![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Last modified 11 months ago
#16422 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001f40f0f40 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, psutil._psutil_osx, psutil._psutil_posix (total: 63)
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{
"uptime" : 740000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 1763,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-12-05 00:19:36.6742 +0100",
"codeSigningMonitor" : 1,
"incident" : "1A45BAC7-6FFC-4440-B61D-232BFACB799D",
"pid" : 231,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-04 19:39:56.2755 +0100",
"procStartAbsTime" : 17373257614560,
"procExitAbsTime" : 17775986940482,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"28FE279B-5C00-53B3-BED9-B0F9D96FA4E2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3610094C-FE23-95D2-FA43-F569A7A5CF1F",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 22019,
"sleepWakeUUID" : "8819E196-7082-49CC-AD74-8CF1DB73C047",
"sip" : "enabled",
"vmRegionInfo" : "0x6e703f3a25d8 is not in any region. Bytes after previous region: 15872038675929 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 6000a0000000-6000c0000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000ee703f3a25d8","rawCodes":[1,262165864523224],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000ee703f3a25d8 -> 0x00006e703f3a25d8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":231},
"vmregioninfo" : "0x6e703f3a25d8 is not in any region. Bytes after previous region: 15872038675929 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 6000a0000000-6000c0000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241125_chimera_for_figures.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.005, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32
Log from Tue Nov 26 17:24:46 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241122_chimera_for_figures.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32
Log from Fri Nov 22 15:12:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1/20241114_v2.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32
Log from Thu Nov 14 15:28:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241017_COPI_leaf_all_AF3_results_aligned.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Log from Thu Oct 17 14:08:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241009_COPI_leaf_AF3_for_figs_v8.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Log from Wed Oct 9 16:21:15 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Log from Wed Sep 25 22:56:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Log from Fri Aug 9 13:21:55 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #58, grid size 292,292,292,
pixel 1.71, shown at level 0.005, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Log from Tue Aug 6 15:17:45 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v4.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00585, step 1, values float32
Log from Wed Jul 24 16:40:43 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3
> /fold_20240711_copi_golph3/20240711_leaf_fitting_alphafold_withGolph3AF3_v2.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00736, step 1, values float32
Log from Sat Jul 13 09:14:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v5.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00736, step 1, values float32
Log from Fri Jul 12 14:16:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v4.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00465, step 1, values float32
Log from Wed Jul 10 18:08:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v2.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00465, step 1, values float32
Log from Wed Jul 10 17:31:38 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00404, step 1, values float32
Log from Wed Jul 10 16:36:09 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00404, step 1, values float32
Log from Wed Jul 10 16:07:37 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v39_labelled.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 1, values float32
Log from Tue Jul 9 17:02:08 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240708_leaf_fitting_v36_labelled.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00463, step 1, values float32
Log from Mon Jul 8 16:31:05 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240522_leaf_fitting_v32_labelled.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00733, step 1, values float32
Log from Mon Jun 3 13:56:09 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera
> sessions/20240521_leaf_fitting_v31_mutations_interactions_labeled.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00733, step 1, values float32
Log from Tue May 21 23:56:29 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v25.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32
Log from Mon Apr 15 16:36:47 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v21.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32
Log from Mon Apr 15 15:35:58 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240328_leaf_fitting_v17.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32
Opened cryosparc_P126_J1413_005_volume_map.mrc as #35, grid size 480,480,480,
pixel 0.953, shown at level 0.136, step 1, values float32
Opened cryosparc_P126_J1449_008_volume_map_sharp.mrc as #36, grid size
480,480,480, pixel 0.953, shown at level 0.227, step 1, values float32
Log from Fri Mar 29 15:25:34 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v13.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00747, step 1, values float32
Log from Tue Mar 26 13:48:19 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v10.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Log from Thu Feb 15 12:14:52 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v2.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00338, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Log from Mon Feb 12 10:40:16 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240126_linkage_3_fitting_v1.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.00376, step 1, values float32
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00396, step 1, values float32
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32
Opened postprocess_20231221.mrc as #48, grid size 156,156,156, pixel 2.55,
shown at level 0.00387, step 1, values float32
Opened emd_3720_2017_leaf.map as #49, grid size 128,128,128, pixel 1.78, shown
at level 0.226, step 1, values float32
Log from Fri Jan 26 14:05:24 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_3_fitting.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.0033, step 1, values float32
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00303, step 1, values float32
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32
Log from Thu Jan 25 18:04:25 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_1_fitting.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 3.38, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.0033, step 1, values float32
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00453, step 1, values float32
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32
Log from Thu Jan 25 16:06:42 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240124_Golph3_fitting.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #18, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #19, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #20, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #22, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #23, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #24, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32
Opened emd_3720_2017_leaf.map as #26, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32
Opened postprocess_20231221.mrc as #27, grid size 156,156,156, pixel 2.55,
shown at level 0.00356, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00402, step 1, values float32
Log from Wed Jan 24 14:57:19 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/All_Linkages_fitting_Golph_AF_RT.cxs"
Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.01, step 1, values float32
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #18, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #19, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #20, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #22, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #23, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #24, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32
Opened emd_3720_2017_leaf.map as #26, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32
Log from Tue Dec 5 16:56:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/Linkage_1_fitting_Golph_AF_RT.cxs" format
> session
Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.193, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.372, step 1, values float32
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Log from Tue Dec 5 14:45:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI-GOLPH
> dataset/Chimera_COPI_golph/alphafold_copi_colored_RT_4.cxs"
Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32
Log from Tue Nov 7 12:35:14 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open alphafold_copi_colored_RT_2.cxs
Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32
Log from Tue Nov 7 08:56:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/alphafold_copi_colored_RT.cxs
> format session
Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32
Log from Mon Nov 6 14:26:30 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open alphafold_copi_gt_colored.cxs
Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00914, step 1, values float32
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.155, step 1, values float32
Log from Sun Nov 5 21:56:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open alphafold_copi_gt.cxs
Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.012, step 1, values float32
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.155, step 1, values float32
Log from Sun Nov 5 03:35:04 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/warpV1_erase/relion/PostProcess/job062/postprocess.mrc
Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00604, step 1, values float32
> open 5nzr
Summary of feedback from opening 5nzr fetched from pdb
---
note | Fetching compressed mmCIF 5nzr from http://files.rcsb.org/download/5nzr.cif
5nzr title:
The structure of the COPI coat leaf [more info...]
Chain information for 5nzr #2
---
Chain | Description | UniProt
A | Coatomer subunit alpha | COPA_MOUSE 1-1224
B | Coatomer subunit beta | COPB_MOUSE 16-968
C | Coatomer subunit beta' | COPB2_MOUSE 1-905
D | Coatomer subunit delta | COPD_MOUSE 1-511
F M R | ADP-ribosylation factor 1 | ARF1_YEAST 1-181
G K | Coatomer subunit gamma-1 | COPG1_MOUSE 1-874
L Z | Coatomer subunit zeta-1 | COPZ1_MOUSE 1-177
> select add #2
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> volume #1 level 0.0087
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models #2,1,0,0,-37.882,0,1,0,64.414,0,0,1,202.79
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.52562,-0.43202,0.73286,-19.37,-0.17024,0.79062,0.58817,39.912,-0.83351,-0.43392,0.34202,421.68
> view matrix models
> #2,0.7,0.68406,-0.20508,-62.275,0.0068065,0.28077,0.95975,37.92,0.71411,-0.67322,0.19188,297.56
> view matrix models
> #2,0.28224,0.88452,-0.37142,-20.952,-0.65525,0.46053,0.5988,130.99,0.7007,0.074371,0.70957,150.66
> view matrix models
> #2,0.49213,0.75481,-0.43366,-21.427,-0.82839,0.25296,-0.49979,301.54,-0.26755,0.6052,0.74977,189.39
> view matrix models
> #2,0.36057,0.92393,-0.12783,-62.367,-0.57964,0.11459,-0.80677,326.12,-0.73076,0.365,0.57687,288.65
> view matrix models
> #2,-0.61475,0.27359,-0.73975,192.39,-0.35757,-0.93266,-0.047782,338.05,-0.70301,0.23514,0.67118,290.08
> view matrix models
> #2,-0.91301,0.40193,0.069771,116.36,-0.4071,-0.9087,-0.092394,345.81,0.026265,-0.11276,0.99328,214.04
> view matrix models
> #2,-0.88167,0.40879,0.2357,92.928,-0.40453,-0.91196,0.068457,327.32,0.24293,-0.034992,0.96941,183.81
> view matrix models
> #2,-0.5303,0.84267,0.093238,19.456,-0.82612,-0.53832,0.16656,317.99,0.19054,0.011299,0.98161,182.67
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.5303,0.84267,0.093238,263.37,-0.82612,-0.53832,0.16656,455.06,0.19054,0.011299,0.98161,199.63
> fitmap #1 #2
Missing required "in_map" argument
> fitmap #2 inMap #1
Fit molecule 5nzr (#2) to map postprocess.mrc (#1) using 18970 atoms
average map value = 0.01091, steps = 116
shifted from previous position = 7.15
rotated from previous position = 12 degrees
atoms outside contour = 7834, contour level = 0.0087005
Position of 5nzr (#2) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
-0.53470562 0.84443643 -0.03189051 278.17154273
-0.84484986 -0.53500265 -0.00093313 482.55400590
-0.01784948 0.02644375 0.99949093 224.67222139
Axis 0.01620349 -0.00831044 -0.99983418
Axis point 273.19248819 162.79104531 0.00000000
Rotation angle (degrees) 122.35128157
Shift along axis -224.13785000
> select subtract #2
Nothing selected
> close #2
> open 3720
Fetching url http://files.rcsb.org/download/3720.cif failed:
HTTP Error 404: Not Found
> open emdb3720
'emdb3720' has no suffix
> open 3720 fromDatabase emdb
Summary of feedback from opening 3720 fetched from emdb
---
note | Fetching compressed map 3720 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-3720/map/emd_3720.map.gz
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.226, step 1, values float32
> volume #2 level 0.09618
> select add #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,223.78,0,1,0,-35.337,0,0,1,158.95
> view matrix models #2,1,0,0,225.18,0,1,0,9.8187,0,0,1,170.58
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.76316,0.27646,-0.58409,288.27,-0.32541,0.94531,0.022268,51.04,0.5583,0.17307,0.81138,108.15
> view matrix models
> #2,0.95657,0.056083,-0.28607,257.23,-0.28053,-0.089841,-0.95563,285,-0.079296,0.99438,-0.070206,187.24
> view matrix models
> #2,-0.25273,0.83078,0.49592,211.05,-0.38627,0.3833,-0.83897,226.83,-0.88708,-0.4036,0.22403,412.13
> view matrix models
> #2,-0.051655,0.96539,0.25564,200.28,-0.9833,-0.093889,0.15587,234.85,0.17448,-0.24332,0.95412,185.06
> view matrix models
> #2,0.02585,0.7816,-0.62325,317.1,-0.70553,-0.42742,-0.56528,327.98,-0.70821,0.45433,0.54039,251.79
> view matrix models
> #2,-0.58335,0.28587,0.76025,282.85,-0.81203,-0.1846,-0.55366,309.81,-0.017932,-0.94032,0.33982,362.91
> view matrix models
> #2,-0.98042,-0.17156,0.096691,461.36,-0.048228,-0.26686,-0.96253,280.32,0.19094,-0.94834,0.25336,350.12
> view matrix models
> #2,-0.92285,0.28368,-0.26051,442.55,-0.18618,-0.92069,-0.34304,301.1,-0.33716,-0.26807,0.90248,252.78
> view matrix models
> #2,-0.93117,0.30503,-0.1997,433.78,-0.29572,-0.95227,-0.07566,285.87,-0.21324,-0.011399,0.97693,199.12
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.93117,0.30503,-0.1997,397.2,-0.29572,-0.95227,-0.07566,498.67,-0.21324,-0.011399,0.97693,255.17
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess.mrc using 114393 points
correlation = 0.6691, correlation about mean = 0.05303, overlap = 91.28
steps = 100, shift = 27.4, angle = 14.2 degrees
Position of emdb 3720 (#2) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
-0.90384624 0.23353058 -0.35850446 426.60125938
-0.28809092 -0.95167357 0.10640039 474.89273455
-0.31633147 0.19945147 0.92744462 222.06398803
Axis 0.17506212 -0.07934236 -0.98135521
Axis point 264.85851560 196.87446978 0.00000000
Rotation angle (degrees) 164.58753247
Shift along axis -180.92104267
> volume #2 level 0.136
> select clear
> ui mousemode right "translate selected models"
> select #2
2 models selected
> view matrix models
> #2,-0.90385,0.23353,-0.3585,425.99,-0.28809,-0.95167,0.1064,430.09,-0.31633,0.19945,0.92744,249.04
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.93137,0.093427,-0.35189,445.01,-0.15388,-0.97696,0.14789,412.92,-0.32997,0.19189,0.92428,251.87
> view matrix models
> #2,-0.3246,0.87931,-0.3485,282.32,-0.83775,-0.43832,-0.32566,483.27,-0.43911,0.18625,0.87892,270.36
> view matrix models
> #2,-0.71374,0.63847,-0.28798,347.66,-0.6764,-0.73504,0.046791,455.31,-0.18181,0.22819,0.95649,226.9
> view matrix models
> #2,-0.30923,0.92464,-0.22232,259.88,-0.94209,-0.32976,-0.06112,450.03,-0.12982,0.19054,0.97306,223.52
> view matrix models
> #2,-0.79733,0.57614,-0.1798,351.42,-0.59927,-0.79112,0.1225,444.11,-0.071665,0.20542,0.97605,214.81
> view matrix models
> #2,-0.58975,0.77816,-0.21604,308.27,-0.80056,-0.59852,0.029561,455.12,-0.1063,0.19039,0.97594,220.53
> view matrix models
> #2,-0.86768,0.45921,-0.1904,374.6,-0.48592,-0.8643,0.12984,439.16,-0.10494,0.20518,0.97308,218.96
> view matrix models
> #2,-0.74473,0.62297,-0.23933,347.11,-0.64295,-0.76587,0.0071296,460.02,-0.17885,0.15918,0.97091,233.05
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.74473,0.62297,-0.23933,342.91,-0.64295,-0.76587,0.0071296,479.3,-0.17885,0.15918,0.97091,239.3
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.79959,0.57272,-0.1807,347.99,-0.59537,-0.79538,0.11357,464.54,-0.078687,0.19839,0.97696,222.58
> view matrix models
> #2,-0.67006,0.71251,-0.20821,320.02,-0.73726,-0.67144,0.074925,470.46,-0.086418,0.20371,0.97521,223.03
> view matrix models
> #2,-0.91364,0.36722,-0.17437,384.62,-0.37083,-0.92862,-0.012671,470.39,-0.16657,0.053082,0.9846,248.92
> view matrix models
> #2,-0.75132,0.63901,-0.16488,332.72,-0.64038,-0.76631,-0.051852,486.21,-0.15948,0.066629,0.98495,246.46
> view matrix models
> #2,-0.77803,0.62815,-0.010172,318.27,-0.62601,-0.77654,-0.071466,488.18,-0.052791,-0.049235,0.99739,246.73
> view matrix models
> #2,-0.65763,0.75315,0.017269,286.44,-0.75149,-0.65422,-0.085182,489.42,-0.052856,-0.068995,0.99622,249.24
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.65763,0.75315,0.017269,300.45,-0.75149,-0.65422,-0.085182,488.98,-0.052856,-0.068995,0.99622,232.81
> view matrix models
> #2,-0.65763,0.75315,0.017269,297.73,-0.75149,-0.65422,-0.085182,497.05,-0.052856,-0.068995,0.99622,233.9
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess.mrc using 73589 points
correlation = 0.8646, correlation about mean = 0.3064, overlap = 147.1
steps = 96, shift = 6.01, angle = 10.4 degrees
Position of emdb 3720 (#2) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
-0.53666347 0.84316340 -0.03267727 278.66671757
-0.84365691 -0.53687633 0.00261266 482.08926923
-0.01534075 0.02897052 0.99946254 223.65484556
Axis 0.01562303 -0.01027584 -0.99982515
Axis point 272.76166410 162.45158774 0.00000000
Rotation angle (degrees) 122.48227196
Shift along axis -224.21599001
> select clear
> volume #2 level 0.1256
> volume #1 level 0.007442
> volume #2 level 0.07023
> volume #2 level 0.1775
> volume #1 level 0.005345
> volume #1 level 0.009819
> ui tool show AlphaFold
> alphafold match
> MLTKFETKSARVKGLSFHPKRPWILTSLHNGVIQLWDYRMCTLIDKFDEHDGPVRGIDFHKQQPLFVSGGDDYKIKVWNYKLRRCLFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRVWNWQSRTCVCVLTGHNHYVMCAQFHPSEDLVVSASLDQTVRVWDISGLRKKNLSPGAVESDVRGITGVDLFGTTDAVVKHVLEGHDRGVNWAAFHPTMPLIVSGADDRQVKIWRMNESKAWEVDTCRGHYNNVSCAVFHPRQELILSNSEDKSIRVWDMSKRTGVQTFRRDHDRFWVLAAHPNLNLFAAGHDGGMIVFKLERERPAYAVHGNMLHYVKDRFLRQLDFNSSKDVAVMQLRSGSKFPVFNMSYNPAENAVLLCTRASNLENSTYDLYTIPKDADSQNPDAPEGKRSSGLTAVWVARNRFAVLDRMHSLLIKNLKNEITKKIQVPNCDEIFYAGTGNLLLRDADSITLFDVQQKRTLASVKISKVKYVIWSADMSHVALLAKHEHSCPLPLTAIVICNRKLDALCNIHENIRVKSGAWDESGVFIYTTSNHIKYAVTTGDHGIIRTLDLPIYVTRVKGNNVYCLDRECRPRVLTIDPTEFKFKLALINRKYDEVLHMVRNAKLVGQSIIAYLQKKGYPEVALHFVKDEKTRFSLALECGNIEIALEAAKALDDKNCWEKLGEVALLQGNHQIVEMCYQRTKNFDKLSFLYLITGNLEKLRKMMKIAEIRKDMSGHYQNALYLGDVSERVRILKNCGQKSLAYLSAATHGLDEEAESLKETFDPEKETIPDIDPNAKLLQPPAPIMPLDTNWPLLTVSKGFFEGSIASKGKGGALAADIDIDTVGTEGWGEDAELQLDEDGFVEAPEGLGEDVLGKGQEEGGGWDVEEDLELPPELDVPSGVSGSAEDGFFVPPTKGTSPTQIWCNNSQLPVDHILAGSFETAMRLLHDQVGVIQFGPYKQLFLQTYARGRTTYQALPCLPSMYSYPNRNWKDAGLKNGVPAVGLKLNDLIQRLQLCYQLTTVGKFEEAVEKFRSILLSVPLLVVDNKQEIAEAQQLITICREYIVGLCMEIERKKLPKETLDQQKRICEMAAYFTHSNLQPVHMILVLRTALNLFFKLKNFKTAATFARRLLELGPKPEVAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEFKGQICRVTTVTEIGKDVIGLRISPLQFR
AlphaFold sequence search web service failed (404) "Not Found"
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py
No AlphaFold model with similar sequence for 1 sequences
Opened 0 AlphaFold model
Fetching compressed F8WHL2 UniProt info from
https://www.uniprot.org/uniprot/F8WHL2.xml
> alphafold match F8WHL2
Fetching compressed AlphaFold F8WHL2 from
https://alphafold.ebi.ac.uk/files/AF-F8WHL2-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: F8WHL2 (UniProt F8WHL2)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
F8WHL2 | F8WHL2 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #39810 atoms, 10032 bonds, 1233 residues, 1 model selected
> ui mousemode right "translate selected models"> view matrix models
> #3,1,0,0,303.28,0,1,0,304.96,0,0,1,11.166> view matrix models
> #3,1,0,0,324.74,0,1,0,283.74,0,0,1,319.33> view matrix models
> #3,1,0,0,209.64,0,1,0,387.4,0,0,1,429.36> ui mousemode right "translate
> selected models"[Repeated 1 time(s)]> view matrix models
> #3,1,0,0,222.42,0,1,0,405.56,0,0,1,420.95> ui mousemode right "rotate
> selected models"> view matrix models
> #3,0.32639,-0.23212,-0.91629,218.55,-0.93865,-0.1938,-0.28526,399.27,-0.11137,0.95319,-0.28113,421.32>
> view matrix models
> #3,-0.60439,0.30546,-0.7358,196.12,-0.51637,-0.85352,0.069815,409.29,-0.60669,0.42214,0.67359,409.09>
> view matrix models
> #3,-0.96723,0.14467,-0.20868,186.74,-0.15733,-0.9865,0.045344,417.05,-0.1993,0.076689,0.97693,416.89>
> view matrix models
> #3,-0.9522,0.23336,-0.19714,186.28,-0.23562,-0.97177,-0.01224,415.93,-0.19443,0.034795,0.9803,417.26>
> view matrix models
> #3,-0.97348,-0.079573,-0.21447,188.33,0.038436,-0.98112,0.18956,419.54,-0.2255,0.17629,0.95816,415.81>
> view matrix models
> #3,-0.22693,-0.37305,-0.89963,209.3,0.58137,0.68921,-0.43244,421.75,0.78135,-0.62115,0.060477,446.87>
> view matrix models
> #3,0.21155,-0.58135,-0.78567,218.06,0.9196,-0.15386,0.36146,428.33,-0.33102,-0.79897,0.50207,424.47>
> view matrix models
> #3,-0.12158,-0.084379,-0.98899,209.76,-0.25211,-0.96108,0.11299,414.62,-0.96003,0.26307,0.095579,408.05>
> view matrix models
> #3,0.84817,0.13727,0.51163,214.82,-0.089352,-0.91493,0.3936,415.19,0.52213,-0.37955,-0.76375,446.42>
> view matrix models
> #3,0.32531,0.49583,-0.80518,212.31,0.69626,0.45057,0.55876,418.28,0.63984,-0.74239,-0.19865,447.08>
> view matrix models
> #3,0.4134,0.56919,-0.71072,212.69,0.6828,0.32261,0.65552,418.27,0.6024,-0.75627,-0.25528,446.92>
> view matrix models
> #3,-0.13517,-0.24305,-0.96055,210.47,0.45069,0.84827,-0.27806,417.02,0.88239,-0.4705,-0.0051158,448.09>
> view matrix models
> #3,-0.8766,0.28966,-0.38428,188.63,0.43236,0.82468,-0.36465,417.5,0.21128,-0.4858,-0.84815,442.12>
> view matrix models
> #3,-0.75554,0.47772,0.44827,183.3,-0.087054,0.60499,-0.79146,412.75,-0.6493,-0.637,-0.4155,424.22>
> view matrix models
> #3,-0.17993,0.68527,0.70571,190.43,-0.77714,0.3408,-0.52907,400.08,-0.60306,-0.64363,0.47123,418.55>
> view matrix models
> #3,0.38482,0.64397,0.66123,201.45,-0.54337,0.73715,-0.40169,400.49,-0.7461,-0.20471,0.63358,411.47>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.38482,0.64397,0.66123,209.11,-0.54337,0.73715,-0.40169,352.77,-0.7461,-0.20471,0.63358,346.78>
> view matrix models
> #3,0.38482,0.64397,0.66123,272.84,-0.54337,0.73715,-0.40169,341.51,-0.7461,-0.20471,0.63358,359.04>
> view matrix models
> #3,0.38482,0.64397,0.66123,275.5,-0.54337,0.73715,-0.40169,343.71,-0.7461,-0.20471,0.63358,340.28>
> volume #1 level 0.009245> volume #1 transparency .5> view matrix models
> #3,0.38482,0.64397,0.66123,277.74,-0.54337,0.73715,-0.40169,343.45,-0.7461,-0.20471,0.63358,342.76>
> view matrix models
> #3,0.38482,0.64397,0.66123,274.73,-0.54337,0.73715,-0.40169,335.94,-0.7461,-0.20471,0.63358,326.51>
> view matrix models
> #3,0.38482,0.64397,0.66123,273,-0.54337,0.73715,-0.40169,338.08,-0.7461,-0.20471,0.63358,327.8>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.2206,0.77424,0.5932,269.52,-0.66437,0.56456,-0.48978,337.79,-0.7141,-0.28606,0.63893,328.95>
> view matrix models
> #3,0.46242,0.64706,0.60621,274.81,-0.30974,0.75851,-0.57335,343.48,-0.8308,0.077362,0.55116,324.76>
> view matrix models
> #3,0.1596,0.83662,0.52402,268.45,-0.68532,0.47596,-0.55117,338.51,-0.71054,-0.27116,0.64932,328.83>
> view matrix models
> #3,0.48141,0.60575,0.63349,275.26,-0.24765,0.78731,-0.56464,344.35,-0.84078,0.11494,0.52903,324.46>
> view matrix models
> #3,0.22271,0.44453,0.86764,269.97,-0.69434,0.69705,-0.1789,333.95,-0.68431,-0.56259,0.4639,332.84>
> view matrix models
> #3,0.25107,0.90985,0.33037,271.02,-0.74263,0.39997,-0.53714,337.92,-0.62085,-0.11048,0.7761,328.35>
> view matrix models
> #3,0.60545,0.57661,0.54859,278.39,-0.6801,0.73285,-0.01969,332.77,-0.41339,-0.36117,0.83586,333.57>
> view matrix models
> #3,0.5141,0.75687,0.40355,276.45,-0.8383,0.54295,0.049627,330.76,-0.18154,-0.3638,0.91361,337.28>
> view matrix models
> #3,0.68948,0.49522,0.52856,280.68,-0.57485,0.81809,-0.016621,334.05,-0.44064,-0.29238,0.84873,332.47>
> view matrix models
> #3,0.76356,0.52587,0.37475,282.96,-0.51319,0.84643,-0.14212,335.9,-0.39194,-0.083795,0.91617,331.32>
> view matrix models
> #3,0.20308,0.96515,0.16504,270.96,-0.89543,0.25126,-0.36754,334.96,-0.3962,-0.073139,0.91525,331.17>
> select clear> volume #1 level 0.007668> volume #1 level 0.008528> select add
> #39810 atoms, 10032 bonds, 1233 residues, 1 model selected
> select subtract #3Nothing selected
> select add #39810 atoms, 10032 bonds, 1233 residues, 1 model selected
> view matrix models
> #3,0.24506,0.95994,0.13585,271.98,-0.89492,0.27787,-0.34914,334.63,-0.3729,-0.036017,0.92717,331.23>
> view matrix models
> #3,0.1572,0.79158,0.5905,268.25,-0.72926,0.49624,-0.47109,336.96,-0.66593,-0.35657,0.65528,330.24>
> view matrix models
> #3,0.28322,0.87764,0.3867,271.44,-0.81992,0.43074,-0.37709,335.08,-0.49751,-0.21027,0.84159,330.87>
> view matrix models
> #3,-0.017812,0.84232,0.53868,265.04,-0.76613,0.33468,-0.54867,338.06,-0.64244,-0.42247,0.63937,331.27>
> view matrix models
> #3,-0.0031655,0.85903,0.51192,265.38,-0.72124,0.35264,-0.5962,339.1,-0.69268,-0.37111,0.61845,330.13>
> view matrix models
> #3,-0.27124,0.8759,0.39904,261.17,-0.68704,0.11416,-0.7176,342.39,-0.67409,-0.4688,0.57081,331.54>
> view matrix models
> #3,0.13566,0.93162,0.33715,268.69,-0.77565,0.31159,-0.54889,338.05,-0.61641,-0.18705,0.76489,329.08>
> select clear> select /A:7789 atoms, 8 bonds, 1 residue, 1 model selected
> select clear> select /A:19910 atoms, 10 bonds, 1 residue, 1 model selected
> select add /A:78015 atoms, 14 bonds, 2 residues, 1 model selected
> select up111 atoms, 110 bonds, 14 residues, 1 model selected
> select up9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> select down111 atoms, 110 bonds, 14 residues, 1 model selected
> ui mousemode right "translate selected models"> view matrix models
> #3,0.13566,0.93162,0.33715,267.62,-0.77565,0.31159,-0.54889,339.05,-0.61641,-0.18705,0.76489,326.53>
> view matrix models
> #3,0.13566,0.93162,0.33715,263.83,-0.77565,0.31159,-0.54889,331.53,-0.61641,-0.18705,0.76489,323.99>
> view matrix models
> #3,0.13566,0.93162,0.33715,264.39,-0.77565,0.31159,-0.54889,331.73,-0.61641,-0.18705,0.76489,323.13>
> view matrix models
> #3,0.13566,0.93162,0.33715,264.12,-0.77565,0.31159,-0.54889,329.56,-0.61641,-0.18705,0.76489,322.14>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.27221,0.90106,0.33763,266.85,-0.73533,0.42111,-0.531,329.36,-0.62064,-0.10372,0.77721,321.36>
> view matrix models
> #3,0.2643,0.91061,0.31769,266.78,-0.70061,0.40766,-0.58563,330.5,-0.66279,-0.0678,0.74573,320.55>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.2643,0.91061,0.31769,268.7,-0.70061,0.40766,-0.58563,332.37,-0.66279,-0.0678,0.74573,325.34>
> view matrix models
> #3,0.2643,0.91061,0.31769,268.14,-0.70061,0.40766,-0.58563,333.45,-0.66279,-0.0678,0.74573,326.51>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.41107,0.83158,0.37349,271.01,-0.59062,0.55504,-0.58574,334.38,-0.6944,0.02019,0.71931,325.47>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.41107,0.83158,0.37349,268.91,-0.59062,0.55504,-0.58574,338.04,-0.6944,0.02019,0.71931,328.38>
> view matrix models
> #3,0.41107,0.83158,0.37349,266.29,-0.59062,0.55504,-0.58574,340.47,-0.6944,0.02019,0.71931,325.69>
> view matrix models
> #3,0.41107,0.83158,0.37349,266.62,-0.59062,0.55504,-0.58574,340.35,-0.6944,0.02019,0.71931,326.17>
> view matrix models
> #3,0.41107,0.83158,0.37349,266.32,-0.59062,0.55504,-0.58574,341.97,-0.6944,0.02019,0.71931,326.79>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.57049,0.67618,0.46618,269.71,-0.47052,0.73431,-0.4893,342.13,-0.67317,0.05979,0.73706,326.76>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.57049,0.67618,0.46618,257.51,-0.47052,0.73431,-0.4893,347.5,-0.67317,0.05979,0.73706,322.97>
> view matrix models
> #3,0.57049,0.67618,0.46618,259.1,-0.47052,0.73431,-0.4893,342.4,-0.67317,0.05979,0.73706,325.89>
> view matrix models
> #3,0.57049,0.67618,0.46618,263.37,-0.47052,0.73431,-0.4893,342.64,-0.67317,0.05979,0.73706,327.49>
> view matrix models
> #3,0.57049,0.67618,0.46618,262.68,-0.47052,0.73431,-0.4893,346.65,-0.67317,0.05979,0.73706,329>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.57248,0.67477,0.46578,262.74,-0.49429,0.73727,-0.46055,345.97,-0.65417,0.033424,0.75561,329.4>
> view matrix models
> #3,0.63127,0.69884,0.33633,264.6,-0.52003,0.70313,-0.48495,345.94,-0.57539,0.13123,0.80729,329.74>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.63127,0.69884,0.33633,266.39,-0.52003,0.70313,-0.48495,345.55,-0.57539,0.13123,0.80729,331.04>
> view matrix models
> #3,0.63127,0.69884,0.33633,268.56,-0.52003,0.70313,-0.48495,343.51,-0.57539,0.13123,0.80729,331.68>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.6514,0.67692,0.34272,269.04,-0.52428,0.7281,-0.4416,342.92,-0.54846,0.10797,0.82918,332.18>
> view matrix models
> #3,0.59614,0.71527,0.3647,267.58,-0.54988,0.69472,-0.46367,342.86,-0.58502,0.075871,0.80746,331.91>
> view matrix models
> #3,0.71756,0.63247,0.2917,270.97,-0.45126,0.74119,-0.49699,344.58,-0.53053,0.22499,0.81726,331.73>
> view matrix models
> #3,0.7144,0.66742,0.2102,271.25,-0.51692,0.70585,-0.48432,343.54,-0.47161,0.23735,0.84927,332.49>
> view matrix models
> #3,0.73441,0.65932,0.16107,272.04,-0.52134,0.69996,-0.48813,343.53,-0.43457,0.27451,0.85778,332.83>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.73441,0.65932,0.16107,274.91,-0.52134,0.69996,-0.48813,343.26,-0.43457,0.27451,0.85778,335.65>
> view matrix models
> #3,0.73441,0.65932,0.16107,274.57,-0.52134,0.69996,-0.48813,341.68,-0.43457,0.27451,0.85778,338>
> view matrix models
> #3,0.73441,0.65932,0.16107,275.14,-0.52134,0.69996,-0.48813,341.4,-0.43457,0.27451,0.85778,337.25>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.7541,0.63707,0.15963,275.68,-0.50041,0.71476,-0.48858,341.68,-0.42536,0.28856,0.85779,337.31>
> view matrix models
> #3,0.74291,0.63667,0.20673,275.12,-0.46536,0.71322,-0.52417,342.6,-0.48117,0.29321,0.82614,336.49>
> view matrix models
> #3,0.80342,0.55155,0.22432,276.74,-0.39022,0.77229,-0.50129,343.37,-0.44972,0.31521,0.8357,336.83>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.80342,0.55155,0.22432,271.95,-0.39022,0.77229,-0.50129,347.63,-0.44972,0.31521,0.8357,338.54>
> view matrix models
> #3,0.80342,0.55155,0.22432,271.53,-0.39022,0.77229,-0.50129,347.65,-0.44972,0.31521,0.8357,339.94>
> view matrix models
> #3,0.80342,0.55155,0.22432,271.45,-0.39022,0.77229,-0.50129,347.37,-0.44972,0.31521,0.8357,339.41>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.87916,0.44751,0.16375,274.06,-0.32398,0.81332,-0.48327,348.15,-0.34945,0.37182,0.86002,340.65>
> view matrix models
> #3,0.8903,0.43345,0.1396,274.55,-0.32015,0.81379,-0.48502,348.23,-0.32383,0.38712,0.86329,340.98>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.8903,0.43345,0.1396,274.05,-0.32015,0.81379,-0.48502,351.03,-0.32383,0.38712,0.86329,342.82>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.90023,0.42579,0.091041,274.64,-0.30651,0.76821,-0.56205,352.19,-0.30925,0.47807,0.82208,342.72>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.90023,0.42579,0.091041,276.29,-0.30651,0.76821,-0.56205,352.94,-0.30925,0.47807,0.82208,345.52>
> view matrix models
> #3,0.90023,0.42579,0.091041,276.64,-0.30651,0.76821,-0.56205,351.93,-0.30925,0.47807,0.82208,348.52>
> view matrix models
> #3,0.90023,0.42579,0.091041,276.5,-0.30651,0.76821,-0.56205,353.45,-0.30925,0.47807,0.82208,349.29>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.90732,0.40924,0.096353,276.71,-0.27468,0.75051,-0.60107,354.45,-0.3183,0.5189,0.79337,349.04>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.90732,0.40924,0.096353,276.03,-0.27468,0.75051,-0.60107,353.78,-0.3183,0.5189,0.79337,350.72>
> view matrix models
> #3,0.90732,0.40924,0.096353,275.78,-0.27468,0.75051,-0.60107,353.7,-0.3183,0.5189,0.79337,350.42>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.86593,0.44239,0.23337,273.76,-0.19734,0.73091,-0.65332,355.65,-0.4596,0.51967,0.72021,348.36>
> view matrix models
> #3,0.87467,0.42973,0.22423,274.08,-0.18031,0.71787,-0.67242,356.2,-0.44993,0.54772,0.70538,348.44>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.87467,0.42973,0.22423,274.15,-0.18031,0.71787,-0.67242,356.66,-0.44993,0.54772,0.70538,349.67>
> view matrix models
> #3,0.87467,0.42973,0.22423,273.1,-0.18031,0.71787,-0.67242,357.41,-0.44993,0.54772,0.70538,350.66>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.8751,0.43332,0.2155,273.15,-0.20188,0.73155,-0.65121,356.76,-0.43983,0.52637,0.72766,350.84>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.8751,0.43332,0.2155,271.79,-0.20188,0.73155,-0.65121,356.91,-0.43983,0.52637,0.72766,350.01>
> view matrix models
> #3,0.8751,0.43332,0.2155,271.87,-0.20188,0.73155,-0.65121,357.52,-0.43983,0.52637,0.72766,349.85>
> select clear> select #12 models selected
> select clear> hide #!1 models> select /A:7826 atoms, 5 bonds, 1 residue, 1
> model selected
> select /A:6409 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:77818 atoms, 16 bonds, 2 residues, 1 model selected
> select clearDrag select of 3 residues
> select up63 atoms, 62 bonds, 8 residues, 1 model selected
> select up9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> select down63 atoms, 62 bonds, 8 residues, 1 model selected
> select down23 atoms, 3 residues, 1 model selected
> select up63 atoms, 62 bonds, 8 residues, 1 model selected
> select down23 atoms, 3 residues, 1 model selected
> select #3:200-300832 atoms, 855 bonds, 101 residues, 1 model selected
> select #3:626-7831252 atoms, 1269 bonds, 158 residues, 1 model selected
> volume #1 level 0.003653> volume #1 level 0.006521> volume #1 level
> 0.007524> fitmap sel inMap #1Fit molecule AlphaFold F8WHL2 (#3) to map
> postprocess.mrc (#1) using 1252 atoms
average map value = 0.008076, steps = 68
shifted from previous position = 0.881
rotated from previous position = 5.6 degrees
atoms outside contour = 530, contour level = 0.0075244
Position of AlphaFold F8WHL2 (#3) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.91479768 0.37496522 0.15015414 272.72163633
-0.20072021 0.74461830 -0.63659640 357.53578289
-0.35050903 0.55221794 0.75643820 352.78881648
Axis 0.84159616 0.35443398 -0.40754442
Axis point 0.00000000 -509.89936941 647.89739820
Rotation angle (degrees) 44.93349247
Shift along axis 212.46720010
> volume #1 level 0.008672> volume #1 level 0.009102> select clear> select
> /A:6037 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 598 residues
> ui tool show "Fit in Map"> fitmap sel inMap #1 moveWholeMolecules falseFit
> molecule AlphaFold F8WHL2 (#3) to map postprocess.mrc (#1) using 4818 atoms
average map value = 0.007747, steps = 96
shifted from previous position = 11.7
rotated from previous position = 23.8 degrees
atoms outside contour = 3249, contour level = 0.0091018
> show #!1 models> select clear> ui tool show AlphaFoldFetching compressed
> O55029 UniProt info from https://www.uniprot.org/uniprot/O55029.xml
> alphafold match O55029Fetching compressed AlphaFold O55029 from
> https://alphafold.ebi.ac.uk/files/AF-O55029-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: O55029 (UniProt O55029)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
O55029 | O55029 | 100.0 | 100.0
Opened 1 AlphaFold model
Drag select of 905 residues
> rename #3 "acop F8WHL2"> rename #4 "b1cop O55029"> ui mousemode right
> "translate selected models"> view matrix models
> #4,1,0,0,370.38,0,1,0,247.17,0,0,1,216.75> view matrix models
> #4,1,0,0,335.12,0,1,0,270.36,0,0,1,361.07> view matrix models
> #4,1,0,0,277,0,1,0,291.15,0,0,1,334.99> ui mousemode right "rotate selected
> models"> view matrix models
> #4,0.90253,0.38282,0.1972,270.62,0.033459,-0.51889,0.85418,271.85,0.42933,-0.76433,-0.48113,377.38>
> view matrix models
> #4,0.77302,-0.058303,-0.63169,290.22,0.58343,-0.32566,0.74401,280.54,-0.2491,-0.94369,-0.21773,363.43>
> view matrix models
> #4,0.074915,0.65545,-0.75151,284.66,0.23799,0.7201,0.65178,277.9,0.96837,-0.22768,-0.10205,373.44>
> view matrix models
> #4,0.24709,0.54101,-0.8039,288,0.57248,-0.75086,-0.32936,307.53,-0.7818,-0.37884,-0.49524,363.79>
> view matrix models
> #4,0.45878,-0.60051,-0.65491,287.84,0.77685,-0.086693,0.62369,285.45,-0.43131,-0.79491,0.42673,345.23>
> view matrix models
> #4,-0.15329,-0.58727,-0.79475,284.45,0.83983,-0.50125,0.20841,296.9,-0.52076,-0.6355,0.57004,340.5>
> view matrix models
> #4,0.11761,-0.10952,-0.987,291.77,0.62392,-0.76509,0.15924,295.98,-0.77258,-0.63454,-0.021653,352.39>
> view matrix models
> #4,0.34012,-0.0025252,-0.94038,292.99,0.60524,-0.76477,0.22096,294.24,-0.71973,-0.6443,-0.25858,358.87>
> view matrix models
> #4,0.32988,-0.012843,-0.94393,292.98,0.59671,-0.77198,0.21904,294.19,-0.73152,-0.63551,-0.247,358.45>
> ui mousemode right "translate selected models"> view matrix models
> #4,0.32988,-0.012843,-0.94393,312.66,0.59671,-0.77198,0.21904,304.98,-0.73152,-0.63551,-0.247,365.85>
> fitmap sel inMap #1Fit molecule b1cop O55029 (#4) to map postprocess.mrc
> (#1) using 7214 atoms
average map value = 0.008522, steps = 168
shifted from previous position = 20.5
rotated from previous position = 49.4 degrees
atoms outside contour = 3879, contour level = 0.0091018
Position of b1cop O55029 (#4) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
-0.17500586 -0.17837291 -0.96827478 300.31538503
-0.01101922 -0.98303557 0.18308371 289.63776415
-0.98450572 0.04271036 0.17007146 350.80591372
Axis -0.64087816 0.07410279 0.76405756
Axis point 287.13093608 140.83628611 0.00000000
Rotation angle (degrees) 173.71256043
Shift along axis 97.03330679
> select clear> volume #1 level 0.005373> volume #1 level 0.003509> volume #1
> level 0.01125> ui tool show AlphaFoldFetching compressed Q9JIF7 UniProt info
> from https://www.uniprot.org/uniprot/Q9JIF7.xml
> alphafold match Q9JIF7Fetching compressed AlphaFold Q9JIF7 from
> https://alphafold.ebi.ac.uk/files/AF-Q9JIF7-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: Q9JIF7 (UniProt Q9JIF7)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q9JIF7 | Q9JIF7 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #57501 atoms, 7619 bonds, 953 residues, 1 model selected
> ui mousemode right "translate selected models"> view matrix models
> #5,1,0,0,271.36,0,1,0,317.01,0,0,1,50.878> view matrix models
> #5,1,0,0,318.9,0,1,0,281.77,0,0,1,334.98> view matrix models
> #5,1,0,0,278.73,0,1,0,199.54,0,0,1,360.27> ui mousemode right "rotate
> selected models"> view matrix models
> #5,0.88745,-0.36435,-0.28227,281.8,0.44595,0.52412,0.72555,194.37,-0.11641,-0.76977,0.62761,364.88>
> view matrix models
> #5,0.67107,0.33535,0.66121,275.67,-0.73977,0.24385,0.62712,201.35,0.049071,-0.90999,0.41172,365.68>
> view matrix models
> #5,0.017555,0.80719,0.59003,278.07,-0.79428,0.36969,-0.48212,207.72,-0.60729,-0.46019,0.64763,366.37>
> view matrix models
> #5,-0.10559,0.20105,0.97387,277.94,-0.90536,-0.42452,-0.010521,207.48,0.41131,-0.88281,0.22685,364.93>
> view matrix models
> #5,-0.55224,-0.11726,0.8254,281.74,-0.42401,0.89195,-0.15697,202.76,-0.71781,-0.43666,-0.54229,373.73>
> view matrix models
> #5,-0.594,-0.055194,0.80257,281.92,-0.10836,0.99404,-0.01184,200.15,-0.79713,-0.094001,-0.59644,373.58>
> view matrix models
> #5,-0.48192,-0.54854,0.68327,283.28,-0.30994,0.8361,0.45263,198.82,-0.81957,0.0063597,-0.57294,373.31>
> view matrix models
> #5,-0.16222,-0.5084,0.84571,280.7,-0.39977,0.81743,0.41472,199.52,-0.90215,-0.27081,-0.33585,373.02>
> view matrix models
> #5,-0.1128,-0.50446,0.85603,280.39,-0.47173,0.78544,0.4007,200.03,-0.8745,-0.35862,-0.32656,373.05>
> view matrix models
> #5,0.025474,-0.37173,0.92799,278.98,-0.34416,0.86829,0.35726,199.46,-0.93857,-0.32848,-0.10581,372>
> view matrix models
> #5,0.33949,-0.64321,0.68632,279.53,-0.36106,0.58464,0.72652,198.11,-0.86855,-0.49445,-0.033758,371.66>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.33949,-0.64321,0.68632,276.35,-0.36106,0.58464,0.72652,288.45,-0.86855,-0.49445,-0.033758,402.83>
> view matrix models
> #5,0.33949,-0.64321,0.68632,250.38,-0.36106,0.58464,0.72652,309,-0.86855,-0.49445,-0.033758,398.1>
> view matrix models
> #5,0.33949,-0.64321,0.68632,285.01,-0.36106,0.58464,0.72652,319.3,-0.86855,-0.49445,-0.033758,353.89>
> view matrix models
> #5,0.33949,-0.64321,0.68632,283.3,-0.36106,0.58464,0.72652,331.55,-0.86855,-0.49445,-0.033758,349.45>
> hide #5 models> hide #4 models> view matrix models
> #5,0.33949,-0.64321,0.68632,279.14,-0.36106,0.58464,0.72652,302.8,-0.86855,-0.49445,-0.033758,343.44>
> show #5 models> show #4 models> hide #3 models> hide #4 models> view matrix
> models
> #5,0.33949,-0.64321,0.68632,270.08,-0.36106,0.58464,0.72652,305.66,-0.86855,-0.49445,-0.033758,339.27>
> view matrix models
> #5,0.33949,-0.64321,0.68632,273.26,-0.36106,0.58464,0.72652,296.36,-0.86855,-0.49445,-0.033758,339.61>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.1583,-0.75472,0.63666,274.7,-0.22837,0.59932,0.76724,295.45,-0.96062,-0.26685,-0.077487,339.75>
> view matrix models
> #5,0.31702,-0.77002,0.55368,274.45,-0.044004,0.57122,0.81961,294.32,-0.9474,-0.2842,0.14721,338.42>
> view matrix models
> #5,-0.1688,-0.83643,0.52143,277.15,0.15518,0.49987,0.85209,293.35,-0.97336,0.22475,0.045415,337.89>
> view matrix models
> #5,-0.29859,-0.756,0.5825,277.22,-0.055259,0.62302,0.78026,294.48,-0.95278,0.20079,-0.2278,339.43>
> view matrix models
> #5,-0.31587,-0.77827,0.54269,277.59,0.0031861,0.5711,0.82087,294.09,-0.9488,0.26102,-0.17791,338.97>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.31587,-0.77827,0.54269,293.23,0.0031861,0.5711,0.82087,320.12,-0.9488,0.26102,-0.17791,348.52>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.22491,-0.76691,0.60105,292.43,-0.062203,0.62689,0.77662,320.56,-0.97239,0.13728,-0.1887,349>
> view matrix models
> #5,-0.22093,-0.79312,0.56759,292.67,-0.096038,0.59683,0.7966,320.68,-0.97055,0.12149,-0.20803,349.14>
> fitmap sel inMap #1Fit molecule AlphaFold Q9JIF7 (#5) to map postprocess.mrc
> (#1) using 7501 atoms
average map value = 0.00647, steps = 148
shifted from previous position = 5.87
rotated from previous position = 8.11 degrees
atoms outside contour = 6135, contour level = 0.011253
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.12743314 -0.78566653 0.60538327 287.87538541
-0.18888952 0.61841267 0.76281486 319.45283965
-0.97369479 -0.01714266 -0.22721044 353.10812983
Axis -0.41943118 0.84916750 0.32092374
Axis point 330.24827580 0.00000000 -43.29109963
Rotation angle (degrees) 111.59943904
Shift along axis 263.84583665
> view matrix models
> #5,-0.11909,-0.79329,0.59708,287.9,-0.21644,0.60764,0.76415,319.6,-0.969,-0.03823,-0.24407,353.23>
> view matrix models
> #5,-0.13997,-0.7806,0.60915,287.9,-0.23845,0.62368,0.74443,319.79,-0.96101,-0.041054,-0.27343,353.37>
> fitmap sel inMap #1Fit molecule AlphaFold Q9JIF7 (#5) to map postprocess.mrc
> (#1) using 7501 atoms
average map value = 0.00647, steps = 84
shifted from previous position = 0.25
rotated from previous position = 3.09 degrees
atoms outside contour = 6133, contour level = 0.011253
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.12796009 -0.78606814 0.60475043 287.89645555
-0.18929672 0.61791074 0.76312062 319.45704475
-0.97354659 -0.01682829 -0.22786803 353.09674124
Axis -0.41957740 0.84905276 0.32103617
Axis point 330.19750182 0.00000000 -43.20868706
Rotation angle (degrees) 111.65141172
Shift along axis 263.79786166
> view matrix models
> #5,-0.013632,-0.77278,0.63452,287.14,-0.21506,0.622,0.75291,319.63,-0.97651,-0.1262,-0.17467,353.07>
> view matrix models
> #5,-0.041711,-0.77488,0.63073,287.3,-0.1704,0.62755,0.7597,319.36,-0.98449,-0.075789,-0.15822,352.89>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.041711,-0.77488,0.63073,290,-0.1704,0.62755,0.7597,317.67,-0.98449,-0.075789,-0.15822,354.39>
> view matrix models
> #5,-0.041711,-0.77488,0.63073,290,-0.1704,0.62755,0.7597,318.98,-0.98449,-0.075789,-0.15822,355>
> view matrix models
> #5,-0.041711,-0.77488,0.63073,288.25,-0.1704,0.62755,0.7597,313.73,-0.98449,-0.075789,-0.15822,356.75>
> view matrix models
> #5,-0.041711,-0.77488,0.63073,287.59,-0.1704,0.62755,0.7597,314.9,-0.98449,-0.075789,-0.15822,356.71>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.055916,-0.77902,0.6245,287.71,-0.13246,0.62573,0.76871,314.67,-0.98961,-0.03974,-0.13818,356.53>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.055916,-0.77902,0.6245,286.88,-0.13246,0.62573,0.76871,316.68,-0.98961,-0.03974,-0.13818,356.49>
> view matrix models
> #5,-0.055916,-0.77902,0.6245,286.02,-0.13246,0.62573,0.76871,317.58,-0.98961,-0.03974,-0.13818,355.6>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.055916,-0.77902,0.6245,282.11,-0.13246,0.62573,0.76871,313.86,-0.98961,-0.03974,-0.13818,352.7>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.12597,-0.76708,0.62907,282.39,-0.15988,0.64153,0.75025,314.06,-0.97906,-0.0060659,-0.20346,352.94>
> view matrix models
> #5,-0.11811,-0.76841,0.62896,282.36,-0.16267,0.63981,0.75112,314.07,-0.97959,-0.013602,-0.20056,352.94>
> hide #!1 models> select clear> select #5/A:2486 atoms, 5 bonds, 1 residue, 1
> model selected
> select add #5/A:61913 atoms, 11 bonds, 2 residues, 1 model selected
> select #3:248-6192987 atoms, 3052 bonds, 372 residues, 1 model selected
> select #5:248-6192917 atoms, 2955 bonds, 372 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9JIF7 (#5) to map postprocess.mrc
> (#1) using 2917 atoms
average map value = 0.008991, steps = 92
shifted from previous position = 1.33
rotated from previous position = 9.66 degrees
atoms outside contour = 1911, contour level = 0.011253
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04538395 -0.75064039 0.65915044 284.75500060
-0.14313055 0.64813639 0.74795244 314.22146667
-0.98866270 -0.12828960 -0.07802459 347.64202153
Axis -0.44644928 0.83956824 0.30952901
Axis point 359.26930118 0.00000000 -77.14856130
Rotation angle (degrees) 101.08424479
Shift along axis 244.28698872
> show #!1 models> hide #!1 models> select clear[Repeated 2 time(s)]> select
> #5/A:6257 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:66111 atoms, 10 bonds, 1 residue, 1 model selected
> select #5:625-661304 atoms, 305 bonds, 37 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9JIF7 (#5) to map postprocess.mrc
> (#1) using 304 atoms
average map value = 0.008099, steps = 96
shifted from previous position = 3.7
rotated from previous position = 18.7 degrees
atoms outside contour = 241, contour level = 0.011253
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.02186533 -0.51118779 0.85919087 281.99306344
-0.21164457 0.84228549 0.49574360 318.48989776
-0.97710208 -0.17100349 -0.12660697 349.71050382
Axis -0.33735033 0.92909895 0.15155822
Axis point 342.36646040 0.00000000 -20.66281678
Rotation angle (degrees) 98.80623687
Shift along axis 253.77967932
> select up220 atoms, 219 bonds, 27 residues, 1 model selected
> select up7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select up24525 atoms, 25024 bonds, 3091 residues, 7 models selected
> select #5:248-6192917 atoms, 2955 bonds, 372 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9JIF7 (#5) to map postprocess.mrc
> (#1) using 2917 atoms
average map value = 0.008992, steps = 92
shifted from previous position = 3.51
rotated from previous position = 18.7 degrees
atoms outside contour = 1915, contour level = 0.011253
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04673051 -0.75025969 0.65948969 284.75211128
-0.14540060 0.64807045 0.74757164 314.20252886
-0.98826865 -0.13082460 -0.07880354 347.60466200
Axis -0.44752446 0.83949831 0.30816302
Axis point 359.78743319 0.00000000 -76.92474568
Rotation angle (degrees) 101.06960017
Shift along axis 243.45786006
> show #!1 models> ui tool show "Fit in Map"> select #5:625-661304 atoms, 305
> bonds, 37 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9JIF7
> (#5) to map postprocess.mrc (#1) using 304 atoms
average map value = 0.008098, steps = 108
shifted from previous position = 3.71
rotated from previous position = 18.9 degrees
atoms outside contour = 242, contour level = 0.011253
> select clear> select add #5/A:2556 atoms, 5 bonds, 1 residue, 1 model
> selected
> hide #!1 models> select add #5/A:82714 atoms, 12 bonds, 2 residues, 1 model
> selected
> select #5/A:2556 atoms, 5 bonds, 1 residue, 1 model selected
> select clear[Repeated 1 time(s)]> select add #5/A:82912 atoms, 12 bonds, 1
> residue, 1 model selected
> select clear[Repeated 1 time(s)]> select #5/A:2566 atoms, 5 bonds, 1
> residue, 1 model selected
> select #5/A:199 atoms, 8 bonds, 1 residue, 1 model selected
> select #5:19-2561934 atoms, 1972 bonds, 238 residues, 1 model selected
> ui tool show "Fit in Map"> fitmap sel inMap #1 moveWholeMolecules falseFit
> molecule AlphaFold Q9JIF7 (#5) to map postprocess.mrc (#1) using 1934 atoms
average map value = 0.009335, steps = 84
shifted from previous position = 9.44
rotated from previous position = 19.9 degrees
atoms outside contour = 1289, contour level = 0.011253
> show #!1 models> hide #5 models> volume #1 level 0.007811> show #5 models>
> show #4 models> show #3 models> volume #1 level 0.009245> volume #1 level
> 0.005087> volume #1 level 0.009389> hide #3 models> hide #4 models> hide #5
> models> volume #1 level 0.007955> volume #1 level 0.006951> ui tool show
> AlphaFoldFetching compressed P84078 UniProt info from
> https://www.uniprot.org/uniprot/P84078.xml
> alphafold match P84078Fetching AlphaFold database settings from
> https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold P84078 from
https://alphafold.ebi.ac.uk/files/AF-P84078-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: P84078 (UniProt P84078)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P84078 | P84078 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #63391 atoms, 3455 bonds, 419 residues, 2 models selected
> ui mousemode right "translate selected models"[Repeated 1 time(s)]> view
> matrix models
> #5,0.046731,-0.75026,0.65949,358.15,-0.1454,0.64807,0.74757,273.41,-0.98827,-0.13082,-0.078804,676.69,#6,1,0,0,73.4,0,1,0,-40.79,0,0,1,329.09>
> view matrix models
> #5,0.046731,-0.75026,0.65949,488.25,-0.1454,0.64807,0.74757,635.09,-0.98827,-0.13082,-0.078804,585.3,#6,1,0,0,203.5,0,1,0,320.89,0,0,1,237.7>
> view matrix models
> #5,0.046731,-0.75026,0.65949,509.25,-0.1454,0.64807,0.74757,660.67,-0.98827,-0.13082,-0.078804,614.35,#6,1,0,0,224.5,0,1,0,346.47,0,0,1,266.74>
> view matrix models
> #5,0.046731,-0.75026,0.65949,505.66,-0.1454,0.64807,0.74757,658.86,-0.98827,-0.13082,-0.078804,611.53,#6,1,0,0,220.91,0,1,0,344.66,0,0,1,263.93>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.45029,0.28448,0.84635,697.73,-0.88308,-0.28199,-0.37504,549.91,0.13197,-0.91627,0.3782,425.79,#6,0.32368,0.88255,0.34109,209.69,-0.077031,-0.33472,0.93916,350.56,0.94303,-0.33026,-0.040359,275.06>
> view matrix models
> #5,-0.64611,0.34327,0.6817,701.97,-0.72307,-0.56124,-0.40271,497.44,0.24436,-0.75311,0.61083,465.1,#6,0.16184,0.82603,0.5399,208.67,0.12171,-0.55964,0.81975,353.67,0.97928,-0.066957,-0.1911,273.71>
> volume #1 level 0.008815> volume #1 level 0.007668> ui mousemode right
> "rotate selected models"> view matrix models
> #5,-0.37127,-0.68688,0.62479,642.13,-0.38801,-0.49655,-0.77646,224.25,0.84357,-0.5307,-0.082162,-39.636,#6,0.91003,0.07591,0.40754,217.48,-0.15766,-0.84584,0.5096,357.76,0.38339,-0.52801,-0.75777,280.5>
> view matrix models
> #5,0.46673,-0.10013,0.87871,396.42,-0.88433,-0.065543,0.46224,863.68,0.01131,-0.99281,-0.11914,280.92,#6,0.67644,0.52415,-0.5174,218.96,0.3127,0.43167,0.8461,344.9,0.66683,-0.73412,0.1281,277.17>
> view matrix models
> #5,0.55973,-0.02731,0.82823,337.98,-0.72757,-0.49463,0.47539,837.56,0.39668,-0.86868,-0.29673,62.067,#6,0.59285,0.52008,-0.61485,219.48,0.65061,0.14062,0.74628,348.7,0.47458,-0.84246,-0.255,280.27>
> view matrix models
> #5,0.55281,-0.035838,0.83254,342.74,-0.74921,-0.45875,0.47773,844.23,0.36481,-0.88784,-0.28045,81.337,#6,0.60177,0.51878,-0.60724,219.46,0.62423,0.16877,0.76279,348.3,0.4982,-0.83809,-0.22227,280.06>
> view matrix models
> #5,0.017758,-0.75813,0.65186,513.84,-0.92289,-0.26324,-0.28102,600.1,0.38465,-0.59661,-0.70435,-109.32,#6,0.99952,-0.0065926,0.030264,220.78,-0.030955,-0.24649,0.96865,349.66,0.0010739,-0.96912,-0.24658,280.59>
> view matrix models
> #5,-0.97931,-0.10943,0.17021,653.05,-0.17636,0.049126,-0.9831,32.019,0.099216,-0.99278,-0.067408,268.73,#6,0.14859,0.19872,0.96873,211.56,-0.69344,-0.67746,0.24534,357.06,0.70502,-0.70821,0.03714,277.58>
> view matrix models
> #5,-0.86351,0.34359,0.36917,660.07,-0.32165,0.18859,-0.92789,98.453,-0.38844,-0.91999,-0.052331,449.68,#6,-0.054673,0.62421,0.77934,208.61,-0.76845,-0.52468,0.36633,354.79,0.63757,-0.57886,0.50836,273.31>
> view matrix models
> #5,-0.848,0.34752,0.40014,666.2,-0.34914,0.20172,-0.9151,112.75,-0.39874,-0.91572,-0.049725,454.23,#6,-0.036469,0.64766,0.76106,208.54,-0.77116,-0.50261,0.39077,354.43,0.6356,-0.57265,0.51778,273.19>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.848,0.34752,0.40014,675.82,-0.34914,0.20172,-0.9151,66.483,-0.39874,-0.91572,-0.049725,473.97,#6,-0.036469,0.64766,0.76106,218.16,-0.77116,-0.50261,0.39077,308.16,0.6356,-0.57265,0.51778,292.93>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.848,0.34752,0.40014,688.49,-0.34914,0.20172,-0.9151,71.033,-0.39874,-0.91572,-0.049725,471.57,#6,-0.036469,0.64766,0.76106,230.83,-0.77116,-0.50261,0.39077,312.71,0.6356,-0.57265,0.51778,290.53>
> view matrix models
> #5,-0.848,0.34752,0.40014,693.85,-0.34914,0.20172,-0.9151,69.786,-0.39874,-0.91572,-0.049725,472.74,#6,-0.036469,0.64766,0.76106,236.19,-0.77116,-0.50261,0.39077,311.46,0.6356,-0.57265,0.51778,291.69>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#6) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006422, steps = 2000
shifted from previous position = 223
rotated from previous position = 48.9 degrees
atoms outside contour = 2952, contour level = 0.0076678
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.78544199 -0.47592112 0.39570188 715.46000326
-0.51313102 0.14321967 -0.84627696 160.72942314
0.34608878 -0.86774836 -0.35670063 67.50377065
Axis -0.32716750 0.75597252 -0.56698058
Axis point 392.31439396 0.00000000 86.79523471
Rotation angle (degrees) 178.11955374
Shift along axis -150.84155657
Position of AlphaFold P84078 (#6) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.58132163 0.10158882 0.80730717 237.38423842
-0.68954175 -0.46522666 0.55506427 310.31035722
0.43196914 -0.87934286 -0.20039659 290.45018442
Axis -0.85352803 0.22334073 -0.47075346
Axis point -0.00000000 238.34586381 -38.53694803
Rotation angle (degrees) 122.83017374
Shift along axis -270.03958986
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.82136,-0.26559,0.50481,758.27,-0.56919,0.43962,-0.69481,222.17,-0.037383,-0.85802,-0.51225,147.42,#6,0.4938,0.32468,0.80669,235.24,-0.81465,-0.15176,0.55975,307.26,0.30416,-0.93357,0.18956,288.25>
> view matrix models
> #5,-0.49775,-0.37352,0.78277,754.22,-0.85254,0.37659,-0.36242,460.08,-0.15941,-0.84774,-0.50589,194.2,#6,0.7732,0.41548,0.47909,236.96,-0.56139,0.097083,0.82183,303.76,0.29494,-0.90441,0.30831,287.21>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.49775,-0.37352,0.78277,752.99,-0.85254,0.37659,-0.36242,463.44,-0.15941,-0.84774,-0.50589,195.37,#6,0.7732,0.41548,0.47909,235.74,-0.56139,0.097083,0.82183,307.12,0.29494,-0.90441,0.30831,288.38>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.38026,-0.5892,0.71291,695.78,-0.92487,0.23958,-0.29532,524.71,0.0031968,-0.77165,-0.63604,80.022,#6,0.89444,0.2064,0.39671,238.34,-0.41773,0.068975,0.90595,307.07,0.15963,-0.97603,0.14791,289.82>
> view matrix models
> #5,-0.5285,-0.28376,0.80011,765.54,-0.81897,0.41863,-0.39249,436.75,-0.22357,-0.86269,-0.45363,240.31,#6,0.71586,0.49108,0.49637,234.85,-0.61119,0.096966,0.78552,307.27,0.33763,-0.8657,0.36956,287.71>
> view matrix models
> #5,-0.51604,-0.53596,0.66817,725.04,-0.85145,0.23586,-0.4684,430.37,0.093449,-0.81062,-0.57806,71.813,#6,0.81865,0.22719,0.52745,237.2,-0.52565,-0.073503,0.84752,308.55,0.23132,-0.97107,0.059251,290.46>
> view matrix models
> #5,0.13499,-0.86453,0.48411,433.78,-0.94222,-0.26318,-0.20726,596.47,0.30659,-0.42816,-0.85011,-136.41,#6,0.9742,-0.218,-0.058457,245.19,0.01674,-0.1885,0.98193,309.61,-0.22508,-0.95757,-0.17999,291.12>
> view matrix models
> #5,-0.2051,-0.47242,0.85718,680.36,-0.97757,0.056064,-0.20301,591.45,0.047851,-0.87959,-0.47332,133.72,#6,0.91015,0.36446,0.19695,238.22,-0.22163,0.026705,0.97477,307.33,0.35001,-0.93083,0.10508,290>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.2051,-0.47242,0.85718,680.48,-0.97757,0.056064,-0.20301,589.73,0.047851,-0.87959,-0.47332,130.59,#6,0.91015,0.36446,0.19695,238.33,-0.22163,0.026705,0.97477,305.62,0.35001,-0.93083,0.10508,286.87>
> view matrix models
> #5,-0.2051,-0.47242,0.85718,679,-0.97757,0.056064,-0.20301,590.84,0.047851,-0.87959,-0.47332,131,#6,0.91015,0.36446,0.19695,236.86,-0.22163,0.026705,0.97477,306.72,0.35001,-0.93083,0.10508,287.28>
> view matrix models
> #5,-0.2051,-0.47242,0.85718,679.45,-0.97757,0.056064,-0.20301,594.98,0.047851,-0.87959,-0.47332,131.08,#6,0.91015,0.36446,0.19695,237.31,-0.22163,0.026705,0.97477,310.86,0.35001,-0.93083,0.10508,287.36>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.95483,-0.2827,0.091546,645.11,0.025199,-0.384,-0.92299,-28.007,0.29608,-0.87899,0.37378,370.13,#6,0.22785,0.02406,0.9734,234.31,-0.31943,-0.94252,0.098068,325,0.91981,-0.33327,-0.20707,284.9>
> view matrix models
> #5,-0.84993,0.079467,-0.52086,345.21,0.34319,-0.66661,-0.6617,-25.719,-0.3998,-0.74116,0.5393,682.44,#6,-0.44284,-0.2143,0.87061,236.02,0.079783,-0.97658,-0.19981,327.86,0.89304,-0.019022,0.44957,277.85>
> view matrix models
> #5,-0.98119,0.14656,-0.12566,543.59,0.028815,-0.53242,-0.84599,9.8618,-0.19089,-0.8337,0.51818,602.99,#6,-0.23868,0.14371,0.96041,232.56,-0.15712,-0.98167,0.10784,325.56,0.9583,-0.12516,0.25688,280.14>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.98119,0.14656,-0.12566,550.85,0.028815,-0.53242,-0.84599,-0.71247,-0.19089,-0.8337,0.51818,614.04,#6,-0.23868,0.14371,0.96041,239.82,-0.15712,-0.98167,0.10784,314.99,0.9583,-0.12516,0.25688,291.19>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.98945,0.13416,0.054668,625.01,-0.078216,-0.17707,-0.98108,-35.936,-0.12194,-0.97501,0.1857,467.66,#6,-0.11084,0.27168,0.95598,238.91,-0.51782,-0.83681,0.17778,312.65,0.84828,-0.47532,0.23344,294.31>
> view matrix models
> #5,-0.97538,0.074364,0.20762,683.2,-0.21728,-0.16286,-0.96243,21.676,-0.037756,-0.98384,0.17501,433.03,#6,0.035553,0.34523,0.93785,238.6,-0.52267,-0.79344,0.31188,311.4,0.85179,-0.50128,0.15223,295.07>
> view matrix models
> #5,-0.94584,-0.32042,-0.052228,595.3,-0.02913,0.24399,-0.96934,-75.412,0.32334,-0.91531,-0.24011,133.88,#6,0.16175,-0.10917,0.98077,242.62,-0.82369,-0.56229,0.073256,310.34,0.54349,-0.8197,-0.18088,299.55>
> view matrix models
> #5,-0.95651,-0.28552,-0.059666,594.18,-0.02128,0.27232,-0.96197,-77.176,0.29091,-0.91887,-0.26655,135.73,#6,0.13016,-0.090561,0.98735,242.36,-0.83971,-0.53957,0.061211,310.19,0.5272,-0.83706,-0.14628,299.46>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.95651,-0.28552,-0.059666,584.96,-0.02128,0.27232,-0.96197,-73.984,0.29091,-0.91887,-0.26655,126.76,#6,0.13016,-0.090561,0.98735,233.14,-0.83971,-0.53957,0.061211,313.38,0.5272,-0.83706,-0.14628,290.49>
> view matrix models
> #5,-0.95651,-0.28552,-0.059666,586.7,-0.02128,0.27232,-0.96197,-73.161,0.29091,-0.91887,-0.26655,127.44,#6,0.13016,-0.090561,0.98735,234.88,-0.83971,-0.53957,0.061211,314.21,0.5272,-0.83706,-0.14628,291.18>
> view matrix models
> #5,-0.95651,-0.28552,-0.059666,586.01,-0.02128,0.27232,-0.96197,-72.51,0.29091,-0.91887,-0.26655,126.77,#6,0.13016,-0.090561,0.98735,234.19,-0.83971,-0.53957,0.061211,314.86,0.5272,-0.83706,-0.14628,290.5>
> view matrix models
> #5,-0.95651,-0.28552,-0.059666,586.93,-0.02128,0.27232,-0.96197,-70.705,0.29091,-0.91887,-0.26655,125.92,#6,0.13016,-0.090561,0.98735,235.11,-0.83971,-0.53957,0.061211,316.66,0.5272,-0.83706,-0.14628,289.65>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#6) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006833, steps = 2000
shifted from previous position = 35.4
rotated from previous position = 6.86 degrees
atoms outside contour = 2846, contour level = 0.0076678
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.96231226 -0.25463330 -0.09548300 575.09609390
0.04958688 0.18092578 -0.98224590 -102.68057512
0.26738785 -0.94996197 -0.16148063 179.64811468
Axis 0.06802008 -0.76454471 0.64097164
Axis point 280.58340423 0.00000000 90.80899720
Rotation angle (degrees) 166.27206933
Shift along axis 232.77132307
Position of AlphaFold P84078 (#6) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.08310170 -0.09647993 0.99185973 236.97187835
-0.78120515 -0.62425648 0.00472976 314.26811764
0.61871854 -0.77523898 -0.12724739 291.28053862
Axis -0.70718474 0.33832095 -0.62082902
Axis point 0.00000000 243.78687797 -42.59228603
Rotation angle (degrees) 146.53274098
Shift along axis -242.09482207
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.59055,-0.24829,-0.76786,-259.42,0.70109,-0.31337,0.64052,321.03,-0.39966,-0.9166,-0.010989,481.93,#6,-0.29252,-0.8208,-0.49063,252.32,0.69029,0.17381,-0.70235,314,0.66176,-0.54412,0.51575,285.18>
> view matrix models
> #5,0.7237,0.28678,-0.62771,-286.79,0.30928,-0.94789,-0.07649,224.72,-0.61694,-0.13878,-0.77468,215.99,#6,-0.59531,-0.38863,-0.70326,249.29,0.67517,-0.71645,-0.17562,318.62,-0.4356,-0.57937,0.6889,282.6>
> view matrix models
> #5,0.48684,0.83037,0.27104,117.52,0.74137,-0.22872,-0.63092,-195.07,-0.4619,0.5081,-0.72697,137.6,#6,-0.4215,0.66998,-0.61112,239.46,-0.20984,-0.72768,-0.65303,320.32,-0.88222,-0.14701,0.4473,279.52>
> view matrix models
> #5,-0.1243,0.97397,-0.18956,154,0.87072,0.19868,0.44985,152.58,0.4758,-0.10914,-0.87275,-226.48,#6,-0.86155,0.50756,0.010362,236.25,0.1883,0.33845,-0.92195,313.09,-0.47145,-0.79236,-0.38717,291.31>
> view matrix models
> #5,-0.11846,0.94765,0.29653,343.11,0.9592,0.18642,-0.21256,-137.68,-0.25671,0.25925,-0.93107,-2.2351,#6,-0.52096,0.85304,-0.030271,233.95,-0.23522,-0.17756,-0.95559,317.26,-0.82053,-0.49071,0.29315,283.69>
> view matrix models
> #5,0.38244,0.69187,-0.61242,-180.16,-0.34259,0.72174,0.60144,626.22,0.85812,-0.020207,0.51305,167.91,#6,-0.90509,-0.065052,-0.42021,244.07,-0.16086,0.96717,0.19675,299.74,0.39361,0.24568,-0.88584,286.56>
> view matrix models
> #5,-0.010124,0.85975,0.51061,392.17,0.13388,-0.50488,0.85275,624.51,0.99095,0.076994,-0.10999,-130.07,#6,-0.30877,0.94037,-0.14271,234.23,0.94742,0.29083,-0.13346,309.74,-0.083995,-0.17641,-0.98073,290.18>
> view matrix models
> #5,-0.47691,0.62752,0.61544,619.28,0.80676,0.034608,0.58987,240.89,0.34886,0.77783,-0.52276,-97.925,#6,-0.087213,0.93611,0.34072,231.55,0.40075,0.3461,-0.8483,312.9,-0.91203,0.06256,-0.40533,283.01>
> view matrix models
> #5,-0.26096,0.59122,0.76313,599.62,0.96303,0.10471,0.2482,45.716,0.066835,0.79969,-0.59668,-24.265,#6,0.047515,0.99159,0.12042,232.68,0.13013,0.11338,-0.98499,315.42,-0.99036,0.062472,-0.12365,281.09>
> view matrix models
> #5,-0.95651,0.065195,0.28433,701.4,0.28764,0.048556,0.95651,574.22,0.048553,0.99669,-0.065196,177.67,#6,0.093902,0.39389,0.91435,233.07,0.60782,0.7047,-0.36599,306.94,-0.7885,0.59013,-0.17324,276.99>
> view matrix models
> #5,-0.4407,0.038915,0.89681,752.05,0.84001,-0.33436,0.4273,187.99,0.31649,0.94164,0.11467,152.57,#6,0.54165,0.75973,0.35977,234.04,0.57191,-0.019389,-0.82008,316.29,-0.61606,0.64995,-0.445,278.47>
> view matrix models
> #5,0.015963,0.0070203,0.99985,626.06,0.36125,-0.93247,0.00077988,234.78,0.93233,0.36118,-0.017421,-89.91,#6,0.65487,0.74969,-0.095485,237.22,0.71699,-0.65625,-0.23508,318.53,-0.2389,0.085485,-0.96727,287.49>
> view matrix models
> #5,-0.060137,0.76102,0.64593,469.47,-0.21824,-0.64147,0.73545,716.84,0.97404,-0.096742,0.20466,9.6358,#6,-0.14779,0.98482,-0.09103,233.76,0.95609,0.16581,0.24165,308.49,0.25307,-0.051321,-0.96609,289.51>
> view matrix models
> #5,0.42809,0.027838,0.90331,435.35,0.79791,-0.48097,-0.36332,-95.922,0.42435,0.8763,-0.22811,-16.842,#6,0.59484,0.63108,-0.4979,240.75,0.15853,-0.69933,-0.697,320.95,-0.78806,0.33567,-0.51603,281.47>
> view matrix models
> #5,0.2184,0.60798,0.76332,422.15,0.74111,-0.61222,0.27558,182.36,0.63487,0.50552,-0.58429,-210.44,#6,0.057465,0.9329,-0.35553,236.25,0.6757,-0.2985,-0.67404,318.04,-0.73494,-0.2015,-0.64751,287.22>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#6) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006369, steps = 2000
shifted from previous position = 47.6
rotated from previous position = 11.7 degrees
atoms outside contour = 2902, contour level = 0.0076678
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.30252382 0.72278836 0.62133431 332.10274732
0.73609320 -0.59129658 0.32944673 198.61776044
0.60551312 0.35769448 -0.71092090 -235.47233701
Axis 0.80699148 0.45198534 0.38009736
Axis point 0.00000000 8.13542212 -195.52778063
Rotation angle (degrees) 178.99716459
Shift along axis 268.27399044
Position of AlphaFold P84078 (#6) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.11837831 0.88892254 -0.44249665 240.32340880
0.69529073 -0.24394520 -0.67606327 312.28320062
-0.70891281 -0.38769505 -0.58918178 293.00918140
Axis 0.65874746 0.60860025 -0.44233191
Axis point 0.00000000 12.35318661 242.25345413
Rotation angle (degrees) 167.35696729
Shift along axis 218.76075747
> view matrix models
> #5,-0.2533,0.92841,0.27182,387.72,0.081794,-0.25943,0.96229,665.97,0.96392,0.26598,-0.010227,-88.419,#6,-0.52912,0.84171,0.10744,236.57,0.83308,0.53936,-0.12273,301.94,-0.16125,0.024573,-0.98661,292.73>
> view matrix models
> #5,-0.080396,0.95861,-0.27315,109.58,-0.50547,0.19698,0.84006,806.36,0.85909,0.20561,0.46871,140.76,#6,-0.9031,0.42874,-0.024432,240.52,0.38261,0.82915,0.40758,295.22,0.195,0.35873,-0.91284,289.83>
> ui mousemode right "rotate selected models"> ui mousemode right "translate
> selected models"> view matrix models
> #5,-0.080396,0.95861,-0.27315,113.92,-0.50547,0.19698,0.84006,812.52,0.85909,0.20561,0.46871,133.27,#6,-0.9031,0.42874,-0.024432,244.86,0.38261,0.82915,0.40758,301.37,0.195,0.35873,-0.91284,282.33>
> view matrix models
> #5,-0.080396,0.95861,-0.27315,109.21,-0.50547,0.19698,0.84006,820.14,0.85909,0.20561,0.46871,139.18,#6,-0.9031,0.42874,-0.024432,240.16,0.38261,0.82915,0.40758,309,0.195,0.35873,-0.91284,288.24>
> view matrix models
> #5,-0.080396,0.95861,-0.27315,108.57,-0.50547,0.19698,0.84006,824.36,0.85909,0.20561,0.46871,140.38,#6,-0.9031,0.42874,-0.024432,239.51,0.38261,0.82915,0.40758,313.22,0.195,0.35873,-0.91284,289.45>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.091143,0.9467,0.30895,273.24,-0.16968,-0.29094,0.94157,770.43,0.98128,-0.13824,0.13412,-13.934,#6,-0.50226,0.83124,-0.23827,237.91,0.83131,0.54002,0.13155,318.31,0.23802,-0.132,-0.96225,294.25>
> view matrix models
> #5,0.63807,0.72115,0.26983,70.505,-0.17926,-0.20168,0.96291,776.77,0.74882,-0.66278,0.00058407,51.936,#6,-0.33328,0.5763,-0.7462,243.71,0.77796,0.6152,0.12766,317.57,0.53263,-0.53797,-0.65337,296.41>
> view matrix models
> #5,0.53579,0.82092,0.19753,73.802,-0.12537,-0.154,0.98008,760.69,0.83499,-0.54989,0.020404,20.971,#6,-0.4606,0.60178,-0.65247,242.68,0.75604,0.65111,0.066811,317.6,0.46503,-0.46252,-0.75486,296.27>
> view matrix models
> #5,0.19065,0.96194,0.19575,191.5,-0.028672,-0.19387,0.98061,727.75,0.98124,-0.19256,-0.0093789,-66.552,#6,-0.5837,0.74202,-0.32968,239.16,0.79081,0.61161,-0.023577,318.59,0.18414,-0.27448,-0.9438,295.32>
> view matrix models
> #5,-0.062999,0.98925,-0.13198,155.35,-0.13769,0.12236,0.98289,749.26,0.98847,0.080093,0.1285,-32.246,#6,-0.83218,0.5516,-0.056758,238.73,0.54997,0.8341,0.042615,315.77,0.070848,0.0042482,-0.99748,292.97>
> view matrix models
> #5,-0.19218,0.97766,0.085187,288.36,0.077415,-0.071431,0.99444,686.52,0.9783,0.19771,-0.061957,-110.07,#6,-0.6863,0.72522,0.055312,236.69,0.71303,0.68586,-0.14553,318.57,-0.14347,-0.060435,-0.98781,293.14>
> view matrix models
> #5,0.41028,0.85223,0.32461,167.67,0.16147,-0.41821,0.89388,637.74,0.89755,-0.31433,-0.30919,-145.19,#6,-0.40615,0.73532,-0.54254,240.87,0.91082,0.37374,-0.17531,321.89,0.07386,-0.56535,-0.82153,296.98>
> view matrix models
> #5,0.34369,0.68075,0.64689,328.5,0.33116,-0.73245,0.59485,477.98,0.87876,0.0097805,-0.47717,-223.81,#6,-0.068061,0.87479,-0.47969,239.76,0.9573,-0.078141,-0.27833,326.69,-0.28096,-0.47815,-0.83212,295.68>
> view matrix models
> #5,0.16198,0.73523,0.65818,396.46,0.33802,-0.66797,0.66299,498.06,0.9271,0.11509,-0.35672,-201.11,#6,-0.10998,0.94497,-0.30813,237.97,0.95418,0.013589,-0.29891,325.99,-0.27828,-0.32689,-0.90316,294.78>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.16198,0.73523,0.65818,392.54,0.33802,-0.66797,0.66299,486.45,0.9271,0.11509,-0.35672,-202.35,#6,-0.10998,0.94497,-0.30813,234.06,0.95418,0.013589,-0.29891,314.38,-0.27828,-0.32689,-0.90316,293.55>
> view matrix models
> #5,0.16198,0.73523,0.65818,392.9,0.33802,-0.66797,0.66299,484.42,0.9271,0.11509,-0.35672,-202.32,#6,-0.10998,0.94497,-0.30813,234.41,0.95418,0.013589,-0.29891,312.35,-0.27828,-0.32689,-0.90316,293.58>
> view matrix models
> #5,0.16198,0.73523,0.65818,397.84,0.33802,-0.66797,0.66299,485.66,0.9271,0.11509,-0.35672,-198.61,#6,-0.10998,0.94497,-0.30813,239.35,0.95418,0.013589,-0.29891,313.59,-0.27828,-0.32689,-0.90316,297.28>
> view matrix models
> #5,0.16198,0.73523,0.65818,399.84,0.33802,-0.66797,0.66299,484.43,0.9271,0.11509,-0.35672,-202.16,#6,-0.10998,0.94497,-0.30813,241.35,0.95418,0.013589,-0.29891,312.36,-0.27828,-0.32689,-0.90316,293.73>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#6) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006527, steps = 2000
shifted from previous position = 57.2
rotated from previous position = 12.8 degrees
atoms outside contour = 2926, contour level = 0.0076678
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04834974 0.70373818 0.70881229 499.38635257
0.37624850 -0.64453776 0.66558855 468.54924077
0.92525637 0.29887060 -0.23361721 -164.79401783
Axis -0.68265201 -0.40291451 -0.60962787
Axis point 0.00000000 44.16621885 -335.00198418
Rotation angle (degrees) 164.41914190
Shift along axis -429.22935818
Position of AlphaFold P84078 (#6) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.06279140 0.99298997 -0.10014066 240.07573806
0.94010178 0.02516248 -0.33996394 311.12020767
-0.33506099 -0.11548923 -0.93509163 291.94452474
Axis 0.68187636 0.71360654 -0.16065598
Axis point -8.49428540 0.00000000 180.46874782
Rotation angle (degrees) 170.52595832
Shift along axis 338.81675107
> view matrix models
> #5,-0.04835,0.70374,0.70881,497.88,0.37625,-0.64454,0.66559,469.9,0.92526,0.29887,-0.23362,-167.1,#6,-0.062791,0.99299,-0.10014,238.57,0.9401,0.025162,-0.33996,312.47,-0.33506,-0.11549,-0.93509,289.64>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.25589,0.96045,0.10979,324.76,-0.29595,-0.18595,0.93693,794.98,0.92029,0.20726,0.33183,60.99,#6,-0.66014,0.74172,0.11858,238.46,0.74358,0.62294,0.24297,303.06,0.10635,0.24857,-0.96276,287.27>
> view matrix models
> #5,-0.26553,0.96312,-0.043574,268.31,-0.40314,-0.069863,0.91247,817.74,0.87577,0.25985,0.40682,103.4,#6,-0.76373,0.6302,0.13985,239.16,0.63534,0.69548,0.33565,301.64,0.11427,0.3452,-0.93155,286.21>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.26553,0.96312,-0.043574,265.25,-0.40314,-0.069863,0.91247,819.82,0.87577,0.25985,0.40682,101.72,#6,-0.76373,0.6302,0.13985,236.1,0.63534,0.69548,0.33565,303.71,0.11427,0.3452,-0.93155,284.53>
> view matrix models
> #5,-0.26553,0.96312,-0.043574,264.6,-0.40314,-0.069863,0.91247,824.29,0.87577,0.25985,0.40682,102.95,#6,-0.76373,0.6302,0.13985,235.45,0.63534,0.69548,0.33565,308.18,0.11427,0.3452,-0.93155,285.76>
> view matrix models
> #5,-0.26553,0.96312,-0.043574,265.77,-0.40314,-0.069863,0.91247,822.97,0.87577,0.25985,0.40682,103.9,#6,-0.76373,0.6302,0.13985,236.62,0.63534,0.69548,0.33565,306.86,0.11427,0.3452,-0.93155,286.71>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.096354,0.96226,-0.25451,121.23,-0.71537,0.11084,0.6899,839.95,0.69207,0.24855,0.67769,277.91,#6,-0.89429,0.44735,-0.010607,239.01,0.33839,0.6916,0.63811,304.48,0.2928,0.56707,-0.76987,283.98>
> view matrix models
> #5,-0.41274,-0.045038,-0.90974,44.264,-0.90109,-0.12566,0.41503,815.7,-0.13301,0.99105,0.011283,275.92,#6,-0.58546,-0.64927,0.48548,246.22,0.32588,0.35985,0.87425,305.94,-0.74232,0.67004,0.0009085,276.45>
> view matrix models
> #5,-0.59233,-0.74854,-0.29805,392.45,-0.67701,0.66298,-0.31957,397.92,0.43681,0.012488,-0.89947,-228.84,#6,0.33736,-0.62179,0.7068,246.07,-0.7398,0.28919,0.60751,306.54,-0.58215,-0.72783,-0.36244,291.6>
> view matrix models
> #5,-0.88795,-0.45286,-0.080415,567.97,0.28284,-0.39976,-0.87189,-105.43,0.3627,-0.79694,0.48306,387.78,#6,0.24524,-0.22449,0.94311,240.84,-0.26186,-0.952,-0.15852,323.36,0.93343,-0.20809,-0.29225,288.95>
> view matrix models
> #5,-0.88787,-0.45545,-0.065149,574.06,0.085665,-0.024526,-0.99602,-104.41,0.45204,-0.88992,0.060792,195.88,#6,0.25725,-0.21477,0.94218,240.78,-0.63446,-0.77295,-0.0029616,320.15,0.72889,-0.59701,-0.33511,292.39>
> view matrix models
> #5,-0.84528,-0.53404,-0.017379,581.86,-0.0041565,0.039095,-0.99923,-76.507,0.53431,-0.84455,-0.035266,125.31,#6,0.34971,-0.23618,0.9066,241.35,-0.68851,-0.72105,0.077736,319.08,0.63535,-0.65138,-0.41477,293.24>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.84528,-0.53404,-0.017379,577.09,-0.0041565,0.039095,-0.99923,-81.656,0.53431,-0.84455,-0.035266,122.35,#6,0.34971,-0.23618,0.9066,236.58,-0.68851,-0.72105,0.077736,313.93,0.63535,-0.65138,-0.41477,290.28>
> view matrix models
> #5,-0.84528,-0.53404,-0.017379,575.68,-0.0041565,0.039095,-0.99923,-81.253,0.53431,-0.84455,-0.035266,119.47,#6,0.34971,-0.23618,0.9066,235.17,-0.68851,-0.72105,0.077736,314.34,0.63535,-0.65138,-0.41477,287.4>
> view matrix models
> #5,-0.84528,-0.53404,-0.017379,575.42,-0.0041565,0.039095,-0.99923,-80.212,0.53431,-0.84455,-0.035266,121.31,#6,0.34971,-0.23618,0.9066,234.91,-0.68851,-0.72105,0.077736,315.38,0.63535,-0.65138,-0.41477,289.24>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.898,-0.43956,0.019715,603.47,-0.0080542,-0.028378,-0.99956,-74.745,0.43993,-0.89776,0.021943,181.67,#6,0.30082,-0.13956,0.94341,233.73,-0.63829,-0.76447,0.090441,315.77,0.70859,-0.62938,-0.31905,288.55>
> view matrix models
> #5,-0.73058,-0.67803,0.080783,580.37,-0.29541,0.20719,-0.93263,42.645,0.61561,-0.70523,-0.35167,-40.668,#6,0.52783,-0.27279,0.80435,236.18,-0.78432,-0.51998,0.33834,311.75,0.32595,-0.80945,-0.48842,290.62>
> view matrix models
> #5,-0.82117,-0.54947,0.15417,634.42,-0.23969,0.0869,-0.96695,16.16,0.51791,-0.83098,-0.20306,61.046,#6,0.47555,-0.12144,0.87127,234.31,-0.71409,-0.6317,0.30171,313.1,0.51374,-0.76564,-0.38712,289.89>
> view matrix models
> #5,-0.86724,-0.44653,0.22026,670.82,-0.32028,0.16161,-0.93344,54.301,0.38121,-0.88006,-0.28317,83.161,#6,0.43974,0.0013758,0.89812,232.98,-0.75181,-0.54651,0.36894,311.85,0.49134,-0.83745,-0.23929,289.56>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#6) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006896, steps = 2000
shifted from previous position = 102
rotated from previous position = 20.5 degrees
atoms outside contour = 2836, contour level = 0.0076678
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.97686247 -0.21016135 0.03964732 631.50637819
-0.05878614 0.08561538 -0.99459247 -62.25688663
0.20563048 -0.97391077 -0.09598903 229.87395164
Axis 0.09167666 -0.73576092 0.67100764
Axis point 309.69104936 0.00000000 109.91985102
Rotation angle (degrees) 173.52342786
Shift along axis 257.94776112
Position of AlphaFold P84078 (#6) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.13817331 0.03547624 0.98977248 236.96498569
-0.72290436 -0.67949678 0.12527331 313.54567562
0.67699144 -0.73282027 -0.06824239 291.07456381
Axis -0.72282519 0.26347478 -0.63883079
Axis point 0.00000000 226.26842741 -46.97006814
Rotation angle (degrees) 143.58929744
Shift along axis -274.62027921
> ui tool show AlphaFold> alphafold match P840781 AlphaFold model found using
> UniProt identifier: P84078 (UniProt P84078)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P84078 | P84078 | 100.0 | 100.0
Opened 1 AlphaFold model
> select subtract #61934 atoms, 1972 bonds, 238 residues, 1 model selected
> select add #73391 atoms, 3455 bonds, 419 residues, 2 models selected
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.97686,-0.21016,0.039647,976.12,-0.058786,0.085615,-0.99459,70.39,0.20563,-0.97391,-0.095989,418.44,#7,1,0,0,344.62,0,1,0,132.65,0,0,1,188.56>
> view matrix models
> #5,-0.97686,-0.21016,0.039647,914.72,-0.058786,0.085615,-0.99459,296.23,0.20563,-0.97391,-0.095989,481.88,#7,1,0,0,283.21,0,1,0,358.48,0,0,1,252.01>
> view matrix models
> #5,-0.97686,-0.21016,0.039647,898.61,-0.058786,0.085615,-0.99459,313.49,0.20563,-0.97391,-0.095989,495.6,#7,1,0,0,267.11,0,1,0,375.75,0,0,1,265.73>
> view matrix models
> #5,-0.97686,-0.21016,0.039647,874.97,-0.058786,0.085615,-0.99459,288.55,0.20563,-0.97391,-0.095989,517.06,#7,1,0,0,243.47,0,1,0,350.81,0,0,1,287.18>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.85125,-0.13258,-0.50773,735.11,0.24578,-0.9556,-0.16254,548.99,-0.46364,-0.26316,0.84604,714,#7,0.83929,0.54368,0.0028187,238.3,-0.045712,0.065399,0.99681,352.79,0.54176,-0.83674,0.079742,301.46>
> view matrix models
> #5,-0.57508,-0.29644,-0.7625,617.64,-0.20794,-0.84847,0.48669,817.01,-0.79123,0.43844,0.42629,618.56,#7,0.59384,0.7668,0.24365,234.35,0.40074,-0.54448,0.73686,360.66,0.69768,-0.33994,-0.63062,301.77>
> volume #1 level 0.006976> volume #1 level 0.01071> view matrix models
> #5,-0.092924,-0.41978,-0.90286,377.16,-0.46451,-0.78378,0.41222,934.2,-0.88068,0.45769,-0.12216,621.65,#7,0.1432,0.8675,0.47638,231.23,0.63483,-0.44979,0.62824,360.88,0.75927,0.21246,-0.61512,296.8>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.092924,-0.41978,-0.90286,349.18,-0.46451,-0.78378,0.41222,934.92,-0.88068,0.45769,-0.12216,595.75,#7,0.1432,0.8675,0.47638,203.25,0.63483,-0.44979,0.62824,361.61,0.75927,0.21246,-0.61512,270.9>
> volume #1 level 0.0067> view matrix models
> #5,-0.092924,-0.41978,-0.90286,374.03,-0.46451,-0.78378,0.41222,927.65,-0.88068,0.45769,-0.12216,624.03,#7,0.1432,0.8675,0.47638,228.1,0.63483,-0.44979,0.62824,354.34,0.75927,0.21246,-0.61512,299.18>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.78353,-0.53891,-0.30928,853.27,-0.52511,0.3082,0.79327,600.83,-0.33218,0.78395,-0.52447,165.9,#7,0.8664,0.30753,0.39342,234.85,0.47963,-0.73172,-0.48428,363.71,0.13894,0.60828,-0.78147,295.66>
> view matrix models
> #5,-0.49504,-0.20081,-0.84535,528.72,-0.8214,-0.20904,0.53067,934.23,-0.28328,0.95707,-0.061463,110.84,#7,0.49227,0.85268,0.17492,230.72,0.86736,-0.49741,-0.016255,359.25,0.073149,0.15972,-0.98445,300.88>
> view matrix models
> #5,-0.31735,0.55711,-0.76741,163.09,-0.71256,-0.67406,-0.19467,984.26,-0.62573,0.48505,0.61089,524,#7,0.1625,0.82961,-0.53417,234.91,0.83002,0.1778,0.52864,349.65,0.53354,-0.52928,-0.6597,305.77>
> view matrix models
> #5,-0.42011,0.76147,-0.49364,168.97,-0.86041,-0.50714,-0.05003,1019.5,-0.28844,0.40371,0.86823,380.5,#7,0.23079,0.58086,-0.7806,238.83,0.9451,0.056921,0.32178,352.24,0.23134,-0.81201,-0.53583,307.03>
> view matrix models
> #5,-0.59175,0.80293,0.071683,293.85,-0.77375,-0.5408,-0.32991,961.41,-0.22613,-0.25069,0.94129,584.05,#7,0.41216,0.032235,-0.91054,244.89,0.85643,0.32731,0.39925,349.17,0.3109,-0.94437,0.1073,304.25>
> view matrix models
> #5,-0.60495,0.24786,-0.7567,437.69,-0.53688,-0.82878,0.15775,965.88,-0.58804,0.50169,0.63444,498.4,#7,0.50886,0.80939,-0.29315,234.12,0.70489,-0.19629,0.68162,351.83,0.49415,-0.55349,-0.67042,305.99>
> view matrix models
> #5,-0.32974,0.62176,-0.71042,151.31,-0.43463,-0.76799,-0.47041,839.27,-0.83807,0.15366,0.52347,756.42,#7,0.16328,0.77919,-0.60515,235.81,0.56733,0.42767,0.70373,345.85,0.80714,-0.45822,-0.37223,303.74>
> view matrix models
> #5,-0.00082256,-0.62086,-0.78392,402.3,-0.99976,0.017546,-0.012847,914.25,0.02173,0.78373,-0.62073,-42.334,#7,0.1002,0.72658,0.67974,228,0.97243,0.073052,-0.22144,355.6,-0.21055,0.68319,-0.69923,293.9>
> view matrix models
> #5,-0.30162,0.011223,-0.95336,335.08,-0.95287,-0.037697,0.30102,930.7,-0.03256,0.99923,0.022064,-40.478,#7,0.25448,0.9669,0.01856,230.3,0.95068,-0.2466,-0.18812,358.23,-0.17732,0.065518,-0.98197,301.31>
> view matrix models
> #5,-0.22656,0.75112,-0.62007,53.238,-0.70375,-0.56636,-0.42892,923.37,-0.67335,0.3392,0.65692,606.54,#7,0.038882,0.69435,-0.71859,237.1,0.78949,0.41948,0.44805,347.92,0.61253,-0.58474,-0.53187,305.58>
> view matrix models
> #5,-0.1711,-0.05398,-0.98377,281.9,-0.77949,-0.60328,0.16868,1024.1,-0.60259,0.7957,0.061145,359.03,#7,0.13948,0.98389,0.11182,229.37,0.89493,-0.17359,0.41106,353.66,0.42385,0.042734,-0.90472,302>
> view matrix models
> #5,0.31548,0.11853,-0.9415,-53.054,-0.91235,0.3107,-0.2666,741.05,0.26093,0.94309,0.20617,-173.53,#7,-0.37042,0.92801,0.039805,229.5,0.81538,0.34539,-0.46461,354.44,-0.44491,-0.13965,-0.88462,302.1>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.31548,0.11853,-0.9415,-41.293,-0.91235,0.3107,-0.2666,742.29,0.26093,0.94309,0.20617,-185.05,#7,-0.37042,0.92801,0.039805,241.26,0.81538,0.34539,-0.46461,355.68,-0.44491,-0.13965,-0.88462,290.57>
> view matrix models
> #5,0.31548,0.11853,-0.9415,-39.115,-0.91235,0.3107,-0.2666,741.63,0.26093,0.94309,0.20617,-182.57,#7,-0.37042,0.92801,0.039805,243.43,0.81538,0.34539,-0.46461,355.02,-0.44491,-0.13965,-0.88462,293.05>
> view matrix models
> #5,0.31548,0.11853,-0.9415,-38.981,-0.91235,0.3107,-0.2666,737.98,0.26093,0.94309,0.20617,-182.3,#7,-0.37042,0.92801,0.039805,243.57,0.81538,0.34539,-0.46461,351.37,-0.44491,-0.13965,-0.88462,293.32>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#7) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.00607, steps = 2000
shifted from previous position = 207
rotated from previous position = 33.5 degrees
atoms outside contour = 2860, contour level = 0.0066997
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.70129333 0.30350009 -0.64503902 -301.43057902
-0.66567175 0.60257977 -0.44020305 479.70630653
0.25508580 0.73809573 0.62461662 -80.49754857
Axis 0.66517422 -0.50813923 -0.54711771
Axis point 0.00000000 496.85702895 179.18523971
Rotation angle (degrees) 62.33863827
Shift along axis -400.21980655
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.77442520 0.62630892 -0.08945806 247.17999696
0.50617791 0.52854501 -0.68148668 349.61333079
-0.37953857 -0.57304215 -0.72634232 290.47483922
Axis 0.32647079 0.87328350 -0.36165279
Axis point 77.01233711 0.00000000 210.18703682
Rotation angle (degrees) 170.43966562
Shift along axis 280.95756714
> view matrix models
> #5,0.70129,0.3035,-0.64504,-301.05,-0.66567,0.60258,-0.4402,479.69,0.25509,0.7381,0.62462,-80.042,#7,-0.77443,0.62631,-0.089458,247.56,0.50618,0.52855,-0.68149,349.6,-0.37954,-0.57304,-0.72634,290.93>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.64904,0.39252,-0.65167,-303.62,-0.72842,0.56773,-0.38351,532.01,0.21944,0.72361,0.6544,-52.392,#7,-0.74235,0.6436,-0.18627,248.07,0.57705,0.47287,-0.66589,350.12,-0.34049,-0.60181,-0.72242,291.23>
> view matrix models
> #5,0.61859,0.44518,-0.64742,-304.79,-0.7605,0.54632,-0.35097,560.31,0.19745,0.70947,0.67651,-33.203,#7,-0.72351,0.64567,-0.24422,248.45,0.61417,0.44056,-0.65476,350.4,-0.31516,-0.62372,-0.7153,291.42>
> view matrix models
> #5,0.61336,0.44471,-0.6527,-302.04,-0.7266,0.64166,-0.24561,514.88,0.30958,0.6249,0.7167,-63.763,#7,-0.71851,0.65119,-0.24434,248.41,0.5652,0.34194,-0.75075,351.82,-0.40534,-0.67752,-0.61374,291.11>
> view matrix models
> #5,0.61839,0.40672,-0.67244,-292.81,-0.59513,0.80117,-0.062717,396.87,0.51323,0.43898,0.73749,-111.61,#7,-0.71622,0.66727,-0.2044,248.02,0.4105,0.16596,-0.89663,354.07,-0.56438,-0.72609,-0.39278,289.88>
> view matrix models
> #5,0.62873,0.64782,-0.43015,-366.67,-0.73016,0.68211,-0.039965,517.79,0.26752,0.3392,0.90187,75.891,#7,-0.76739,0.44633,-0.46034,251.55,0.56833,0.14107,-0.81062,354.01,-0.29686,-0.88368,-0.36191,291.54>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.62873,0.64782,-0.43015,-373.64,-0.73016,0.68211,-0.039965,516.13,0.26752,0.3392,0.90187,76.782,#7,-0.76739,0.44633,-0.46034,244.58,0.56833,0.14107,-0.81062,352.35,-0.29686,-0.88368,-0.36191,292.43>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#7) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006366, steps = 2000
shifted from previous position = 68.3
rotated from previous position = 12.9 degrees
atoms outside contour = 2782, contour level = 0.0066997
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.62743406 0.74307018 -0.23275136 -389.00714335
-0.75912757 0.65026798 0.02961206 547.56145841
0.17335459 0.15810837 0.97208534 199.59025622
Axis 0.08229454 -0.26008764 -0.96207174
Axis point 303.22479500 634.96258447 0.00000000
Rotation angle (degrees) 51.32561454
Shift along axis -366.44727440
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.77830940 0.25822657 -0.57232292 250.13871784
0.60607608 0.07084719 -0.79224520 351.34780734
-0.16403129 -0.96348312 -0.21164598 291.84550134
Axis -0.30412633 -0.72514452 0.61779657
Axis point 13.26729456 0.00000000 315.83389237
Rotation angle (degrees) 163.64879838
Shift along axis -150.55055819
> view matrix models
> #5,0.62743,0.74307,-0.23275,-393.66,-0.75913,0.65027,0.029612,544.8,0.17335,0.15811,0.97209,196.96,#7,-0.77831,0.25823,-0.57232,245.49,0.60608,0.070847,-0.79225,348.59,-0.16403,-0.96348,-0.21165,289.22>
> volume #1 level 0.007668> view matrix models
> #5,0.62743,0.74307,-0.23275,-389.57,-0.75913,0.65027,0.029612,546.54,0.17335,0.15811,0.97209,197.91,#7,-0.77831,0.25823,-0.57232,249.57,0.60608,0.070847,-0.79225,350.33,-0.16403,-0.96348,-0.21165,290.16>
> view matrix models
> #5,0.62743,0.74307,-0.23275,-394.31,-0.75913,0.65027,0.029612,546.08,0.17335,0.15811,0.97209,198.81,#7,-0.77831,0.25823,-0.57232,244.83,0.60608,0.070847,-0.79225,349.86,-0.16403,-0.96348,-0.21165,291.07>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.21109,0.74123,-0.6372,-187.17,-0.97471,0.11072,-0.1941,844.46,-0.073321,0.66206,0.74586,142.32,#7,-0.38725,0.6848,-0.61732,241.92,0.9212,0.25983,-0.28963,345.48,-0.037943,-0.68083,-0.73146,292.04>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.21109,0.74123,-0.6372,-185.42,-0.97471,0.11072,-0.1941,853.15,-0.073321,0.66206,0.74586,142.55,#7,-0.38725,0.6848,-0.61732,243.67,0.9212,0.25983,-0.28963,354.17,-0.037943,-0.68083,-0.73146,292.27>
> view matrix models
> #5,0.21109,0.74123,-0.6372,-185.65,-0.97471,0.11072,-0.1941,852.57,-0.073321,0.66206,0.74586,140.9,#7,-0.38725,0.6848,-0.61732,243.44,0.9212,0.25983,-0.28963,353.58,-0.037943,-0.68083,-0.73146,290.62>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.003999,0.81501,-0.57943,-89.972,-0.94546,0.19182,0.26328,841.08,0.32573,0.54678,0.77132,-42.862,#7,-0.19816,0.64584,-0.73731,244.86,0.8937,-0.18986,-0.4065,358.33,-0.40252,-0.73949,-0.53957,289.33>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#7) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006182, steps = 2000
shifted from previous position = 726
rotated from previous position = 171 degrees
atoms outside contour = 2996, contour level = 0.0076678
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.50985198 0.62390399 0.59227929 352.88224092
0.48726269 0.77683931 -0.39886807 -230.28494929
-0.70896122 0.08523193 -0.70007820 614.27879090
Axis 0.34700498 0.93273485 -0.09794507
Axis point 349.83451264 0.00000000 206.65062897
Rotation angle (degrees) 135.76999700
Shift along axis -152.50848503
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.39041705 -0.50568852 -0.76932025 251.69547574
-0.65506429 0.43457629 -0.61808917 352.53029652
0.64688894 0.74526677 -0.16159250 289.30819786
Axis 0.69154220 -0.71835123 -0.07576866
Axis point 130.13070659 0.00000000 314.93649546
Rotation angle (degrees) 99.68896785
Shift along axis -101.10302239
> view matrix models
> #5,0.89829,0.066059,0.4344,-260.13,-0.42278,0.39926,0.81354,512.01,-0.1197,-0.91445,0.38658,717.07,#7,-0.87417,-0.4792,0.078683,243.99,0.36134,-0.75011,-0.55387,364.44,0.32444,-0.45575,0.82888,293.28>
> view matrix models
> #5,0.51536,0.72527,-0.45649,-344.11,-0.58927,0.68668,0.42572,475.17,0.62222,0.049593,0.78127,-19.189,#7,-0.67396,0.48582,-0.55656,239.68,0.4482,-0.32999,-0.8308,362.57,-0.58727,-0.80937,0.0046558,300.22>
> view matrix models
> #5,0.46109,0.74604,-0.48044,-322.46,-0.54373,0.66542,0.51144,463.26,0.70125,0.025407,0.71246,-60.599,#7,-0.62626,0.51461,-0.58564,239.69,0.41158,-0.41974,-0.80896,363.17,-0.66212,-0.74766,0.051065,299.25>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.46109,0.74604,-0.48044,-319.66,-0.54373,0.66542,0.51144,457.08,0.70125,0.025407,0.71246,-62.663,#7,-0.62626,0.51461,-0.58564,242.49,0.41158,-0.41974,-0.80896,356.99,-0.66212,-0.74766,0.051065,297.18>
> view matrix models
> #5,0.46109,0.74604,-0.48044,-318.48,-0.54373,0.66542,0.51144,456.87,0.70125,0.025407,0.71246,-67.025,#7,-0.62626,0.51461,-0.58564,243.67,0.41158,-0.41974,-0.80896,356.78,-0.66212,-0.74766,0.051065,292.82>
> view matrix models
> #5,0.46109,0.74604,-0.48044,-314.54,-0.54373,0.66542,0.51144,452.06,0.70125,0.025407,0.71246,-67.762,#7,-0.62626,0.51461,-0.58564,247.61,0.41158,-0.41974,-0.80896,351.97,-0.66212,-0.74766,0.051065,292.08>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#7) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006379, steps = 2000
shifted from previous position = 67.3
rotated from previous position = 13.3 degrees
atoms outside contour = 2933, contour level = 0.0076678
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.44864812 0.85024754 -0.27530707 -329.44673535
-0.61386395 0.51706217 0.59650461 550.06356967
0.64952745 -0.09861958 0.75391528 9.22943609
Axis -0.37251122 -0.49561105 -0.78460505
Axis point 271.63371182 632.46002380 0.00000000
Rotation angle (degrees) 68.91130081
Shift along axis -157.13644207
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.62787187 0.32023832 -0.70938306 250.06408612
0.51464398 -0.51292383 -0.68705947 351.06664711
-0.58388225 -0.79646504 0.15724172 292.22359140
Axis -0.42743859 -0.49032137 0.75952696
Axis point 193.59344878 279.40290037 0.00000000
Rotation angle (degrees) 172.64722909
Shift along axis -57.07082358
> view matrix models
> #5,0.44865,0.85025,-0.27531,-336.59,-0.61386,0.51706,0.5965,546.49,0.64953,-0.09862,0.75392,3.5019,#7,-0.62787,0.32024,-0.70938,242.92,0.51464,-0.51292,-0.68706,347.49,-0.58388,-0.79647,0.15724,286.5>
> volume #1 level 0.006838> ui mousemode right "rotate selected models"> view
> matrix models
> #5,0.64185,0.35969,-0.67724,-301.3,-0.33561,0.92585,0.17367,210.96,0.68949,0.11582,0.71497,-98.634,#7,-0.72944,0.66664,-0.15332,236.09,0.14015,-0.07373,-0.98738,344.84,-0.66953,-0.74172,-0.039649,287.12>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.64185,0.35969,-0.67724,-291.82,-0.33561,0.92585,0.17367,216.24,0.68949,0.11582,0.71497,-97.428,#7,-0.72944,0.66664,-0.15332,245.57,0.14015,-0.07373,-0.98738,350.12,-0.66953,-0.74172,-0.039649,288.32>
> view matrix models
> #5,0.64185,0.35969,-0.67724,-292.85,-0.33561,0.92585,0.17367,215.82,0.68949,0.11582,0.71497,-97.348,#7,-0.72944,0.66664,-0.15332,244.54,0.14015,-0.07373,-0.98738,349.7,-0.66953,-0.74172,-0.039649,288.4>
> view matrix models
> #5,0.64185,0.35969,-0.67724,-293.69,-0.33561,0.92585,0.17367,219.17,0.68949,0.11582,0.71497,-95.847,#7,-0.72944,0.66664,-0.15332,243.7,0.14015,-0.07373,-0.98738,353.04,-0.66953,-0.74172,-0.039649,289.91>
> view matrix models
> #5,0.64185,0.35969,-0.67724,-294.11,-0.33561,0.92585,0.17367,218.78,0.68949,0.11582,0.71497,-97.168,#7,-0.72944,0.66664,-0.15332,243.29,0.14015,-0.07373,-0.98738,352.65,-0.66953,-0.74172,-0.039649,288.58>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.64185,0.35969,-0.67724,-298.59,-0.33561,0.92585,0.17367,215.26,0.68949,0.11582,0.71497,-99.717,#7,-0.72944,0.66664,-0.15332,238.8,0.14015,-0.07373,-0.98738,349.14,-0.66953,-0.74172,-0.039649,286.03>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.54906,0.059004,-0.83369,-150.22,-0.03859,0.99823,0.045234,11.057,0.83489,0.0073364,0.55037,-155.91,#7,-0.58181,0.80196,0.13547,235.99,-0.1703,0.042744,-0.98446,347.57,-0.79529,-0.59585,0.1117,283.55>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.54906,0.059004,-0.83369,-141.32,-0.03859,0.99823,0.045234,18.757,0.83489,0.0073364,0.55037,-154.01,#7,-0.58181,0.80196,0.13547,244.89,-0.1703,0.042744,-0.98446,355.27,-0.79529,-0.59585,0.1117,285.45>
> view matrix models
> #5,0.54906,0.059004,-0.83369,-143.94,-0.03859,0.99823,0.045234,17.226,0.83489,0.0073364,0.55037,-153.35,#7,-0.58181,0.80196,0.13547,242.26,-0.1703,0.042744,-0.98446,353.73,-0.79529,-0.59585,0.1117,286.11>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#7) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006548, steps = 2000
shifted from previous position = 258
rotated from previous position = 39.9 degrees
atoms outside contour = 2731, contour level = 0.006838
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.22428746 -0.36126596 -0.90508675 195.02323000
0.53371593 0.82261567 -0.19608866 -259.73434724
0.81537870 -0.43907899 0.37731577 12.95402397
Axis -0.12432405 -0.88026230 0.45791027
Axis point 174.57812190 0.00000000 94.74078612
Rotation angle (degrees) 77.75399990
Shift along axis 210.32005694
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.17905812 0.85607757 0.48483955 249.94431746
-0.70202348 0.23408177 -0.67258365 352.78061951
-0.68927587 -0.46080031 0.55907231 291.03197901
Axis 0.10791967 0.59830087 -0.79397067
Axis point 325.32005194 156.97099682 -0.00000000
Rotation angle (degrees) 101.12511134
Shift along axis 6.97200511
> view matrix models
> #5,0.22429,-0.36127,-0.90509,195.35,0.53372,0.82262,-0.19609,-260.19,0.81538,-0.43908,0.37732,14.033,#7,-0.17906,0.85608,0.48484,250.27,-0.70202,0.23408,-0.67258,352.32,-0.68928,-0.4608,0.55907,292.11>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.70978,0.63664,0.3015,-346.75,-0.55163,0.76852,-0.32417,366.41,-0.43809,0.063771,0.89667,585.7,#7,-0.8152,-0.28709,-0.50302,265.81,0.3645,0.42064,-0.83078,353.4,0.4501,-0.8606,-0.23826,302.65>
> view matrix models
> #5,0.66322,0.65557,0.36106,-322.61,-0.53819,0.753,-0.37862,360.26,-0.52009,0.056794,0.85222,631.48,#7,-0.77134,-0.34197,-0.53675,266.59,0.35247,0.47268,-0.80767,352.76,0.5299,-0.81218,-0.24406,302.38>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.66322,0.65557,0.36106,-337.36,-0.53819,0.753,-0.37862,356.84,-0.52009,0.056794,0.85222,616.61,#7,-0.77134,-0.34197,-0.53675,251.84,0.35247,0.47268,-0.80767,349.34,0.5299,-0.81218,-0.24406,287.51>
> view matrix models
> #5,0.66322,0.65557,0.36106,-338.79,-0.53819,0.753,-0.37862,355.48,-0.52009,0.056794,0.85222,617.05,#7,-0.77134,-0.34197,-0.53675,250.41,0.35247,0.47268,-0.80767,347.98,0.5299,-0.81218,-0.24406,287.95>
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #5,0.2758,-0.8891,0.36528,432.91,0.72305,-0.058499,-0.68831,-94.846,0.63335,0.45395,0.62673,-197.02,#7,-0.06808,-0.45564,0.88756,243.51,-0.72132,0.63708,0.27172,337.87,-0.68925,-0.62171,-0.37203,285.07>
> view matrix models
> #5,0.061441,-0.99715,0.043751,569.33,0.38122,0.063955,0.92227,175.75,-0.92244,-0.039987,0.38406,845.38,#7,0.15128,-0.1325,0.97957,240.38,-0.34927,-0.93422,-0.072424,354.81,0.92473,-0.33118,-0.1876,283.91>
> view matrix models
> #5,-0.7462,-0.66541,-0.02044,905.19,-0.31624,0.32729,0.89043,475.81,-0.58581,0.67091,-0.45465,337.89,#7,0.86797,0.007227,0.49657,243.37,0.27545,-0.83901,-0.46925,357.5,0.41323,0.54407,-0.73022,278.66>
> view matrix models
> #5,-0.63461,-0.77228,-0.029406,879.23,-0.46761,0.3534,0.81022,546.54,-0.61532,0.52792,-0.58539,395.94,#7,0.78106,0.00043442,0.62446,242.47,0.41464,-0.74809,-0.51811,357.22,0.46692,0.6636,-0.58448,276.74>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.63461,-0.77228,-0.029406,884.6,-0.46761,0.3534,0.81022,541.46,-0.61532,0.52792,-0.58539,415.9,#7,0.78106,0.00043442,0.62446,247.84,0.41464,-0.74809,-0.51811,352.14,0.46692,0.6636,-0.58448,296.71>
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #5,-0.82896,-0.42798,-0.36008,847.56,0.24322,-0.85558,0.45698,542.55,-0.50366,0.29124,0.81333,541.12,#7,0.88545,0.37022,0.28091,246.87,-0.03966,-0.54206,0.8394,340.89,0.46304,-0.75439,-0.46528,308.7>
> view matrix models
> #5,-0.59898,0.79915,0.050885,309.59,-0.63535,-0.51296,0.57723,928.58,0.4874,0.31342,0.81499,-29.926,#7,0.41919,0.053021,-0.90635,256.52,0.75134,-0.58068,0.31353,345.88,-0.50967,-0.8124,-0.28325,306.47>
> view matrix models
> #5,0.3685,0.76002,-0.53532,-269.99,-0.91323,0.40363,-0.055587,712.28,0.17383,0.50936,0.84282,80.444,#7,-0.54093,0.57584,-0.61303,248.38,0.80507,0.14353,-0.57555,345.12,-0.24344,-0.80487,-0.54123,308.48>
> view matrix models
> #5,0.41519,0.70403,-0.57616,-279.58,-0.77489,0.60549,0.18146,579.3,0.47661,0.37112,0.79694,-45.734,#7,-0.57639,0.60892,-0.54498,247.59,0.63691,-0.083088,-0.76645,348.1,-0.51198,-0.78887,-0.33993,306.62>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.41519,0.70403,-0.57616,-278.89,-0.77489,0.60549,0.18146,587.01,0.47661,0.37112,0.79694,-58.465,#7,-0.57639,0.60892,-0.54498,248.29,0.63691,-0.083088,-0.76645,355.81,-0.51198,-0.78887,-0.33993,293.89>
> view matrix models
> #5,0.41519,0.70403,-0.57616,-281.13,-0.77489,0.60549,0.18146,585.25,0.47661,0.37112,0.79694,-62.233,#7,-0.57639,0.60892,-0.54498,246.05,0.63691,-0.083088,-0.76645,354.05,-0.51198,-0.78887,-0.33993,290.12>
> view matrix models
> #5,0.41519,0.70403,-0.57616,-281.48,-0.77489,0.60549,0.18146,586.28,0.47661,0.37112,0.79694,-63.996,#7,-0.57639,0.60892,-0.54498,245.7,0.63691,-0.083088,-0.76645,355.08,-0.51198,-0.78887,-0.33993,288.35>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#7) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006232, steps = 2000
shifted from previous position = 208
rotated from previous position = 32.9 degrees
atoms outside contour = 2802, contour level = 0.006838
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.49426653 0.86558393 -0.08040543 -344.35273626
-0.86785105 0.49667874 0.01203166 664.87484119
0.05035008 0.06383309 0.99668961 305.04246661
Axis 0.02978581 -0.07518439 -0.99672469
Axis point 381.74609833 608.33370844 0.00000000
Rotation angle (degrees) 60.40819812
Shift along axis -364.28839048
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.66793058 0.12502192 -0.73364723 253.87954964
0.74386548 0.08157435 -0.66333233 352.68043687
-0.02308428 -0.98879479 -0.14748549 291.96412449
Axis -0.32647729 -0.71277854 0.62077317
Axis point -26.30236893 0.00000000 337.75189081
Rotation angle (degrees) 150.10277176
Shift along axis -153.02546054
> view matrix models
> #5,0.49427,0.86558,-0.080405,-352.99,-0.86785,0.49668,0.012032,666.63,0.05035,0.063833,0.99669,306.76,#7,-0.66793,0.12502,-0.73365,245.24,0.74387,0.081574,-0.66333,354.44,-0.023084,-0.98879,-0.14749,293.68>
> view matrix models
> #5,0.49427,0.86558,-0.080405,-354.63,-0.86785,0.49668,0.012032,665.67,0.05035,0.063833,0.99669,304.22,#7,-0.66793,0.12502,-0.73365,243.6,0.74387,0.081574,-0.66333,353.47,-0.023084,-0.98879,-0.14749,291.14>
> view matrix models
> #5,0.49427,0.86558,-0.080405,-353.85,-0.86785,0.49668,0.012032,665.32,0.05035,0.063833,0.99669,305.73,#7,-0.66793,0.12502,-0.73365,244.38,0.74387,0.081574,-0.66333,353.12,-0.023084,-0.98879,-0.14749,292.65>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.59564,0.78626,0.1643,-364.93,-0.79935,0.56008,0.2176,619.08,0.079066,-0.26095,0.96211,402.72,#7,-0.74059,-0.13111,-0.65904,246.09,0.67177,-0.12148,-0.73073,355.26,0.015749,-0.9839,0.17805,290.59>
> view matrix models
> #5,0.61081,0.63952,0.46683,-298.64,-0.73957,0.67137,0.047949,532.75,-0.28275,-0.37454,0.88305,643,#7,-0.71257,-0.44546,-0.54205,248.22,0.58327,0.053267,-0.81053,354.05,0.38993,-0.89372,0.22186,290.12>
> view matrix models
> #5,0.58754,0.80917,-0.0055779,-381.16,-0.71413,0.52175,0.46669,602.88,0.38054,-0.27022,0.8844,228.9,#7,-0.74423,0.040286,-0.66671,244.59,0.60646,-0.37752,-0.69978,357.26,-0.27989,-0.92513,0.25653,289.08>
> view matrix models
> #5,0.59766,0.78541,-0.16105,-390.01,-0.59194,0.56775,0.57207,524.88,0.54075,-0.24657,0.80424,123.44,#7,-0.75528,0.19229,-0.62656,242.95,0.48161,-0.48557,-0.72957,358.22,-0.44453,-0.85279,0.27413,288.05>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.59766,0.78541,-0.16105,-390.28,-0.59194,0.56775,0.57207,520.84,0.54075,-0.24657,0.80424,131.04,#7,-0.75528,0.19229,-0.62656,242.68,0.48161,-0.48557,-0.72957,354.18,-0.44453,-0.85279,0.27413,295.66>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.59766,0.78541,-0.16105,-387.3,-0.59194,0.56775,0.57207,520.83,0.54075,-0.24657,0.80424,129.09,#7,-0.75528,0.19229,-0.62656,245.67,0.48161,-0.48557,-0.72957,354.17,-0.44453,-0.85279,0.27413,293.71>
> view matrix models
> #5,0.59766,0.78541,-0.16105,-388.87,-0.59194,0.56775,0.57207,517.58,0.54075,-0.24657,0.80424,128.32,#7,-0.75528,0.19229,-0.62656,244.1,0.48161,-0.48557,-0.72957,350.92,-0.44453,-0.85279,0.27413,292.94>
> view matrix models
> #5,0.59766,0.78541,-0.16105,-387.38,-0.59194,0.56775,0.57207,518.01,0.54075,-0.24657,0.80424,126.64,#7,-0.75528,0.19229,-0.62656,245.59,0.48161,-0.48557,-0.72957,351.35,-0.44453,-0.85279,0.27413,291.26>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#7) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.006304, steps = 2000
shifted from previous position = 21.9
rotated from previous position = 4.12 degrees
atoms outside contour = 2805, contour level = 0.006838
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.63160113 0.74678337 -0.20831371 -392.06980546
-0.55856585 0.62464466 0.54573182 477.26828316
0.53766549 -0.22832791 0.81165397 121.78106461
Axis -0.45774393 -0.44113837 -0.77192450
Axis point 263.86758263 731.84909322 0.00000000
Rotation angle (degrees) 57.72727694
Shift along axis -125.07956684
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.78219153 0.23399400 -0.57742810 249.19255277
0.43600266 -0.45646565 -0.77559061 351.79976917
-0.44505964 -0.85842060 0.25502156 290.77365896
Axis -0.32441286 -0.51843579 0.79118937
Axis point 170.65668667 280.82372829 0.00000000
Rotation angle (degrees) 172.66552652
Shift along axis -33.16983103
> hide #7 models> select subtract #71934 atoms, 1972 bonds, 238 residues, 1
> model selected
> show #5 models> show #4 models> show #3 models> select add #73391 atoms,
> 3455 bonds, 419 residues, 2 models selected
> show #7 models> view matrix models
> #5,0.6316,0.74678,-0.20831,-292.46,-0.55857,0.62464,0.54573,428.58,0.53767,-0.22833,0.81165,182.31,#7,-0.78219,0.23399,-0.57743,348.81,0.436,-0.45647,-0.77559,303.11,-0.44506,-0.85842,0.25502,351.3>
> view matrix models
> #5,0.6316,0.74678,-0.20831,-284.18,-0.55857,0.62464,0.54573,440.14,0.53767,-0.22833,0.81165,179.11,#7,-0.78219,0.23399,-0.57743,357.08,0.436,-0.45647,-0.77559,314.67,-0.44506,-0.85842,0.25502,348.1>
> volume #1 level 0.008913> ui mousemode right "rotate selected models"> view
> matrix models
> #5,0.63195,0.73976,-0.23108,-283.85,-0.52078,0.62615,0.58029,431.7,0.57397,-0.24637,0.78094,172.09,#7,-0.78195,0.25602,-0.56833,356.54,0.40014,-0.49293,-0.7726,325.92,-0.47795,-0.83155,0.283,357.1>
> view matrix models
> #5,0.40608,0.87634,-0.25909,-252.01,-0.912,0.40659,-0.054141,543.3,0.057898,0.25828,0.96433,220.46,#7,-0.59113,0.30885,-0.74511,311.8,0.80331,0.14227,-0.57832,177.81,-0.072604,-0.94041,-0.3322,284.12>
> view matrix models
> #5,0.43696,0.86229,-0.25597,-257.59,-0.88687,0.46051,0.03736,531.74,0.15009,0.21069,0.96596,204.43,#7,-0.61822,0.30272,-0.72537,318.41,0.77105,0.054404,-0.63445,194.05,-0.1526,-0.95152,-0.26705,302.95>
> view matrix models
> #5,0.62956,0.71297,-0.30874,-281.54,-0.44846,0.65796,0.60495,408.43,0.63446,-0.24239,0.73397,154.9,#7,-0.77707,0.33111,-0.53528,352.85,0.32379,-0.51899,-0.79108,353.49,-0.53973,-0.78805,0.29608,378.63>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.62956,0.71297,-0.30874,-274.52,-0.44846,0.65796,0.60495,406.86,0.63446,-0.24239,0.73397,108.93,#7,-0.77707,0.33111,-0.53528,359.87,0.32379,-0.51899,-0.79108,351.92,-0.53973,-0.78805,0.29608,332.66>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.45327,0.82091,-0.34735,-250.42,-0.83142,0.24886,-0.4968,532.21,-0.32138,0.51397,0.79533,221.4,#7,-0.62908,0.38911,-0.67295,325.76,0.74019,0.56429,-0.36565,183.97,0.23746,-0.72813,-0.64299,173.91>
> ui mousemode right "rotate selected models"> ui mousemode right "translate
> selected models"> view matrix models
> #5,0.45327,0.82091,-0.34735,-244.8,-0.83142,0.24886,-0.4968,566.76,-0.32138,0.51397,0.79533,212.32,#7,-0.62908,0.38911,-0.67295,331.38,0.74019,0.56429,-0.36565,218.51,0.23746,-0.72813,-0.64299,164.84>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.45327,0.82091,-0.34735,-204.98,-0.83142,0.24886,-0.4968,685.14,-0.32138,0.51397,0.79533,339.22,#7,-0.62908,0.38911,-0.67295,371.2,0.74019,0.56429,-0.36565,336.89,0.23746,-0.72813,-0.64299,291.74>
> view matrix models
> #5,0.45327,0.82091,-0.34735,-225.24,-0.83142,0.24886,-0.4968,639.6,-0.32138,0.51397,0.79533,355.95,#7,-0.62908,0.38911,-0.67295,350.95,0.74019,0.56429,-0.36565,291.36,0.23746,-0.72813,-0.64299,308.46>
> view matrix models
> #5,0.45327,0.82091,-0.34735,-227.45,-0.83142,0.24886,-0.4968,629.87,-0.32138,0.51397,0.79533,380.08,#7,-0.62908,0.38911,-0.67295,348.74,0.74019,0.56429,-0.36565,281.62,0.23746,-0.72813,-0.64299,332.6>
> view matrix models
> #5,0.45327,0.82091,-0.34735,-218.84,-0.83142,0.24886,-0.4968,647.15,-0.32138,0.51397,0.79533,373.95,#7,-0.62908,0.38911,-0.67295,357.34,0.74019,0.56429,-0.36565,298.9,0.23746,-0.72813,-0.64299,326.46>
> view matrix models
> #5,0.45327,0.82091,-0.34735,-221.31,-0.83142,0.24886,-0.4968,646.06,-0.32138,0.51397,0.79533,381.19,#7,-0.62908,0.38911,-0.67295,354.87,0.74019,0.56429,-0.36565,297.81,0.23746,-0.72813,-0.64299,333.71>
> view matrix models
> #5,0.45327,0.82091,-0.34735,-222.46,-0.83142,0.24886,-0.4968,654.54,-0.32138,0.51397,0.79533,383.99,#7,-0.62908,0.38911,-0.67295,353.72,0.74019,0.56429,-0.36565,306.29,0.23746,-0.72813,-0.64299,336.51>
> view matrix models
> #5,0.45327,0.82091,-0.34735,-222.54,-0.83142,0.24886,-0.4968,652.85,-0.32138,0.51397,0.79533,385.1,#7,-0.62908,0.38911,-0.67295,353.65,0.74019,0.56429,-0.36565,304.6,0.23746,-0.72813,-0.64299,337.62>
> fitmap sel inMap #1Fit molecules AlphaFold Q9JIF7 (#5), AlphaFold P84078
> (#7) to map postprocess.mrc (#1) using 3391 atoms
average map value = 0.008387, steps = 2000
shifted from previous position = 135
rotated from previous position = 20.3 degrees
atoms outside contour = 2803, contour level = 0.0089126
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.55409690 0.62511695 -0.54973213 -218.65297228
-0.83234882 0.40563315 -0.37769984 602.45005605
-0.01311700 0.66685121 0.74507543 146.75071393
Axis 0.55807704 -0.28669981 -0.77868687
Axis point 393.46986018 265.29039526 -0.00000000
Rotation angle (degrees) 69.36565182
Shift along axis -409.02037338
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.69444730 0.56770586 -0.44210067 356.86595497
0.71286713 0.45931644 -0.52995175 302.68762913
-0.09779261 -0.68318260 -0.72366991 332.32740848
Axis -0.37941968 -0.85255192 0.35943835
Axis point 85.30361552 0.00000000 245.10157583
Rotation angle (degrees) 168.35027896
Shift along axis -274.00766921
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.38512,0.91817,0.09297,-196.08,-0.61509,0.18027,0.76758,634.48,0.688,-0.3528,0.63418,136.81,#7,-0.56549,-0.036498,-0.82395,348.16,0.5934,-0.71183,-0.37573,301.8,-0.5728,-0.7014,0.42419,357.36>
> view matrix models
> #5,0.26988,0.96152,-0.051356,-178.93,-0.48414,0.18161,0.85594,603.78,0.83233,-0.20614,0.51452,70.825,#7,-0.46775,0.11753,-0.87601,325.15,0.4687,-0.8073,-0.35858,339.96,-0.74935,-0.57832,0.32253,433.9>
> focus selUnknown command: focus sel
> ui mousemode right "rotate selected models"> ui mousemode right "translate
> selected models"> view matrix models
> #5,0.26988,0.96152,-0.051356,-155.72,-0.48414,0.18161,0.85594,605.27,0.83233,-0.20614,0.51452,71.95,#7,-0.46775,0.11753,-0.87601,348.35,0.4687,-0.8073,-0.35858,341.45,-0.74935,-0.57832,0.32253,435.02>
> view matrix models
> #5,0.26988,0.96152,-0.051356,-227.82,-0.48414,0.18161,0.85594,543.16,0.83233,-0.20614,0.51452,120.55,#7,-0.46775,0.11753,-0.87601,276.25,0.4687,-0.8073,-0.35858,279.34,-0.74935,-0.57832,0.32253,483.63>
> select subtract #71934 atoms, 1972 bonds, 238 residues, 1 model selected
> select add #73391 atoms, 3455 bonds, 419 residues, 2 models selected
> select clear> hide #5 models> show #5 models> hide #5 models> show #5
> models> select add #71457 atoms, 1483 bonds, 181 residues, 1 model selected
> view matrix models
> #7,-0.46775,0.11753,-0.87601,264.54,0.4687,-0.8073,-0.35858,282.89,-0.74935,-0.57832,0.32253,480.54>
> view matrix models
> #7,-0.46775,0.11753,-0.87601,312.97,0.4687,-0.8073,-0.35858,321.84,-0.74935,-0.57832,0.32253,339.06>
> view matrix models
> #7,-0.46775,0.11753,-0.87601,356.18,0.4687,-0.8073,-0.35858,311.73,-0.74935,-0.57832,0.32253,325.59>
> ui mousemode right "rotate selected models"> view matrix models
> #7,-0.31289,0.30669,-0.89891,354.87,0.77534,0.62912,-0.05524,297.38,0.54858,-0.71425,-0.43463,333.76>
> view matrix models
> #7,-0.32942,0.33444,-0.88297,354.5,0.79728,0.59949,-0.070384,297.77,0.50579,-0.72716,-0.46413,333.99>
> ui mousemode right "translate selected models"> view matrix models
> #7,-0.32942,0.33444,-0.88297,356.39,0.79728,0.59949,-0.070384,317.3,0.50579,-0.72716,-0.46413,340>
> view matrix models
> #7,-0.32942,0.33444,-0.88297,353.93,0.79728,0.59949,-0.070384,306.29,0.50579,-0.72716,-0.46413,336.94>
> ui mousemode right "rotate selected models"> view matrix models
> #7,-0.36734,0.92837,-0.056483,343.26,0.7376,0.32778,0.59035,304.43,0.56658,0.1752,-0.80517,331.1>
> view matrix models
> #7,0.96817,0.16059,-0.19199,353.21,0.24775,-0.50581,0.8263,309.63,0.035584,-0.84757,-0.52949,337.67>
> view matrix models
> #7,-0.44229,0.45848,-0.77083,351.91,0.81471,0.56474,-0.13157,307.02,0.375,-0.68619,-0.62331,337.37>
> view matrix models
> #7,-0.4761,0.85565,0.20294,342.08,0.87815,0.45036,0.16131,306.29,0.046626,0.25502,-0.96581,330.55>
> view matrix models
> #7,-0.65814,-0.599,-0.45613,359.07,-0.54692,0.79672,-0.25712,303.51,0.51742,0.080245,-0.85196,332.17>
> view matrix models
> #7,-0.94065,-0.24006,-0.23988,354,-0.067482,0.82504,-0.56104,305.98,0.33259,-0.51155,-0.79227,336.81>
> focus selUnknown command: focus sel
> fitmap sel inMap #1Fit molecule AlphaFold P84078 (#7) to map postprocess.mrc
> (#1) using 1457 atoms
average map value = 0.008691, steps = 80
shifted from previous position = 2.77
rotated from previous position = 17.2 degrees
atoms outside contour = 813, contour level = 0.0089126
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.95086316 -0.13233492 -0.27990481 353.75859723
-0.04679788 0.95509568 -0.29257849 304.12819349
0.30605423 -0.26510316 -0.91435830 333.82641064
Axis 0.04634790 -0.98844918 0.14429168
Axis point 155.79634475 0.00000000 217.07990743
Rotation angle (degrees) 162.75830016
Shift along axis -236.05092359
> view matrix models
> #7,0.89646,-0.11615,-0.42763,357.57,0.15108,0.98733,0.048544,301.99,0.41657,-0.10812,0.90265,321.02>
> view matrix models
> #7,0.24003,-0.9594,-0.14808,362.3,0.61142,0.030929,0.7907,306.62,-0.75402,-0.28033,0.59403,322.62>
> view matrix models
> #7,0.82938,0.2793,-0.48386,354.26,0.55336,-0.29144,0.78029,309.49,0.076921,-0.91491,-0.39627,336>
> fitmap sel inMap #1Fit molecule AlphaFold P84078 (#7) to map postprocess.mrc
> (#1) using 1457 atoms
average map value = 0.008533, steps = 104
shifted from previous position = 5.88
rotated from previous position = 26.3 degrees
atoms outside contour = 806, contour level = 0.0089126
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.70793762 0.63970410 -0.29933753 354.19362259
0.63728879 -0.39588546 0.66116388 305.25131134
0.30444588 -0.65882725 -0.68793847 333.84744266
Axis -0.90937970 -0.41596369 -0.00166398
Axis point 0.00000000 150.36639145 138.65066871
Rotation angle (degrees) 133.46751174
Shift along axis -449.62546628
> view matrix models
> #7,0.65944,0.60816,-0.4419,355.31,0.75098,-0.50616,0.42407,307.94,0.034231,-0.61151,-0.7905,333.63>
> view matrix models
> #7,0.67477,0.61006,-0.41535,355.15,0.7183,-0.41358,0.55946,306.19,0.16952,-0.67585,-0.71728,333.97>
> view matrix models
> #7,0.99296,-0.033915,-0.11349,359.54,0.10378,-0.21285,0.97156,300.76,-0.057107,-0.9765,-0.20783,333.06>
> view matrix models
> #7,0.79178,-0.31663,-0.52233,364.35,-0.036918,-0.87839,0.47651,309.67,-0.60968,-0.35801,-0.70719,329.77>
> view matrix models
> #7,-0.084214,-0.71401,0.69505,358.74,0.043059,-0.69949,-0.71335,315.77,0.99552,-0.030146,0.089651,324.37>
> view matrix models
> #7,-0.72644,-0.50945,0.46125,357.34,-0.639,0.25371,-0.72616,306.16,0.25292,-0.82225,-0.50984,334.1>
> fitmap sel inMap #1Fit molecule AlphaFold P84078 (#7) to map postprocess.mrc
> (#1) using 1457 atoms
average map value = 0.009965, steps = 96
shifted from previous position = 4.5
rotated from previous position = 20.2 degrees
atoms outside contour = 674, contour level = 0.0089126
Position of AlphaFold P84078 (#7) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.82078799 -0.53173104 0.20873226 354.88942843
-0.51806242 0.53896583 -0.66417403 308.12027683
0.24066240 -0.65328242 -0.71784655 333.36238943
Axis 0.29921665 -0.87719085 0.37550715
Axis point 228.19071418 0.00000000 234.53252280
Rotation angle (degrees) 178.95714657
Shift along axis -38.91150075
> volume #1 level 0.01071> select subtract #7Nothing selected
> volume #1 level 0.009051> volume #1 level 0.008083> select add #22 models
> selected
> select subtract #2Nothing selected
> show #!2 models> volume #2 level 0.09363> volume #2 level 0.1809> hide #!2
> models> hide #5 models> show #5 models> select add #57501 atoms, 7619 bonds,
> 953 residues, 1 model selected
> ui mousemode right zoom> ui mousemode right "translate selected models">
> view matrix models
> #5,0.26988,0.96152,-0.051356,-138.83,-0.48414,0.18161,0.85594,363.4,0.83233,-0.20614,0.51452,412.62>
> view matrix models
> #5,0.26988,0.96152,-0.051356,215.52,-0.48414,0.18161,0.85594,313.06,0.83233,-0.20614,0.51452,481.6>
> view matrix models
> #5,0.26988,0.96152,-0.051356,87.067,-0.48414,0.18161,0.85594,304.38,0.83233,-0.20614,0.51452,348.45>
> view matrix models
> #5,0.26988,0.96152,-0.051356,199.47,-0.48414,0.18161,0.85594,297.27,0.83233,-0.20614,0.51452,248.55>
> view matrix models
> #5,0.26988,0.96152,-0.051356,281.71,-0.48414,0.18161,0.85594,328.06,0.83233,-0.20614,0.51452,368.25>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.60313,-0.5776,-0.5501,288.13,-0.33332,-0.80907,0.48405,332.63,-0.72466,-0.10859,-0.6805,378.28>
> view matrix models
> #5,0.083723,0.17341,-0.98128,289.92,-0.76391,0.64349,0.048538,332.57,0.63987,0.74555,0.18634,368.33>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.083723,0.17341,-0.98128,246.28,-0.76391,0.64349,0.048538,203.76,0.63987,0.74555,0.18634,339.11>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.42104,-0.31907,-0.84907,246.08,-0.41555,0.76422,-0.49324,206.34,0.80626,0.5605,0.18918,339.26>
> view matrix models
> #5,0.27316,-0.96179,0.01842,242.35,0.48586,0.12142,-0.86556,208.8,0.83025,0.24539,0.50046,338>
> view matrix models
> #5,0.018184,-0.95114,0.30824,240.9,0.66648,-0.21828,-0.71286,208.35,0.7453,0.2184,0.62994,337.38>
> view matrix models
> #5,-0.86492,-0.14327,0.48102,239.29,0.34551,-0.86511,0.3636,203.59,0.36405,0.48068,0.79775,336.3>
> view matrix models
> #5,-0.73157,-0.37278,0.57082,239.05,0.52599,-0.8413,0.12468,204.76,0.43376,0.39146,0.81155,336.32>
> view matrix models
> #5,-0.1881,-0.86705,0.46136,240.06,0.71994,-0.44124,-0.53572,207.68,0.66806,0.23138,0.70722,336.99>
> view matrix models
> #5,0.24785,-0.96728,0.054255,242.18,0.51183,0.083186,-0.85505,208.78,0.82256,0.23969,0.5157,337.93>
> ui mousemode right "rotate selected models"> view matrix models
> #5,-0.084382,-0.94393,-0.31919,245.07,0.79715,0.12825,-0.59001,206.49,0.59786,-0.30423,0.74163,338.2>
> view matrix models
> #5,0.21946,-0.83157,-0.51022,245.51,0.67192,0.508,-0.53894,205.44,0.70736,-0.22456,0.67023,338.28>
> view matrix models
> #5,0.50938,-0.48951,-0.70776,245.45,0.33656,0.87026,-0.35967,203.97,0.792,-0.054996,0.60804,338.12>
> view matrix models
> #5,-0.10787,-0.94628,-0.30483,245.03,0.80101,0.09889,-0.59043,206.56,0.58886,-0.30787,0.74731,338.19>
> view matrix models
> #5,-0.27101,-0.95907,-0.082092,243.9,0.55729,-0.22587,0.79901,198.87,-0.78485,0.17079,0.59569,340.29>
> view matrix models
> #5,-0.72786,-0.54322,0.41849,240.44,0.34835,0.23275,0.90801,197.39,-0.59065,0.80668,0.019823,342.09>
> view matrix models
> #5,-0.41265,-0.34043,0.84488,236.68,0.80675,0.29409,0.51252,199.01,-0.42295,0.8931,0.15329,340.74>
> view matrix models
> #5,0.30768,-0.07732,0.94834,234.16,0.94345,0.15413,-0.29352,204.29,-0.12347,0.98502,0.12037,340.22>
> view matrix models
> #5,-0.3294,0.67309,0.66215,235.22,0.064826,0.71575,-0.69534,206.95,-0.94196,-0.18612,-0.2794,347.04>
> ui mousemode right "translate selected models"> view matrix models
> #5,-0.3294,0.67309,0.66215,274.07,0.064826,0.71575,-0.69534,330.47,-0.94196,-0.18612,-0.2794,373.87>
> ui mousemode right "rotate selected models"> view matrix models
> #5,0.10641,-0.80959,0.57726,277.53,-0.20523,0.55018,0.80944,321.69,-0.97291,-0.20461,-0.1076,372.87>
> ui mousemode right "translate selected models"> view matrix models
> #5,0.10641,-0.80959,0.57726,282.65,-0.20523,0.55018,0.80944,307.69,-0.97291,-0.20461,-0.1076,351.49>
> view matrix models
> #5,0.10641,-0.80959,0.57726,283.2,-0.20523,0.55018,0.80944,311.64,-0.97291,-0.20461,-0.1076,346.62>
> fitmap sel inMap #1Fit molecule AlphaFold Q9JIF7 (#5) to map postprocess.mrc
> (#1) using 7501 atoms
average map value = 0.007661, steps = 76
shifted from previous position = 4.15
rotated from previous position = 8.09 degrees
atoms outside contour = 4107, contour level = 0.0080828
Position of AlphaFold Q9JIF7 (#5) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04650098 -0.73947641 0.67157448 285.03045903
-0.16587164 0.65725218 0.73519124 314.41918325
-0.98505037 -0.14558228 -0.09209529 347.45631534
Axis -0.44893096 0.84438300 0.29236680
Axis point 361.10500418 0.00000000 -71.56871887
Rotation angle (degrees) 101.19630367
Shift along axis 239.11590829
> select clear> volume #1 level 0.0067> volume #1 level 0.01196> rename #5
> "bcop Q9JIF7"> ui tool show AlphaFoldFetching compressed Q7TNQ1 UniProt info
> from https://www.uniprot.org/uniprot/Q7TNQ1.xml
> alphafold match Q7TNQ1Fetching compressed AlphaFold Q7TNQ1 from
> https://alphafold.ebi.ac.uk/files/AF-Q7TNQ1-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: Q7TNQ1 (UniProt Q7TNQ1)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q7TNQ1 | Q7TNQ1 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #8942 atoms, 957 bonds, 121 residues, 1 model selected
> view matrix models #8,1,0,0,149.9,0,1,0,6.7504,0,0,1,-12.091> view matrix
> models #8,1,0,0,287.33,0,1,0,321.66,0,0,1,265.43> view matrix models
> #8,1,0,0,264.24,0,1,0,366.5,0,0,1,283.32> view matrix models
> #8,1,0,0,229.5,0,1,0,386.19,0,0,1,269.64> view matrix models
> #8,1,0,0,303.82,0,1,0,441.41,0,0,1,243.2> close #8Fetching compressed Q5XJY5
> UniProt info from https://www.uniprot.org/uniprot/Q5XJY5.xml
> alphafold match Q5XJY5Fetching compressed AlphaFold Q5XJY5 from
> https://alphafold.ebi.ac.uk/files/AF-Q5XJY5-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: Q5XJY5 (UniProt Q5XJY5)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q5XJY5 | Q5XJY5 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #84014 atoms, 4083 bonds, 511 residues, 1 model selected
> view matrix models #8,1,0,0,194.37,0,1,0,278.17,0,0,1,-165.99> view matrix
> models #8,1,0,0,330.77,0,1,0,303.4,0,0,1,317.75> view matrix models
> #8,1,0,0,289.13,0,1,0,381.85,0,0,1,374.49> view matrix models
> #8,1,0,0,226.68,0,1,0,354.27,0,0,1,374.38> view matrix models
> #8,1,0,0,182.68,0,1,0,331.4,0,0,1,377.96> view matrix models
> #8,1,0,0,250.96,0,1,0,357.53,0,0,1,329.55> hide #7 models> hide #6 models>
> hide #5 models> hide #4 models> hide #3 models> view matrix models
> #8,1,0,0,251.35,0,1,0,322.13,0,0,1,332.41> view matrix models
> #8,1,0,0,237.89,0,1,0,289.39,0,0,1,319.92> ui mousemode right "rotate
> selected models"> view matrix models
> #8,0.12745,0.73772,-0.66296,217.8,0.41884,0.56586,0.7102,307.24,0.89907,-0.36819,-0.23686,300.45>
> view matrix models
> #8,-0.16135,0.94424,0.287,235.04,-0.14136,-0.30993,0.94019,311.58,0.97672,0.11112,0.18349,308>
> view matrix models
> #8,0.54827,0.71745,0.42972,242.23,-0.64377,0.034086,0.76446,304.44,0.53381,-0.69577,0.48056,314.11>
> view matrix models
> #8,0.43688,0.68885,0.57847,244.77,-0.85392,0.11543,0.50745,297.9,0.28278,-0.71566,0.63865,316.1>
> view matrix models
> #8,0.23358,0.7626,0.60322,244.02,-0.94894,0.043513,0.31244,293.66,0.21202,-0.6454,0.73383,317.47>
> view matrix models
> #8,0.18456,0.89465,0.40686,239.39,-0.88428,-0.029508,0.46602,297.32,0.42893,-0.44579,0.78568,319.05>
> view matrix models
> #8,0.075697,0.89202,0.44562,239.63,-0.87716,-0.15296,0.45519,297.5,0.4742,-0.42533,0.77086,318.92>
> ui mousemode right "translate selected models"> view matrix models
> #8,0.075697,0.89202,0.44562,257.62,-0.87716,-0.15296,0.45519,309.44,0.4742,-0.42533,0.77086,334.32>
> view matrix models
> #8,0.075697,0.89202,0.44562,253.99,-0.87716,-0.15296,0.45519,305.59,0.4742,-0.42533,0.77086,332.93>
> ui mousemode right "rotate selected models"> view matrix models
> #8,0.10729,0.92588,0.36226,252.36,-0.91105,-0.054334,0.4087,304.18,0.39809,-0.37388,0.8377,333.75>
> ui mousemode right "translate selected models"> view matrix models
> #8,0.10729,0.92588,0.36226,254.59,-0.91105,-0.054334,0.4087,304.29,0.39809,-0.37388,0.8377,332.06>
> hide #!1 models> select clear> select #8/A:38 atoms, 7 bonds, 1 residue, 1
> model selected
> select clear> select #8/A:38 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/A:12813 atoms, 11 bonds, 2 residues, 1 model selected
> select up117 atoms, 116 bonds, 16 residues, 1 model selected
> select up4014 atoms, 4083 bonds, 511 residues, 1 model selected
> select up31453 atoms, 32073 bonds, 3964 residues, 10 models selected
> select up31453 atoms, 32073 bonds, 3964 residues, 10 models selected
> select down4014 atoms, 4083 bonds, 511 residues, 1 model selected
> select down117 atoms, 116 bonds, 16 residues, 1 model selected
> select clear> select #8/A:48 atoms, 7 bonds, 1 residue, 1 model selected
> select #8:1-1291037 atoms, 1053 bonds, 129 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q5XJY5 (#8) to map postprocess.mrc
> (#1) using 1037 atoms
average map value = 0.01008, steps = 68
shifted from previous position = 1.88
rotated from previous position = 9.03 degrees
atoms outside contour = 617, contour level = 0.011955
Position of AlphaFold Q5XJY5 (#8) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.20025661 0.94967606 0.24085819 253.94050178
-0.87761546 0.06459277 0.47499355 301.50451746
0.43553230 -0.30650147 0.84638553 331.26549457
Axis -0.39135326 -0.09748796 -0.91506214
Axis point 205.98623285 84.05170203 0.00000000
Rotation angle (degrees) 86.81170934
Shift along axis -431.90201573
> show #!1 models> select clear> show #7 models> show #6 models> show #5
> models> show #4 models> show #3 modelsFetching compressed Q9QXK3 UniProt
> info from https://www.uniprot.org/uniprot/Q9QXK3.xml
> alphafold match Q9QXK3Fetching compressed AlphaFold Q9QXK3 from
> https://alphafold.ebi.ac.uk/files/AF-Q9QXK3-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: Q9QXK3 (UniProt Q9QXK3)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q9QXK3 | Q9QXK3 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #96840 atoms, 6965 bonds, 871 residues, 1 model selected
> view matrix models #9,1,0,0,85.449,0,1,0,271.26,0,0,1,-4.2898> view matrix
> models #9,1,0,0,363.93,0,1,0,413.14,0,0,1,278.06> view matrix models
> #9,1,0,0,279.54,0,1,0,339.8,0,0,1,433.41> view matrix models
> #9,1,0,0,244.3,0,1,0,387.71,0,0,1,324.69> view matrix models
> #9,1,0,0,266.45,0,1,0,316.24,0,0,1,284.51> view matrix models
> #9,1,0,0,300.16,0,1,0,316.61,0,0,1,341.57> view matrix models
> #9,1,0,0,292.4,0,1,0,403.59,0,0,1,378.62> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.99183,0.09982,0.079482,292.2,0.0093959,-0.67835,0.73468,422.34,0.12725,-0.72793,-0.67374,371.99>
> view matrix models
> #9,0.25596,-0.95097,-0.17363,299.29,-0.10833,-0.2067,0.97239,420.44,-0.9606,-0.23008,-0.15592,372.71>
> view matrix models
> #9,0.79745,0.12821,-0.58961,287.21,0.57389,0.14065,0.80676,415.91,0.18636,-0.98172,0.038581,379.2>
> view matrix models
> #9,0.75567,-0.21736,-0.61783,289.78,0.23302,-0.79238,0.56377,421.81,-0.6121,-0.56999,-0.54813,372.25>
> view matrix models
> #9,0.11583,0.2738,-0.95479,283.91,0.71343,-0.69175,-0.11183,415.66,-0.69109,-0.66822,-0.27546,375.1>
> view matrix models
> #9,-0.072123,0.35632,-0.93158,283.57,0.73527,-0.6121,-0.29105,413.69,-0.67393,-0.70595,-0.21784,375.81>
> view matrix models
> #9,-0.10636,0.34632,-0.93207,283.67,0.68464,-0.65428,-0.32123,413.84,-0.72108,-0.67229,-0.16751,375.95>
> ui mousemode right "rotate selected models"> ui mousemode right "translate
> selected models"> view matrix models
> #9,-0.10636,0.34632,-0.93207,327.8,0.68464,-0.65428,-0.32123,352.03,-0.72108,-0.67229,-0.16751,391.1>
> view matrix models
> #9,-0.10636,0.34632,-0.93207,325.86,0.68464,-0.65428,-0.32123,339.75,-0.72108,-0.67229,-0.16751,369.72>
> view matrix models
> #9,-0.10636,0.34632,-0.93207,324.89,0.68464,-0.65428,-0.32123,334.42,-0.72108,-0.67229,-0.16751,360.64>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QXK3 (#9) to map postprocess.mrc
> (#1) using 6840 atoms
average map value = 0.006072, steps = 140
shifted from previous position = 19.4
rotated from previous position = 26.9 degrees
atoms outside contour = 5783, contour level = 0.011955
Position of AlphaFold Q9QXK3 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.29421585 0.14209339 -0.94511719 316.26408008
0.72293810 -0.67990666 0.12283091 351.53253187
-0.62513801 -0.71940003 -0.30276405 352.91229436
Axis -0.78568500 -0.29849632 0.54184779
Axis point 0.00000000 197.21498840 229.44931408
Rotation angle (degrees) 147.58925529
Shift along axis -162.19036505
> view matrix models
> #9,0.29422,0.14209,-0.94512,323.31,0.72294,-0.67991,0.12283,355.25,-0.62514,-0.7194,-0.30276,351.21>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QXK3 (#9) to map postprocess.mrc
> (#1) using 6840 atoms
average map value = 0.006265, steps = 92
shifted from previous position = 6.63
rotated from previous position = 16.6 degrees
atoms outside contour = 5675, contour level = 0.011955
Position of AlphaFold Q9QXK3 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.51174673 -0.00550976 -0.85911869 319.63636780
0.66090437 -0.63639088 0.39775879 360.97301425
-0.54892686 -0.77134706 -0.32202953 352.42782780
Axis -0.84657041 -0.22461544 0.48256237
Axis point 0.00000000 242.22195078 191.54417221
Rotation angle (degrees) 136.33066765
Shift along axis -181.60639881
> select clear> hide #3 models> hide #4 models> hide #5 models> hide #6
> models> hide #7 models> hide #8 models> hide #!1 models> show #!1 models>
> hide #!1 modelsDrag select of 1 residues
> select clearDrag select of 211 residues
> show #8 models> hide #8 models> show #7 models> show #6 models> show #5
> models> show #4 models> hide #4 models> hide #6 models> hide #7 models> hide
> #5 models> show #!1 models> ui tool show "Fit in Map"> fitmap sel inMap #1
> moveWholeMolecules falseFit molecule AlphaFold Q9QXK3 (#9) to map
> postprocess.mrc (#1) using 1678 atoms
average map value = 0.009038, steps = 56
shifted from previous position = 1.03
rotated from previous position = 11.8 degrees
atoms outside contour = 1111, contour level = 0.011955
> view matrix models
> #9,0.51175,-0.0055098,-0.85912,326.87,0.6609,-0.63639,0.39776,356.29,-0.54893,-0.77135,-0.32203,353.26>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 1678 atoms
average map value = 0.01147, steps = 56
shifted from previous position = 4.35
rotated from previous position = 11.3 degrees
atoms outside contour = 900, contour level = 0.011955
> hide #!1 models> select #9/A:2068 atoms, 7 bonds, 1 residue, 1 model
> selected
> select #9:206-316868 atoms, 883 bonds, 111 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 868 atoms
average map value = 0.01128, steps = 68
shifted from previous position = 7.48
rotated from previous position = 28.9 degrees
atoms outside contour = 497, contour level = 0.011955
> show #!1 models> hide #!1 models> select #9:300-5001551 atoms, 1575 bonds,
> 201 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 1551 atoms
average map value = 0.0102, steps = 100
shifted from previous position = 11.7
rotated from previous position = 27.1 degrees
atoms outside contour = 951, contour level = 0.011955
> show #!1 models> select #9:300-9004474 atoms, 4559 bonds, 572 residues, 1
> model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 4474 atoms
average map value = 0.007096, steps = 144
shifted from previous position = 10.5
rotated from previous position = 25.4 degrees
atoms outside contour = 3695, contour level = 0.011955
> select #9:300-7003151 atoms, 3212 bonds, 401 residues, 1 model selected
> select #9:300-6002347 atoms, 2387 bonds, 301 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 2347 atoms
average map value = 0.007995, steps = 64
shifted from previous position = 1.03
rotated from previous position = 5.58 degrees
atoms outside contour = 1793, contour level = 0.011955
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 2347 atoms
average map value = 0.007994, steps = 36
shifted from previous position = 0.0389
rotated from previous position = 0.0318 degrees
atoms outside contour = 1790, contour level = 0.011955
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 2347 atoms
average map value = 0.007994, steps = 44
shifted from previous position = 0.00739
rotated from previous position = 0.0307 degrees
atoms outside contour = 1789, contour level = 0.011955
> select #9:500-600801 atoms, 816 bonds, 101 residues, 1 model selected
> select #9:350-6001971 atoms, 2007 bonds, 251 residues, 1 model selected
> select #9:350-5001175 atoms, 1195 bonds, 151 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 1175 atoms
average map value = 0.01025, steps = 60
shifted from previous position = 3.3
rotated from previous position = 26.6 degrees
atoms outside contour = 741, contour level = 0.011955
> select #9:400-5501192 atoms, 1211 bonds, 151 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 1192 atoms
average map value = 0.0094, steps = 68
shifted from previous position = 1.14
rotated from previous position = 3.49 degrees
atoms outside contour = 837, contour level = 0.011955
> select #9:400-100Nothing selected
> select #9:400-10003708 atoms, 3783 bonds, 472 residues, 1 model selected
> view matrix models
> #9,0.51175,-0.0055098,-0.85912,308.44,0.6609,-0.63639,0.39776,348.7,-0.54893,-0.77135,-0.32203,360.28>
> view matrix models
> #9,0.51175,-0.0055098,-0.85912,297.82,0.6609,-0.63639,0.39776,381.54,-0.54893,-0.77135,-0.32203,377.2>
> ui tool show AlphaFold> close #9Fetching compressed Q9Qxk3 UniProt info from
> https://www.uniprot.org/uniprot/Q9Qxk3.xml
> alphafold match Q9Qxk31 AlphaFold model found using UniProt identifier:
> Q9Qxk3 (UniProt Q9Qxk3)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q9Qxk3 | Q9Qxk3 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #96840 atoms, 6965 bonds, 871 residues, 1 model selected
> view matrix models #9,1,0,0,466.25,0,1,0,157.83,0,0,1,256.46> view matrix
> models #9,1,0,0,305.98,0,1,0,365.44,0,0,1,305.5> view matrix models
> #9,1,0,0,341.52,0,1,0,373.45,0,0,1,300.44> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.81361,-0.12237,-0.56838,338.46,0.5568,-0.1174,0.82231,387.95,-0.16736,-0.98552,-0.027381,300.86>
> view matrix models
> #9,0.82945,-0.12912,-0.54345,338.68,0.5312,-0.11855,0.83891,388.1,-0.17275,-0.98452,-0.029744,300.84>
> view matrix models
> #9,0.54585,0.14577,-0.82511,334.65,0.61472,-0.73883,0.27614,388.82,-0.56936,-0.65794,-0.49289,295.15>
> view matrix models
> #9,0.38754,0.030891,-0.92133,334.98,0.55325,-0.80723,0.20565,388.9,-0.73738,-0.58943,-0.32992,295.94>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.38754,0.030891,-0.92133,322.24,0.55325,-0.80723,0.20565,374.45,-0.73738,-0.58943,-0.32992,358.47>
> view matrix models
> #9,0.38754,0.030891,-0.92133,327.16,0.55325,-0.80723,0.20565,360.18,-0.73738,-0.58943,-0.32992,352.33>
> view matrix models
> #9,0.38754,0.030891,-0.92133,324.22,0.55325,-0.80723,0.20565,360.68,-0.73738,-0.58943,-0.32992,358.31>
> view matrix models
> #9,0.38754,0.030891,-0.92133,322.41,0.55325,-0.80723,0.20565,353.33,-0.73738,-0.58943,-0.32992,357.52>
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.34389,-0.062917,-0.9369,323.07,0.6427,-0.71165,0.2837,353.07,-0.6846,-0.69971,-0.2043,359.27>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.34389,-0.062917,-0.9369,328.81,0.6427,-0.71165,0.2837,356.31,-0.6846,-0.69971,-0.2043,360.58>
> view matrix models
> #9,0.34389,-0.062917,-0.9369,328.8,0.6427,-0.71165,0.2837,351.24,-0.6846,-0.69971,-0.2043,359.5>
> view matrix models
> #9,0.34389,-0.062917,-0.9369,331.26,0.6427,-0.71165,0.2837,360.08,-0.6846,-0.69971,-0.2043,354.24>
> select up38293 atoms, 39038 bonds, 4835 residues, 11 models selected
> select down6840 atoms, 6965 bonds, 871 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9Qxk3 (#9) to map postprocess.mrc
> (#1) using 6840 atoms
average map value = 0.006977, steps = 140
shifted from previous position = 5.07
rotated from previous position = 17 degrees
atoms outside contour = 5336, contour level = 0.011955
Position of AlphaFold Q9Qxk3 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.55353562 -0.14351463 -0.82036691 327.32551199
0.43570473 -0.78957990 0.43211684 362.60212095
-0.70976031 -0.59662980 -0.37453060 353.73929912
Axis -0.86757749 -0.09327835 0.48847564
Axis point 0.00000000 244.06438349 202.94719963
Rotation angle (degrees) 143.63802429
Shift along axis -145.01014236
> hide #9 models> show #9 models> hide #9 models> show #9 models> hide #!1
> models> select #9:250-10004861 atoms, 4956 bonds, 622 residues, 1 model
> selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9Qxk3
> (#9) to map postprocess.mrc (#1) using 4861 atoms
average map value = 0.006192, steps = 108
shifted from previous position = 9.94
rotated from previous position = 28.1 degrees
atoms outside contour = 4157, contour level = 0.011955
> show #!1 models> select #9:300-6002347 atoms, 2387 bonds, 301 residues, 1
> model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9Qxk3
> (#9) to map postprocess.mrc (#1) using 2347 atoms
average map value = 0.0079, steps = 100
shifted from previous position = 6.85
rotated from previous position = 13.6 degrees
atoms outside contour = 1821, contour level = 0.011955
> select #9:100-3001571 atoms, 1595 bonds, 201 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9Qxk3
> (#9) to map postprocess.mrc (#1) using 1571 atoms
average map value = 0.0114, steps = 104
shifted from previous position = 1.54
rotated from previous position = 6.83 degrees
atoms outside contour = 841, contour level = 0.011955
> select #9:300-400777 atoms, 787 bonds, 101 residues, 1 model selected
> select #9:250-4001164 atoms, 1184 bonds, 151 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9Qxk3
> (#9) to map postprocess.mrc (#1) using 1164 atoms
average map value = 0.01073, steps = 72
shifted from previous position = 3.06
rotated from previous position = 30.4 degrees
atoms outside contour = 648, contour level = 0.011955
> select #9:400-100Nothing selected
> select #9:400-10003708 atoms, 3783 bonds, 472 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9Qxk3
> (#9) to map postprocess.mrc (#1) using 3708 atoms
average map value = 0.006659, steps = 104
shifted from previous position = 11.1
rotated from previous position = 11.8 degrees
atoms outside contour = 3193, contour level = 0.011955
> undo> select #9:400-10003708 atoms, 3783 bonds, 472 residues, 1 model
> selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9Qxk3
> (#9) to map postprocess.mrc (#1) using 3708 atoms
average map value = 0.006659, steps = 44
shifted from previous position = 0.0502
rotated from previous position = 0.0896 degrees
atoms outside contour = 3187, contour level = 0.011955
> hide #9 models> close #9> ui tool show AlphaFold> alphafold match Q9QXK31
> AlphaFold model found using UniProt identifier: Q9QXK3 (UniProt Q9QXK3)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q9QXK3 | Q9QXK3 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #96840 atoms, 6965 bonds, 871 residues, 1 model selected
> view matrix models #9,1,0,0,346.28,0,1,0,94.03,0,0,1,328.47> view matrix
> models #9,1,0,0,344.81,0,1,0,325.02,0,0,1,180.28> view matrix models
> #9,1,0,0,329.7,0,1,0,280.23,0,0,1,355.77> view matrix models
> #9,1,0,0,329.94,0,1,0,338.64,0,0,1,391.21> view matrix models
> #9,1,0,0,333.12,0,1,0,343.71,0,0,1,382.63> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.98522,-0.020408,-0.17006,332.04,0.023622,-0.9672,0.25292,361.21,-0.16964,-0.2532,-0.95242,370.41>
> view matrix models
> #9,-0.16807,0.28223,-0.94451,324.86,0.431,-0.84067,-0.3279,355.6,-0.88656,-0.46219,0.019648,379.81>
> view matrix models
> #9,0.037112,0.71778,-0.69528,323.07,0.99928,-0.020977,0.031682,351.27,0.0081554,-0.69595,-0.71804,375.52>
> view matrix models
> #9,0.10857,0.6296,-0.76929,323.17,0.70385,-0.59517,-0.38777,352.99,-0.702,-0.49937,-0.50777,376.07>
> view matrix models
> #9,-0.10772,0.32765,-0.93864,324.49,0.68538,-0.65945,-0.30885,354.09,-0.72017,-0.67659,-0.15353,380.1>
> ui mousemode right "translate selected models"> view matrix models
> #9,-0.10772,0.32765,-0.93864,323.58,0.68538,-0.65945,-0.30885,357.08,-0.72017,-0.67659,-0.15353,353.13>
> view matrix models
> #9,-0.10772,0.32765,-0.93864,326.75,0.68538,-0.65945,-0.30885,348.33,-0.72017,-0.67659,-0.15353,353.08>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.46602,0.20275,-0.86123,327.86,0.56213,-0.81953,0.11124,352.79,-0.68325,-0.53597,-0.49589,349.41>
> view matrix models
> #9,0.54278,0.21877,-0.81088,328.04,0.69587,-0.65774,0.28835,352.7,-0.47027,-0.72078,-0.50924,350.61>
> view matrix models
> #9,0.45333,0.068879,-0.88868,328.73,0.65945,-0.69669,0.2824,353,-0.59968,-0.71406,-0.36126,351.75>
> view matrix models
> #9,0.40612,-0.099249,-0.90841,329.96,0.5666,-0.75258,0.33553,353.91,-0.71696,-0.65098,-0.2494,352.16>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.40612,-0.099249,-0.90841,326.9,0.5666,-0.75258,0.33553,358.95,-0.71696,-0.65098,-0.2494,354.62>
> view matrix models
> #9,0.40612,-0.099249,-0.90841,327.34,0.5666,-0.75258,0.33553,355.75,-0.71696,-0.65098,-0.2494,353.62>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.45446,-0.074433,-0.88765,327.25,0.47841,-0.82019,0.31371,356.19,-0.75139,-0.56723,-0.33713,352.33>
> view matrix models
> #9,0.53338,-0.018393,-0.84568,327.05,0.3716,-0.89303,0.2538,356.42,-0.75988,-0.44962,-0.46949,350.43>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.53338,-0.018393,-0.84568,321.88,0.3716,-0.89303,0.2538,362.63,-0.75988,-0.44962,-0.46949,353.85>
> view matrix models
> #9,0.53338,-0.018393,-0.84568,322.39,0.3716,-0.89303,0.2538,362.93,-0.75988,-0.44962,-0.46949,356.17>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.32662,-0.16027,-0.93147,323.06,0.4011,-0.86887,0.29015,362.98,-0.85583,-0.46838,-0.21951,358.24>
> view matrix models
> #9,0.3621,-0.28466,-0.88761,324.34,0.37433,-0.82767,0.41814,363.62,-0.85367,-0.48367,-0.19315,358.55>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.3621,-0.28466,-0.88761,332.14,0.37433,-0.82767,0.41814,362.08,-0.85367,-0.48367,-0.19315,356.53>
> select up38293 atoms, 39038 bonds, 4835 residues, 11 models selected
> select down6840 atoms, 6965 bonds, 871 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9QXK3 (#9) to map postprocess.mrc
> (#1) using 6840 atoms
average map value = 0.006977, steps = 116
shifted from previous position = 5.47
rotated from previous position = 14.8 degrees
atoms outside contour = 5340, contour level = 0.011955
Position of AlphaFold Q9QXK3 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.55315490 -0.14333117 -0.82065574 327.34325267
0.43605923 -0.78954698 0.43181930 362.59618814
-0.70983943 -0.59671747 -0.37424090 353.73516973
Axis -0.86745823 -0.09346143 0.48865241
Axis point 0.00000000 244.03028062 202.99835241
Rotation angle (degrees) 143.64083195
Shift along axis -144.99181648
> select #9:200-10005268 atoms, 5369 bonds, 672 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9QXK3 (#9) to map postprocess.mrc
> (#1) using 5268 atoms
average map value = 0.006427, steps = 464
shifted from previous position = 15.5
rotated from previous position = 56.2 degrees
atoms outside contour = 4358, contour level = 0.011955
Position of AlphaFold Q9QXK3 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.49099498 -0.67801596 -0.54700849 326.47928845
0.70423224 -0.06071019 0.70736923 354.78229623
-0.51281661 -0.73253576 0.44767230 343.95295021
Axis -0.72129666 -0.01712786 0.69241444
Axis point 0.00000000 399.34894164 97.36011707
Rotation angle (degrees) 93.49844516
Shift along axis -3.40709031
> view matrix models
> #9,0.49099,-0.67802,-0.54701,329.21,0.70423,-0.06071,0.70737,351.41,-0.51282,-0.73254,0.44767,347.28>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.3712,-0.76337,-0.52866,330.12,0.89353,0.13876,0.42702,347.61,-0.25262,-0.63088,0.7336,348.37>
> view matrix models
> #9,0.26797,-0.16146,-0.9498,322.32,0.79568,-0.51877,0.31268,352.08,-0.54321,-0.83953,-0.010544,344.79>
> volume #1 level 0.0114> view matrix models
> #9,-0.068946,0.012243,-0.99755,320.86,0.95859,-0.27615,-0.069642,347.2,-0.27633,-0.96104,0.0073039,345.67>
> ui mousemode right "translate selected models"> view matrix models
> #9,-0.068946,0.012243,-0.99755,326.16,0.95859,-0.27615,-0.069642,383.95,-0.27633,-0.96104,0.0073039,364.3>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.29948,-0.17563,-0.9378,327.8,0.51056,-0.80084,0.31302,391.3,-0.806,-0.57255,-0.15017,360.48>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.29948,-0.17563,-0.9378,331.34,0.51056,-0.80084,0.31302,373.09,-0.806,-0.57255,-0.15017,354.38>
> view matrix models
> #9,0.29948,-0.17563,-0.9378,331.12,0.51056,-0.80084,0.31302,368.68,-0.806,-0.57255,-0.15017,356.95>
> view matrix models
> #9,0.29948,-0.17563,-0.9378,331.87,0.51056,-0.80084,0.31302,368.76,-0.806,-0.57255,-0.15017,357.32>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.2389,-0.24832,-0.93875,332.49,0.49289,-0.80194,0.33757,368.96,-0.83665,-0.54335,-0.069191,357.71>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.2389,-0.24832,-0.93875,331.35,0.49289,-0.80194,0.33757,368.84,-0.83665,-0.54335,-0.069191,354.45>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.25047,-0.32627,-0.91149,332.16,0.48051,-0.77545,0.40962,369.17,-0.84046,-0.54058,-0.037448,354.66>
> view matrix models
> #9,0.25692,-0.30288,-0.91775,331.92,0.48343,-0.782,0.39341,369.1,-0.83683,-0.54474,-0.054491,354.57>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.25692,-0.30288,-0.91775,330.94,0.48343,-0.782,0.39341,368.9,-0.83683,-0.54474,-0.054491,354.54>
> view matrix models
> #9,0.25692,-0.30288,-0.91775,331.19,0.48343,-0.782,0.39341,367.85,-0.83683,-0.54474,-0.054491,351.42>
> view matrix models
> #9,0.25692,-0.30288,-0.91775,331.96,0.48343,-0.782,0.39341,365.6,-0.83683,-0.54474,-0.054491,354.12>
> view matrix models
> #9,0.25692,-0.30288,-0.91775,332.51,0.48343,-0.782,0.39341,364.42,-0.83683,-0.54474,-0.054491,353.64>
> view matrix models
> #9,0.25692,-0.30288,-0.91775,332.06,0.48343,-0.782,0.39341,365.52,-0.83683,-0.54474,-0.054491,351.69>
> view matrix models
> #9,0.25692,-0.30288,-0.91775,332.08,0.48343,-0.782,0.39341,365.35,-0.83683,-0.54474,-0.054491,350.74>
> view matrix models
> #9,0.25692,-0.30288,-0.91775,331.78,0.48343,-0.782,0.39341,364.85,-0.83683,-0.54474,-0.054491,350.82>
> show #8 models> hide #8 models> show #7 models> hide #7 models> show #6
> models> hide #6 models> show #5 models> hide #5 models> show #5 models> hide
> #9 models> volume #1 level 0.007806> hide #5 models> show #9 models> show #5
> models> volume #1 level 0.004348> volume #1 level 0.008913> hide #5 models>
> hide #!1 models> select clear> select #9:1-3542777 atoms, 2820 bonds, 354
> residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QXK3
> (#9) to map postprocess.mrc (#1) using 2777 atoms
average map value = 0.01112, steps = 108
shifted from previous position = 10.6
rotated from previous position = 20.7 degrees
atoms outside contour = 1204, contour level = 0.0089126
> show #!1 models> show #3 models> hide #3 models> show #4 models> hide #4
> models> show #5 models> select clear> show #8 models> show #7 models> show
> #6 models> show #3 models> show #!2 models> show #4 models> hide #!2 models>
> ui tool show AlphaFoldFetching compressed P61924 UniProt info from
> https://www.uniprot.org/uniprot/P61924.xml
> alphafold match P61924Fetching compressed AlphaFold P61924 from
> https://alphafold.ebi.ac.uk/files/AF-P61924-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: P61924 (UniProt P61924)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P61924 | P61924 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #101420 atoms, 1441 bonds, 177 residues, 1 model selected
> view matrix models #10,1,0,0,-76.273,0,1,0,57.541,0,0,1,547.9> view matrix
> models #10,1,0,0,345.73,0,1,0,306.47,0,0,1,357.61> view matrix models
> #10,1,0,0,297.5,0,1,0,315.44,0,0,1,368> view matrix models
> #10,1,0,0,303.89,0,1,0,298.59,0,0,1,364.43> view matrix models
> #10,1,0,0,312.28,0,1,0,288.62,0,0,1,366.79> view matrix models
> #10,1,0,0,342,0,1,0,324.37,0,0,1,361.18> view matrix models
> #10,1,0,0,349.14,0,1,0,327.22,0,0,1,345.56> volume #1 level 0.01209> hide #6
> models> hide #7 models> hide #8 models> hide #9 models> hide #10 models>
> hide #4 models> hide #5 models> hide #3 models> show #10 models> ui
> mousemode right "rotate selected models"> view matrix models
> #10,0.32391,0.15708,-0.93296,340.76,-0.6159,0.78355,-0.081909,322.55,0.71816,0.60114,0.35055,348.14>
> view matrix models
> #10,0.45089,0.75045,-0.48323,347.69,0.79024,-0.083917,0.60702,328.71,0.41499,-0.65557,-0.63088,333.11>
> view matrix models
> #10,0.2643,0.93034,-0.2542,349.33,0.95688,-0.28589,-0.051414,324.04,-0.1205,-0.22965,-0.96578,330.84>
> view matrix models
> #10,0.53133,0.79911,-0.28126,349.66,0.83163,-0.55529,-0.0066568,322.2,-0.1615,-0.23036,-0.95961,330.68>
> view matrix models
> #10,0.44282,0.88902,0.11645,352.36,0.83457,-0.45615,0.30888,324.84,0.32772,-0.039596,-0.94394,334.18>
> view matrix models
> #10,0.35339,0.9199,0.16998,352.46,0.91374,-0.37837,0.14805,324.61,0.20051,0.103,-0.97426,334.2>
> ui mousemode right "move picked models"> ui mousemode right "translate
> selected models"> view matrix models
> #10,0.35339,0.9199,0.16998,339.75,0.91374,-0.37837,0.14805,350.37,0.20051,0.103,-0.97426,343.01>
> view matrix models
> #10,0.35339,0.9199,0.16998,335.09,0.91374,-0.37837,0.14805,353.64,0.20051,0.103,-0.97426,335.73>
> view matrix models
> #10,0.35339,0.9199,0.16998,338.46,0.91374,-0.37837,0.14805,354.76,0.20051,0.103,-0.97426,335.46>
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #10,0.34886,0.90839,0.23049,338.77,0.90686,-0.38926,0.16153,354.75,0.23645,0.15267,-0.95957,336.01>
> view matrix models
> #10,0.31175,0.90646,0.28484,338.94,0.91088,-0.37042,0.18188,355.01,0.27038,0.20276,-0.94116,336.58>
> fitmap sel inMap #1Fit molecule AlphaFold P61924 (#10) to map
> postprocess.mrc (#1) using 1420 atoms
average map value = 0.007729, steps = 132
shifted from previous position = 13.2
rotated from previous position = 32.1 degrees
atoms outside contour = 1082, contour level = 0.012094
Position of AlphaFold P61924 (#10) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.16003408 0.76875563 0.61919615 342.73825944
0.70217047 -0.52954063 0.47596571 350.81279439
0.69379084 0.35861052 -0.62454205 326.83209386
Axis -0.76117753 -0.48382861 -0.43187804
Axis point 0.00000000 68.50464302 64.30358461
Rotation angle (degrees) 175.57880129
Shift along axis -571.76953314
> view matrix models
> #10,0.47263,0.83858,0.27091,342.34,0.88089,-0.44067,-0.17274,347.93,-0.025471,0.32029,-0.94698,321.12>
> view matrix models
> #10,0.24127,0.92096,0.30597,341.95,0.24412,-0.36274,0.89935,352.37,0.93925,-0.14229,-0.31234,327.16>
> view matrix models
> #10,0.089116,0.82987,0.55079,342.31,-0.78026,-0.28555,0.55647,345.75,0.61908,-0.47935,0.62207,329.83>
> view matrix models
> #10,-0.47438,-0.76909,-0.42833,324.11,0.36461,-0.61452,0.69959,350.2,-0.80126,0.17569,0.57193,326.56>
> view matrix models
> #10,0.8148,0.094127,0.57204,341.65,-0.53759,0.49204,0.68476,352.18,-0.21701,-0.86547,0.45151,322.57>
> view matrix models
> #10,-0.87376,-0.081407,-0.47949,325.83,-0.48429,0.054866,0.87319,351.16,-0.044775,0.99517,-0.087364,330.5>
> view matrix models
> #10,-0.40191,0.13704,-0.90537,326.52,-0.52762,0.77344,0.35129,351.66,0.74839,0.61887,-0.23855,331.1>
> view matrix models
> #10,-0.32465,-0.94451,-0.049995,326.28,-0.89222,0.32336,-0.31525,343.02,0.31392,-0.057737,-0.94769,320.55>
> view matrix models
> #10,-0.31501,-0.94741,-0.05641,326.27,-0.82142,0.30193,-0.48384,342.12,0.47543,-0.10608,-0.87334,321.52>
> ui mousemode right "translate selected models"> view matrix models
> #10,-0.31501,-0.94741,-0.05641,341.43,-0.82142,0.30193,-0.48384,348.71,0.47543,-0.10608,-0.87334,331.34>
> view matrix models
> #10,-0.31501,-0.94741,-0.05641,337.08,-0.82142,0.30193,-0.48384,348.47,0.47543,-0.10608,-0.87334,330.53>
> ui mousemode right "rotate selected models"> view matrix models
> #10,0.010611,-0.96565,-0.25962,337.18,-0.51124,0.2179,-0.83136,347.18,0.85937,0.14155,-0.49137,336.25>
> ui mousemode right "translate selected models"> view matrix models
> #10,0.010611,-0.96565,-0.25962,339.55,-0.51124,0.2179,-0.83136,353.43,0.85937,0.14155,-0.49137,329.03>
> fitmap sel inMap #1Fit molecule AlphaFold P61924 (#10) to map
> postprocess.mrc (#1) using 1420 atoms
average map value = 0.009324, steps = 52
shifted from previous position = 2.72
rotated from previous position = 13.3 degrees
atoms outside contour = 889, contour level = 0.012094
Position of AlphaFold P61924 (#10) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.17048332 -0.93854234 -0.30012280 342.77250355
-0.36432141 0.22295977 -0.90418960 353.65281294
0.91553555 0.26349041 -0.30392015 330.16464207
Axis 0.65572776 -0.68267069 0.32246215
Axis point 206.25695508 0.00000000 375.82229589
Rotation angle (degrees) 117.08028278
Shift along axis 89.80263539
> volume #1 level 0.009189> volume #1 level 0.007115> volume #1 level 0.01389>
> hide #10 models> hide #!1 models> show #!1 models> volume #1 level 0.009189>
> show #9 models> hide #9 models> ui tool show AlphaFoldFetching compressed
> Q9QZE5 UniProt info from https://www.uniprot.org/uniprot/Q9QZE5.xml
> alphafold match Q9QZE5Fetching compressed AlphaFold Q9QZE5 from
> https://alphafold.ebi.ac.uk/files/AF-Q9QZE5-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: Q9QZE5 (UniProt Q9QZE5)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q9QZE5 | Q9QZE5 | 100.0 | 100.0
Opened 1 AlphaFold model
> select subtract #10Nothing selected
> select add #116830 atoms, 6947 bonds, 874 residues, 1 model selected
> ui mousemode right "translate selected models"> view matrix models
> #11,1,0,0,356.03,0,1,0,165.68,0,0,1,138.04> view matrix models
> #11,1,0,0,359.53,0,1,0,310.73,0,0,1,363.97> view matrix models
> #11,1,0,0,325.44,0,1,0,350.8,0,0,1,353.56> ui mousemode right "rotate
> selected models"> view matrix models
> #11,0.9222,0.0092431,-0.38659,322.21,0.3867,-0.02198,0.92194,365.83,2.4106e-05,-0.99972,-0.023845,352.54>
> view matrix models
> #11,0.9086,0.21861,-0.3559,320.97,0.37966,-0.077076,0.92191,366.2,0.17411,-0.97276,-0.15303,351.69>
> view matrix models
> #11,0.8827,0.31881,-0.34526,320.3,0.448,-0.34905,0.82308,367.45,0.14189,-0.88121,-0.45093,348.67>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.8827,0.31881,-0.34526,325.98,0.448,-0.34905,0.82308,376,0.14189,-0.88121,-0.45093,348.84>
> ui mousemode right "rotate selected models"> fitmap sel inMap #1Fit molecule
> AlphaFold Q9QZE5 (#11) to map postprocess.mrc (#1) using 6830 atoms
average map value = 0.006168, steps = 184
shifted from previous position = 19
rotated from previous position = 37.2 degrees
atoms outside contour = 4962, contour level = 0.0091892
Position of AlphaFold Q9QZE5 (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64421407 0.04551772 -0.76348960 327.38100329
0.76207078 0.04674821 0.64580394 357.15848158
0.06508729 -0.99786910 -0.00457187 351.49633213
Axis -0.83213029 -0.41947754 0.36276406
Axis point 0.00000000 331.22710000 127.31166795
Rotation angle (degrees) 99.02148331
Shift along axis -294.73337652
> view matrix models
> #11,0.68657,0.17865,-0.70477,327,0.72706,-0.17094,0.66495,358.75,-0.0016791,-0.96895,-0.24726,349.28>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.70704,0.23648,-0.66646,326.93,0.69939,-0.37331,0.60951,359.67,-0.10466,-0.89706,-0.42933,347.16>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.70704,0.23648,-0.66646,317.9,0.69939,-0.37331,0.60951,366.94,-0.10466,-0.89706,-0.42933,348.03>
> view matrix models
> #11,0.70704,0.23648,-0.66646,320.79,0.69939,-0.37331,0.60951,366.61,-0.10466,-0.89706,-0.42933,348.18>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.72406,0.24939,-0.64307,320.91,0.65006,-0.55839,0.51539,367.07,-0.23055,-0.79121,-0.56643,346.13>
> view matrix models
> #11,0.69859,0.21192,-0.68342,320.81,0.71322,-0.28278,0.64137,366.26,-0.057342,-0.93548,-0.34869,349.16>
> view matrix models
> #11,0.70353,0.18375,-0.6865,320.99,0.70318,-0.31989,0.63499,366.45,-0.10293,-0.92947,-0.35426,348.99>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.70353,0.18375,-0.6865,320.82,0.70318,-0.31989,0.63499,367.1,-0.10293,-0.92947,-0.35426,344.89>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.65363,0.082985,-0.75225,320.91,0.72471,-0.35506,0.59053,367.04,-0.21809,-0.93115,-0.29222,345.16>
> view matrix models
> #11,0.70711,0.13906,-0.69329,321.09,0.68996,-0.35029,0.63344,367.27,-0.15477,-0.92626,-0.34365,344.85>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.70711,0.13906,-0.69329,321.8,0.68996,-0.35029,0.63344,368.61,-0.15477,-0.92626,-0.34365,344.63>
> view matrix models
> #11,0.70711,0.13906,-0.69329,322.37,0.68996,-0.35029,0.63344,369.31,-0.15477,-0.92626,-0.34365,344.66>
> view matrix models
> #11,0.70711,0.13906,-0.69329,324.12,0.68996,-0.35029,0.63344,370.34,-0.15477,-0.92626,-0.34365,345.55>
> view matrix models
> #11,0.70711,0.13906,-0.69329,322.98,0.68996,-0.35029,0.63344,370.13,-0.15477,-0.92626,-0.34365,345.67>
> select #9:150-7004326 atoms, 4409 bonds, 551 residues, 1 model selected
> select #11:150-7004309 atoms, 4386 bonds, 551 residues, 1 model selected
> select #11:200-6003131 atoms, 3181 bonds, 401 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#11) to map
> postprocess.mrc (#1) using 3131 atoms
average map value = 0.009322, steps = 128
shifted from previous position = 19.2
rotated from previous position = 36.2 degrees
atoms outside contour = 1622, contour level = 0.0091892
Position of AlphaFold Q9QZE5 (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.30390324 -0.27752474 -0.91138512 331.87408644
0.81454234 -0.42047696 0.39964972 364.79747780
-0.49412913 -0.86381661 0.09827134 355.85181394
Axis -0.73399556 -0.24239984 0.63442323
Axis point 0.00000000 292.03466120 189.63734203
Rotation angle (degrees) 120.60730761
Shift along axis -106.26030233
> ui mousemode right "translate selected models"> view matrix models
> #11,0.3039,-0.27752,-0.91139,332.27,0.81454,-0.42048,0.39965,364.09,-0.49413,-0.86382,0.098271,356.72>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.27029,-0.28399,-0.91994,332.18,0.8111,-0.44762,0.3765,364.09,-0.51871,-0.84793,0.10935,356.65>
> select #11:200-6003131 atoms, 3181 bonds, 401 residues, 1 model selected
> select #11:200-6003131 atoms, 3181 bonds, 401 residues, 1 model selected
> view matrix models
> #11,0.25475,-0.2793,-0.92579,332.07,0.83477,-0.41974,0.35634,363.79,-0.48812,-0.8636,0.12622,356.95>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.25475,-0.2793,-0.92579,331.84,0.83477,-0.41974,0.35634,363.99,-0.48812,-0.8636,0.12622,355.77>
> select #11:200-6003131 atoms, 3181 bonds, 401 residues, 1 model selected
> view matrix models
> #11,0.25475,-0.2793,-0.92579,331.9,0.83477,-0.41974,0.35634,364.24,-0.48812,-0.8636,0.12622,354.72>
> volume #1 level 0.00753> volume #1 level 0.01057> select #11:1-2241761
> atoms, 1788 bonds, 224 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#11) to map postprocess.mrc (#1) using 1761 atoms
average map value = 0.01173, steps = 68
shifted from previous position = 9.15
rotated from previous position = 24.1 degrees
atoms outside contour = 823, contour level = 0.010572
> volume #1 level 0.008774> volume #1 level 0.006146> hide #!1 models> select
> #11:600-100Nothing selected
> select #11:600-10002157 atoms, 2199 bonds, 275 residues, 1 model selected
> show #!1 models> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#11) to
> map postprocess.mrc (#1) using 2157 atoms
average map value = 0.007662, steps = 180
shifted from previous position = 36.1
rotated from previous position = 68.3 degrees
atoms outside contour = 810, contour level = 0.0061465
Position of AlphaFold Q9QZE5 (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.76148885 0.54060767 -0.35760046 330.05520628
0.64193837 -0.55263312 0.53151836 340.37180485
0.08972105 -0.63430276 -0.76786076 354.04518222
Axis -0.93057375 -0.35705791 0.08088350
Axis point 0.00000000 179.94741315 154.00557546
Rotation angle (degrees) 141.21504880
Shift along axis -400.03674317
> view matrix models
> #11,0.76149,0.54061,-0.3576,333.13,0.64194,-0.55263,0.53152,344.1,0.089721,-0.6343,-0.76786,355.44>
> undo[Repeated 1 time(s)]> redo> undo[Repeated 4 time(s)]> redo[Repeated 5
> time(s)]Drag select of 1 postprocess.mrc
> undo[Repeated 3 time(s)]> redo[Repeated 1 time(s)]> undo[Repeated 4
> time(s)]> select add #116830 atoms, 6947 bonds, 874 residues, 1 model
> selected
> view matrix models
> #11,0.76149,0.54061,-0.3576,311.64,0.64194,-0.55263,0.53152,361.96,0.089721,-0.6343,-0.76786,347.28>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.53048,-0.23713,-0.81386,311.44,0.61272,-0.5562,0.56143,362.09,-0.5858,-0.7965,-0.14976,350.16>
> view matrix models
> #11,0.63273,-0.2207,-0.74226,312.29,0.42526,-0.70202,0.57125,362.21,-0.64715,-0.6771,-0.35033,347.77>
> view matrix models
> #11,0.44433,0.080458,-0.89224,308.81,0.697,-0.65675,0.28787,360.89,-0.56282,-0.7498,-0.34789,348.5>
> view matrix models
> #11,0.54362,-0.27815,-0.7919,311.87,0.82504,0.0037442,0.56506,359.97,-0.1542,-0.96053,0.23152,355.62>
> view matrix models
> #11,-0.061484,-0.33761,-0.93927,308.7,0.84092,-0.52444,0.13346,359.59,-0.53765,-0.78165,0.31615,353.8>
> view matrix models
> #11,-0.23566,-0.13852,-0.96191,306.78,0.80998,-0.57494,-0.11565,357.85,-0.53702,-0.80639,0.24769,353.41>
> ui mousemode right "translate selected models"> view matrix models
> #11,-0.23566,-0.13852,-0.96191,332.21,0.80998,-0.57494,-0.11565,366.09,-0.53702,-0.80639,0.24769,356.19>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#11) to map
> postprocess.mrc (#1) using 6830 atoms
average map value = 0.006152, steps = 88
shifted from previous position = 5.62
rotated from previous position = 9.14 degrees
atoms outside contour = 4002, contour level = 0.0061465
Position of AlphaFold Q9QZE5 (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.08853631 -0.08927349 -0.99206430 328.87288070
0.81371062 -0.58091406 -0.02034415 362.70357604
-0.57448790 -0.80905445 0.12407477 357.29597121
Axis -0.62124086 -0.32891103 0.71125054
Axis point 234.92409049 335.88873344 0.00000000
Rotation angle (degrees) 140.59586808
Shift along axis -69.47952713
> volume #1 level 0.01043> view matrix models
> #11,-0.088536,-0.089273,-0.99206,325.48,0.81371,-0.58091,-0.020344,351.26,-0.57449,-0.80905,0.12407,355.86>
> view matrix models
> #11,-0.088536,-0.089273,-0.99206,333.51,0.81371,-0.58091,-0.020344,354.7,-0.57449,-0.80905,0.12407,353.84>
> view matrix models
> #11,-0.088536,-0.089273,-0.99206,328.18,0.81371,-0.58091,-0.020344,355.32,-0.57449,-0.80905,0.12407,354.03>
> ui mousemode right "rotate selected models"> view matrix models
> #11,-0.28036,-0.26113,-0.92369,328.86,0.75357,-0.65594,-0.04329,355.31,-0.59458,-0.70821,0.38068,355.35>
> view matrix models
> #11,-0.030932,-0.050662,-0.99824,328.15,0.76228,-0.64718,0.0092245,355.69,-0.6465,-0.76066,0.058638,352.99>
> view matrix models
> #11,0.061156,-0.1302,-0.9896,329,0.95467,-0.28175,0.096068,355.16,-0.29133,-0.95061,0.10707,355.77>
> view matrix models
> #11,0.04603,-0.17237,-0.98396,329.21,0.96144,-0.2597,0.090472,355.02,-0.27113,-0.95018,0.15377,356.2>
> view matrix models
> #11,0.0023262,-0.10506,-0.99446,328.6,0.8618,-0.50423,0.055288,355.67,-0.50725,-0.85715,0.089372,354.29>
> view matrix models
> #11,-0.18991,-0.3505,-0.91711,329.74,0.88807,-0.45964,-0.0082315,355.06,-0.41865,-0.81601,0.39856,356.75>
> view matrix models
> #11,-0.080938,-0.34798,-0.934,330.03,0.98708,-0.15797,-0.026682,353.69,-0.13826,-0.9241,0.35627,358.11>
> view matrix models
> #11,0.011068,-0.0051088,-0.99993,328.06,0.98507,-0.17174,0.011781,354.05,-0.17179,-0.98513,0.0031317,355.64>
> view matrix models
> #11,0.52954,-0.35911,-0.76852,333.74,0.78751,-0.12862,0.60273,357.51,-0.31529,-0.92439,0.21469,356.35>
> view matrix models
> #11,0.57219,-0.27083,-0.77411,333.39,0.78422,-0.095517,0.61308,357.4,-0.23998,-0.95788,0.15774,356.39>
> ui mousemode right "rotate selected models"> ui mousemode right "translate
> selected models"> view matrix models
> #11,0.57219,-0.27083,-0.77411,335.51,0.78422,-0.095517,0.61308,362.58,-0.23998,-0.95788,0.15774,351.6>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#11) to map
> postprocess.mrc (#1) using 6830 atoms
average map value = 0.0064, steps = 84
shifted from previous position = 5.2
rotated from previous position = 12.7 degrees
atoms outside contour = 5219, contour level = 0.010434
Position of AlphaFold Q9QZE5 (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.66131608 -0.21078491 -0.71988247 333.61865897
0.74780498 0.11012805 0.65472095 360.57382072
-0.05872604 -0.97130919 0.23045545 348.57872255
Axis -0.81301543 -0.33057836 0.47929516
Axis point 0.00000000 392.94052784 96.12016323
Rotation angle (degrees) 89.94558111
Shift along axis -223.36292607
> view matrix models
> #11,0.66132,-0.21078,-0.71988,341.27,0.7478,0.11013,0.65472,365.27,-0.058726,-0.97131,0.23046,355.25>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.53948,-0.29131,-0.79,340.69,0.59896,-0.52665,0.60322,367.7,-0.59178,-0.79861,-0.10964,349.66>
> view matrix models
> #11,0.46778,-0.17957,-0.86541,339.24,0.68801,-0.54066,0.48407,367.22,-0.55482,-0.82185,-0.12936,349.78>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.46778,-0.17957,-0.86541,332.04,0.68801,-0.54066,0.48407,368.06,-0.55482,-0.82185,-0.12936,351.26>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.1232,-0.023189,-0.99211,328.89,0.74196,-0.66175,0.10761,366.07,-0.65902,-0.74937,-0.064325,350.95>
> view matrix models
> #11,0.16935,-0.30285,-0.93787,330.98,0.7448,-0.58389,0.32303,367.3,-0.64544,-0.75323,0.12669,352.47>
> view matrix models
> #11,0.14032,-0.13117,-0.98138,329.62,0.74434,-0.63963,0.19192,366.6,-0.65289,-0.75741,0.0078783,351.57>
> view matrix models
> #11,0.23167,-0.1013,-0.9675,329.92,0.76523,-0.59508,0.24555,366.85,-0.60062,-0.79725,-0.060342,351.47>
> view matrix models
> #11,0.24437,-0.094002,-0.96511,329.95,0.76843,-0.58828,0.25187,366.87,-0.59143,-0.80318,-0.071526,351.45>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.24437,-0.094002,-0.96511,329.54,0.76843,-0.58828,0.25187,361.23,-0.59143,-0.80318,-0.071526,350.08>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.28058,-0.25967,-0.92404,330.88,0.77353,-0.50879,0.37786,361.78,-0.56826,-0.82079,0.058108,351.25>
> view matrix models
> #11,0.28742,-0.25679,-0.92274,330.9,0.75767,-0.5284,0.38305,361.86,-0.58594,-0.80923,0.042695,351>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.28742,-0.25679,-0.92274,333.19,0.75767,-0.5284,0.38305,365.36,-0.58594,-0.80923,0.042695,355.22>
> view matrix models
> #11,0.28742,-0.25679,-0.92274,331.2,0.75767,-0.5284,0.38305,365.15,-0.58594,-0.80923,0.042695,354.9>
> view matrix models
> #11,0.28742,-0.25679,-0.92274,331.85,0.75767,-0.5284,0.38305,365.37,-0.58594,-0.80923,0.042695,355.26>
> select up46543 atoms, 47426 bonds, 5886 residues, 13 models selected
> select up46543 atoms, 47426 bonds, 5886 residues, 13 models selected
> select down6830 atoms, 6947 bonds, 874 residues, 1 model selected
> select #11:1-6004682 atoms, 4756 bonds, 600 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#11) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.01021, steps = 60
shifted from previous position = 1.22
rotated from previous position = 7.73 degrees
atoms outside contour = 2553, contour level = 0.010434
> select #11:600-10002157 atoms, 2199 bonds, 275 residues, 1 model selected
> ui mousemode right "translate selected atoms"> volume #1 level 0.007668> ui
> mousemode right "rotate selected models"> ui mousemode right "translate
> selected atoms"> ui mousemode right "rotate selected models"> view matrix
> models
> #11,0.59822,-0.60725,-0.52286,337.58,0.30921,-0.42703,0.84972,366.3,-0.73927,-0.66999,-0.067694,353.2>
> view matrix models
> #11,0.77041,-0.50997,-0.38262,338.97,0.12293,-0.47006,0.87403,365.81,-0.62559,-0.7204,-0.29944,352.25>
> view matrix models
> #11,0.80145,-0.49595,-0.33423,339.41,0.030481,-0.52426,0.85101,365.44,-0.59728,-0.69223,-0.40505,351.5>
> view matrix models
> #11,0.81806,-0.46811,-0.33414,339.37,0.21046,-0.29705,0.93138,365.91,-0.53524,-0.83225,-0.14448,354.23>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.81806,-0.46811,-0.33414,336.18,0.21046,-0.29705,0.93138,386.15,-0.53524,-0.83225,-0.14448,359.02>
> view matrix models
> #11,0.81806,-0.46811,-0.33414,336.3,0.21046,-0.29705,0.93138,388.9,-0.53524,-0.83225,-0.14448,350.26>
> view matrix models
> #11,0.81806,-0.46811,-0.33414,333.59,0.21046,-0.29705,0.93138,393.22,-0.53524,-0.83225,-0.14448,351.16>
> view matrix models
> #11,0.81806,-0.46811,-0.33414,333.2,0.21046,-0.29705,0.93138,389.47,-0.53524,-0.83225,-0.14448,356.78>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#11) to map postprocess.mrc (#1) using 2157 atoms
average map value = 0.006694, steps = 136
shifted from previous position = 5.04
rotated from previous position = 47.1 degrees
atoms outside contour = 1445, contour level = 0.0076678
> select #11:1-6004682 atoms, 4756 bonds, 600 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#11) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.008066, steps = 172
shifted from previous position = 26
rotated from previous position = 33 degrees
atoms outside contour = 2547, contour level = 0.0076678
> view matrix models
> #11,0.81806,-0.46811,-0.33414,331.26,0.21046,-0.29705,0.93138,386.86,-0.53524,-0.83225,-0.14448,361.45>
> select #11:1-6004682 atoms, 4756 bonds, 600 residues, 1 model selected
> view matrix models
> #11,0.81806,-0.46811,-0.33414,331.71,0.21046,-0.29705,0.93138,389.51,-0.53524,-0.83225,-0.14448,361.48>
> volume #1 level 0.009742> view matrix models
> #11,0.81806,-0.46811,-0.33414,331,0.21046,-0.29705,0.93138,393.38,-0.53524,-0.83225,-0.14448,362.84>
> view matrix models
> #11,0.81806,-0.46811,-0.33414,331.73,0.21046,-0.29705,0.93138,391.47,-0.53524,-0.83225,-0.14448,362.19>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.83824,-0.4494,-0.30887,332.09,0.11909,-0.40187,0.90792,391.51,-0.53214,-0.79784,-0.28334,359.59>
> select #11:1-6004682 atoms, 4756 bonds, 600 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#11) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.008066, steps = 120
shifted from previous position = 7.42
rotated from previous position = 8.32 degrees
atoms outside contour = 3016, contour level = 0.0097424
> view matrix models
> #11,0.84176,-0.43937,-0.31369,331.92,0.02953,-0.54272,0.8394,391.99,-0.53905,-0.71583,-0.44386,356.49>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.84176,-0.43937,-0.31369,331.75,0.02953,-0.54272,0.8394,399.15,-0.53905,-0.71583,-0.44386,356.2>
> select #11:1-6004682 atoms, 4756 bonds, 600 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#11) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.008066, steps = 76
shifted from previous position = 5.51
rotated from previous position = 10.3 degrees
atoms outside contour = 3011, contour level = 0.0097424
> ui mousemode right "translate selected models"> view matrix models
> #11,0.84176,-0.43937,-0.31369,332.74,0.02953,-0.54272,0.8394,408.41,-0.53905,-0.71583,-0.44386,358.5>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.85268,-0.42149,-0.30869,332.59,-0.0092437,-0.60295,0.79773,408.46,-0.52236,-0.67735,-0.51802,356.68>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.85268,-0.42149,-0.30869,330.72,-0.0092437,-0.60295,0.79773,400.46,-0.52236,-0.67735,-0.51802,359.82>
> select #11:1-6004682 atoms, 4756 bonds, 600 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#11) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.008065, steps = 68
shifted from previous position = 7.07
rotated from previous position = 4.73 degrees
atoms outside contour = 3010, contour level = 0.0097424
> view matrix models
> #11,0.85268,-0.42149,-0.30869,335.88,-0.0092437,-0.60295,0.79773,405.4,-0.52236,-0.67735,-0.51802,361.17>
> ui mousemode right "rotate selected models"> view matrix models
> #11,0.81426,-0.46494,-0.34757,336.1,-0.098912,-0.70112,0.70615,405.87,-0.57201,-0.54061,-0.61688,358.39>
> view matrix models
> #11,0.87501,-0.41991,-0.24091,336.8,-0.20539,-0.77263,0.60071,405.97,-0.43838,-0.47615,-0.76231,353.76>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.87501,-0.41991,-0.24091,331.82,-0.20539,-0.77263,0.60071,413.52,-0.43838,-0.47615,-0.76231,351.86>
> select #11:1-6004682 atoms, 4756 bonds, 600 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#11) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.007962, steps = 124
shifted from previous position = 9.84
rotated from previous position = 14.7 degrees
atoms outside contour = 3070, contour level = 0.0097424
> view matrix models
> #11,0.87501,-0.41991,-0.24091,331.62,-0.20539,-0.77263,0.60071,418.42,-0.43838,-0.47615,-0.76231,353.39>
> close #11> show #9 models> close #9> ui tool show AlphaFold> alphafold match
> Q9QZE51 AlphaFold model found using UniProt identifier: Q9QZE5 (UniProt
> Q9QZE5)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q9QZE5 | Q9QZE5 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #96830 atoms, 6947 bonds, 874 residues, 1 model selected
> view matrix models #9,1,0,0,118.39,0,1,0,297.25,0,0,1,-11.337> view matrix
> models #9,1,0,0,245.71,0,1,0,231.28,0,0,1,332.27> view matrix models
> #9,1,0,0,318.92,0,1,0,322.38,0,0,1,318.53> ui mousemode right "rotate
> selected models"> view matrix models
> #9,-0.20377,-0.7111,-0.67292,316.26,-0.33161,-0.59657,0.73084,338.5,-0.92115,0.37207,-0.11425,305.47>
> view matrix models
> #9,0.40243,-0.79107,-0.46073,319.66,-0.60017,-0.60801,0.51973,336.41,-0.69127,0.067364,-0.71945,303.33>
> view matrix models
> #9,0.2352,-0.84344,-0.48301,319.52,-0.43876,-0.53557,0.72157,337.79,-0.86728,0.042207,-0.49603,304.89>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.2352,-0.84344,-0.48301,339.88,-0.43876,-0.53557,0.72157,350.3,-0.86728,0.042207,-0.49603,367.19>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.2352,-0.84344,-0.48301,334.21,-0.43876,-0.53557,0.72157,375.08,-0.86728,0.042207,-0.49603,349.36>
> volume #1 level 0.007391> view matrix models
> #9,0.2352,-0.84344,-0.48301,333.8,-0.43876,-0.53557,0.72157,373.64,-0.86728,0.042207,-0.49603,349.96>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.037657,-0.31194,-0.94935,326.09,0.77359,0.61048,-0.16991,361.13,0.63256,-0.72802,0.26431,364.17>
> view matrix models
> #9,-0.95684,0.046043,-0.28694,326.81,0.27591,-0.16616,-0.94671,359.5,-0.091268,-0.98502,0.14629,363.62>
> ui mousemode right "translate selected models"> view matrix models
> #9,-0.95684,0.046043,-0.28694,331.91,0.27591,-0.16616,-0.94671,384.35,-0.091268,-0.98502,0.14629,352.91>
> view matrix models
> #9,-0.95684,0.046043,-0.28694,334.19,0.27591,-0.16616,-0.94671,381.78,-0.091268,-0.98502,0.14629,351.78>
> ui mousemode right "rotate selected models"> view matrix models
> #9,-0.97567,0.091702,-0.19917,334.52,0.18187,0.84583,-0.50148,378.03,0.12248,-0.5255,-0.84193,341.32>
> view matrix models
> #9,-0.89837,0.36972,0.23715,336.14,0.02583,0.58344,-0.81174,377.13,-0.43848,-0.72312,-0.5337,343.99>
> ui mousemode right "translate selected models"> view matrix models
> #9,-0.89837,0.36972,0.23715,349.82,0.02583,0.58344,-0.81174,385.82,-0.43848,-0.72312,-0.5337,339.33>
> view matrix models
> #9,-0.89837,0.36972,0.23715,367.42,0.02583,0.58344,-0.81174,403.32,-0.43848,-0.72312,-0.5337,355.2>
> view matrix models
> #9,-0.89837,0.36972,0.23715,347.32,0.02583,0.58344,-0.81174,411.68,-0.43848,-0.72312,-0.5337,366.13>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc
> (#1) using 6830 atoms
average map value = 0.00421, steps = 156
shifted from previous position = 18.9
rotated from previous position = 17.4 degrees
atoms outside contour = 5527, contour level = 0.0073912
Position of AlphaFold Q9QZE5 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.73010351 0.53319212 0.42738160 358.86359853
-0.02431141 0.60476967 -0.79602928 406.65494151
-0.68290397 -0.59157401 -0.42858180 351.34455561
Axis 0.16238138 0.88180517 -0.44277752
Axis point 235.81219866 0.00000000 214.20078465
Rotation angle (degrees) 140.98287405
Shift along axis 261.29572483
> view matrix models
> #9,-0.7301,0.53319,0.42738,360.6,-0.024311,0.60477,-0.79603,408.44,-0.6829,-0.59157,-0.42858,351.39>
> ui mousemode right "rotate selected models"> view matrix models
> #9,-0.58923,0.65779,0.46916,360.34,-0.26987,0.38709,-0.88166,408.8,-0.76156,-0.64612,-0.050566,354.56>
> ui mousemode right "translate selected models"> view matrix models
> #9,-0.58923,0.65779,0.46916,366.58,-0.26987,0.38709,-0.88166,401.14,-0.76156,-0.64612,-0.050566,353.1>
> view matrix models
> #9,-0.58923,0.65779,0.46916,367.47,-0.26987,0.38709,-0.88166,401.19,-0.76156,-0.64612,-0.050566,356.86>
> view matrix models
> #9,-0.58923,0.65779,0.46916,363.55,-0.26987,0.38709,-0.88166,400.39,-0.76156,-0.64612,-0.050566,356.65>
> view matrix models
> #9,-0.58923,0.65779,0.46916,359.48,-0.26987,0.38709,-0.88166,398.89,-0.76156,-0.64612,-0.050566,358.85>
> select #11:600-1000Nothing selected
> select #9:600-10002157 atoms, 2199 bonds, 275 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc
> (#1) using 2157 atoms
average map value = 0.007022, steps = 288
shifted from previous position = 27
rotated from previous position = 73.2 degrees
atoms outside contour = 1209, contour level = 0.0073912
Position of AlphaFold Q9QZE5 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.99844607 0.01106931 0.05461602 354.19039505
-0.00738039 0.94517341 -0.32648548 407.33487213
-0.05523558 -0.32638123 -0.94362298 352.18820987
Axis 0.00093588 0.98618731 -0.16563126
Axis point 182.68264138 0.00000000 205.30019773
Rotation angle (degrees) 176.80725389
Shift along axis 343.70658489
> view matrix models
> #9,-0.99845,0.011069,0.054616,346.87,-0.0073804,0.94517,-0.32649,422.05,-0.055236,-0.32638,-0.94362,361.2>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.24304,0.92608,0.28863,344.77,-0.96288,0.1943,0.18735,429.39,0.11742,-0.32345,0.93893,376.16>
> view matrix models
> #9,0.043178,-0.27177,-0.96139,342.97,-0.82891,-0.54693,0.11738,434.25,-0.55772,0.79184,-0.24889,357.85>
> view matrix models
> #9,-0.74057,-0.19028,-0.64448,343.33,0.61567,-0.57643,-0.53729,432.2,-0.26926,-0.79469,0.54403,375.61>
> view matrix models
> #9,-0.74409,-0.15124,-0.65074,343.01,0.29262,0.80185,-0.52096,422.12,0.60059,-0.57806,-0.55239,367.28>
> view matrix models
> #9,-0.46898,0.34464,0.81319,351.49,-0.6805,0.44592,-0.58144,422.21,-0.56301,-0.82606,0.0254,371.21>
> view matrix models
> #9,-0.46134,0.36344,0.80937,351.35,-0.68581,0.43267,-0.5852,422.26,-0.56287,-0.82505,0.049642,371.39>
> view matrix models
> #9,-0.49256,0.49302,0.71716,349.67,-0.52447,0.48945,-0.69669,421.32,-0.69449,-0.71929,0.017488,370.15>
> ui mousemode right "translate selected models"> view matrix models
> #9,-0.49256,0.49302,0.71716,358.65,-0.52447,0.48945,-0.69669,413.12,-0.69449,-0.71929,0.017488,349.65>
> ui mousemode right "translate selected models"> view matrix models
> #9,-0.49256,0.49302,0.71716,356.89,-0.52447,0.48945,-0.69669,395.25,-0.69449,-0.71929,0.017488,359.86>
> view matrix models
> #9,-0.49256,0.49302,0.71716,355.55,-0.52447,0.48945,-0.69669,394.68,-0.69449,-0.71929,0.017488,359.36>
> view matrix models
> #9,-0.49256,0.49302,0.71716,356.39,-0.52447,0.48945,-0.69669,395.57,-0.69449,-0.71929,0.017488,359.67>
> view matrix models
> #9,-0.49256,0.49302,0.71716,356.3,-0.52447,0.48945,-0.69669,392.38,-0.69449,-0.71929,0.017488,359.47>
> view matrix models
> #9,-0.49256,0.49302,0.71716,357.6,-0.52447,0.48945,-0.69669,396.07,-0.69449,-0.71929,0.017488,360.07>
> view matrix models
> #9,-0.49256,0.49302,0.71716,354.2,-0.52447,0.48945,-0.69669,393.79,-0.69449,-0.71929,0.017488,359.11>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.1382,0.98029,-0.14121,345.38,0.67315,0.011612,0.73942,410.63,0.72648,-0.19724,-0.65827,353.01>
> view matrix models
> #9,0.79254,0.13893,-0.59378,348.99,0.40546,0.60723,0.68328,405.53,0.45549,-0.78228,0.42493,364.97>
> view matrix models
> #9,0.75026,-0.15287,-0.64322,350.54,0.30934,-0.77867,0.54588,413.9,-0.58431,-0.60853,-0.53692,354.24>
> view matrix models
> #9,0.71898,-0.24441,-0.65064,351.06,0.24016,-0.7911,0.56256,413.98,-0.65222,-0.56073,-0.51009,353.98>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.71898,-0.24441,-0.65064,340.8,0.24016,-0.7911,0.56256,389.35,-0.65222,-0.56073,-0.51009,364.86>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.62148,-0.42664,-0.65707,341.83,-0.051117,-0.85901,0.50941,388.84,-0.78176,-0.283,-0.55566,362.32>
> view matrix models
> #9,0.5995,-0.46686,-0.65011,342.12,0.045189,-0.79122,0.60986,389.34,-0.7991,-0.39499,-0.45324,363.86>
> view matrix models
> #9,0.65675,-0.47926,-0.58222,342.84,0.073565,-0.72767,0.68197,389.52,-0.75051,-0.49072,-0.44265,364.7>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.65675,-0.47926,-0.58222,344.93,0.073565,-0.72767,0.68197,386.95,-0.75051,-0.49072,-0.44265,365.94>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.66385,-0.55109,-0.50557,346.04,0.076659,-0.62231,0.77901,386.98,-0.74393,-0.5559,-0.37087,366.96>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.66385,-0.55109,-0.50557,344.8,0.076659,-0.62231,0.77901,383.2,-0.74393,-0.5559,-0.37087,361.43>
> view matrix models
> #9,0.66385,-0.55109,-0.50557,344.64,0.076659,-0.62231,0.77901,381.03,-0.74393,-0.5559,-0.37087,365.37>
> view matrix models
> #9,0.66385,-0.55109,-0.50557,341.78,0.076659,-0.62231,0.77901,381.78,-0.74393,-0.5559,-0.37087,365.31>
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.60629,-0.55655,-0.56804,341.22,0.14486,-0.62505,0.76702,381.84,-0.78194,-0.54733,-0.29834,365.74>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc
> (#1) using 2157 atoms
average map value = 0.006693, steps = 80
shifted from previous position = 7.19
rotated from previous position = 31.8 degrees
atoms outside contour = 1351, contour level = 0.0073912
Position of AlphaFold Q9QZE5 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.15378698 -0.84710107 -0.50869376 332.33451652
0.16472506 -0.48563474 0.85850135 387.36757534
-0.97427677 -0.21582094 0.06485448 366.46545007
Axis -0.69423497 0.30086317 0.65384950
Axis point 0.00000000 362.73488489 220.45875682
Rotation angle (degrees) 129.30857204
Shift along axis 125.43964356
> select #9:1-6004682 atoms, 4756 bonds, 600 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.005104, steps = 84
shifted from previous position = 16.1
rotated from previous position = 21.6 degrees
atoms outside contour = 3452, contour level = 0.0073912
> volume #1 level 0.008498> ui mousemode right "rotate selected models"> view
> matrix models
> #9,0.17474,0.1346,-0.97537,320.44,0.98437,-0.046172,0.16998,369.77,-0.022157,-0.98982,-0.14056,361.17>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc
> (#1) using 4682 atoms
average map value = 0.009126, steps = 360
shifted from previous position = 23.3
rotated from previous position = 15.1 degrees
atoms outside contour = 2456, contour level = 0.0084977
Position of AlphaFold Q9QZE5 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.26722214 0.11515920 -0.95672917 313.71512644
0.92844099 -0.29663683 0.22361556 356.10575290
-0.25804972 -0.94802160 -0.18618645 345.95018384
Axis -0.73772342 -0.43992476 0.51208433
Axis point 0.00000000 236.47808024 193.71528561
Rotation angle (degrees) 127.43063905
Shift along axis -210.93906558
> view matrix models
> #9,0.62734,-0.137,-0.7666,315.51,0.62687,-0.49522,0.60149,364.62,-0.46204,-0.8579,-0.22479,346.22>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.007414, steps = 200
shifted from previous position = 10.5
rotated from previous position = 25.5 degrees
atoms outside contour = 2906, contour level = 0.0084977
> view matrix models
> #9,0.62689,-0.13779,-0.76682,315.51,0.62658,-0.49578,0.60133,364.62,-0.46303,-0.85745,-0.22446,346.22>
> view matrix models
> #9,0.78502,-0.30523,-0.53905,321.04,0.40342,-0.40846,0.81879,367.89,-0.47009,-0.86023,-0.19751,346.74>
> view matrix models
> #9,0.65986,-0.47284,-0.58396,321.22,0.32015,-0.52617,0.78781,368.03,-0.67977,-0.7068,-0.19582,345.54>
> view matrix models
> #9,0.63575,-0.49645,-0.59107,321.23,0.30396,-0.54286,0.78289,368.04,-0.70953,-0.67738,-0.19422,345.35>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.63575,-0.49645,-0.59107,329.03,0.30396,-0.54286,0.78289,375.62,-0.70953,-0.67738,-0.19422,346.81>
> view matrix models
> #9,0.63575,-0.49645,-0.59107,329.49,0.30396,-0.54286,0.78289,376.63,-0.70953,-0.67738,-0.19422,349.62>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.007466, steps = 92
shifted from previous position = 9.33
rotated from previous position = 13.4 degrees
atoms outside contour = 2810, contour level = 0.0084977
> view matrix models
> #9,0.63575,-0.49645,-0.59107,323.05,0.30396,-0.54286,0.78289,378.79,-0.70953,-0.67738,-0.19422,355.99>
> view matrix models
> #9,0.63575,-0.49645,-0.59107,325.43,0.30396,-0.54286,0.78289,382.67,-0.70953,-0.67738,-0.19422,356>
> view matrix models
> #9,0.63575,-0.49645,-0.59107,315.63,0.30396,-0.54286,0.78289,385.33,-0.70953,-0.67738,-0.19422,358.5>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.007414, steps = 188
shifted from previous position = 9.6
rotated from previous position = 19.1 degrees
atoms outside contour = 2904, contour level = 0.0084977
> view matrix models
> #9,0.63575,-0.49645,-0.59107,313.27,0.30396,-0.54286,0.78289,391.49,-0.70953,-0.67738,-0.19422,358.97>
> view matrix models
> #9,0.63575,-0.49645,-0.59107,313.87,0.30396,-0.54286,0.78289,390.27,-0.70953,-0.67738,-0.19422,359.2>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4682 atoms
average map value = 0.00756, steps = 60
shifted from previous position = 3.71
rotated from previous position = 6.24 degrees
atoms outside contour = 2853, contour level = 0.0084977
> select #9:600-10002157 atoms, 2199 bonds, 275 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2157 atoms
average map value = 0.006694, steps = 200
shifted from previous position = 32.1
rotated from previous position = 35.8 degrees
atoms outside contour = 1666, contour level = 0.0084977
> select #9:650-10001763 atoms, 1796 bonds, 225 residues, 1 model selected
> view matrix models
> #9,0.63575,-0.49645,-0.59107,330.89,0.30396,-0.54286,0.78289,403.52,-0.70953,-0.67738,-0.19422,367.13>
> view matrix models
> #9,0.63575,-0.49645,-0.59107,339.19,0.30396,-0.54286,0.78289,407.94,-0.70953,-0.67738,-0.19422,382.25>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 1763 atoms
average map value = 0.007481, steps = 236
shifted from previous position = 61.9
rotated from previous position = 41.9 degrees
atoms outside contour = 966, contour level = 0.0084977
> ui tool show AlphaFold> close #9> alphafold match Q9QZE51 AlphaFold model
> found using UniProt identifier: Q9QZE5 (UniProt Q9QZE5)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q9QZE5 | Q9QZE5 | 100.0 | 100.0
Opened 1 AlphaFold model
> hide #9 models> show #9 models> select add #96830 atoms, 6947 bonds, 874
> residues, 1 model selected
> view matrix models #9,1,0,0,231.53,0,1,0,352.98,0,0,1,252.26> view matrix
> models #9,1,0,0,225.37,0,1,0,330.91,0,0,1,352.68> view matrix models
> #9,1,0,0,329.42,0,1,0,337.51,0,0,1,364.07> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.5106,0.057525,0.85789,334.74,-0.81647,-0.28037,0.50474,348.72,0.26957,-0.95817,-0.096191,362.72>
> view matrix models
> #9,-0.33935,0.87755,-0.33875,318.06,-0.86466,-0.14919,0.47969,347.52,0.37041,0.45569,0.80941,360.15>
> view matrix models
> #9,0.93235,0.086502,-0.35105,325.96,0.2537,0.53526,0.80569,347.5,0.2576,-0.84025,0.47711,366.34>
> view matrix models
> #9,0.92134,-0.081696,-0.38007,326.88,0.35814,-0.20192,0.91157,353.65,-0.15122,-0.97599,-0.15678,361.55>
> view matrix models
> #9,0.91582,-0.11413,-0.38503,327.05,0.33247,-0.32231,0.88633,354.24,-0.22525,-0.93973,-0.25723,360.37>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc
> (#1) using 6830 atoms
average map value = 0.006137, steps = 92
shifted from previous position = 17.1
rotated from previous position = 10.5 degrees
atoms outside contour = 4797, contour level = 0.0084977
Position of AlphaFold Q9QZE5 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.87097484 -0.15840588 -0.46509182 332.36931951
0.43604691 -0.18701388 0.88027774 345.85308003
-0.22641979 -0.96950162 -0.09381199 347.41581981
Axis -0.94494368 -0.12192353 0.30367103
Axis point 0.00000000 333.53825216 91.59869353
Rotation angle (degrees) 101.82513874
Shift along axis -250.73779687
> view matrix models
> #9,0.85722,-0.25265,-0.44871,333.12,0.38273,-0.2704,0.88341,346.35,-0.34453,-0.929,-0.13509,346.58>
> view matrix models
> #9,0.86448,-0.2189,-0.4525,332.87,0.40922,-0.21628,0.88643,346.05,-0.29191,-0.95147,-0.097393,347.13>
> view matrix models
> #9,0.36729,0.024632,-0.92978,326.49,0.74423,-0.60736,0.27791,344.69,-0.55786,-0.79405,-0.24141,344.4>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.36729,0.024632,-0.92978,320.35,0.74423,-0.60736,0.27791,367.07,-0.55786,-0.79405,-0.24141,335.26>
> view matrix models
> #9,0.36729,0.024632,-0.92978,319.34,0.74423,-0.60736,0.27791,374.59,-0.55786,-0.79405,-0.24141,351.05>
> view matrix models
> #9,0.36729,0.024632,-0.92978,318.31,0.74423,-0.60736,0.27791,364.69,-0.55786,-0.79405,-0.24141,353.03>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.39074,0.007604,-0.92047,318.55,0.79623,-0.50455,0.33383,364.51,-0.46189,-0.86335,-0.2032,354>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.39074,0.007604,-0.92047,319.03,0.79623,-0.50455,0.33383,361.58,-0.46189,-0.86335,-0.2032,354.38>
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc
> (#1) using 6830 atoms
average map value = 0.006748, steps = 124
shifted from previous position = 5.03
rotated from previous position = 19.9 degrees
atoms outside contour = 4536, contour level = 0.0084977
Position of AlphaFold Q9QZE5 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.52415675 -0.03555277 -0.85087937 323.94798716
0.82736390 -0.21551011 0.51867559 361.60820896
-0.20181346 -0.97585418 -0.08354600 353.04415803
Axis -0.81057848 -0.35202969 0.46801455
Axis point 0.00000000 298.25200642 154.24747069
Rotation angle (degrees) 112.79590387
Shift along axis -224.65229079
> view matrix models
> #9,0.52416,-0.035553,-0.85088,323.62,0.82736,-0.21551,0.51868,361.48,-0.20181,-0.97585,-0.083546,354.84>
> ui mousemode right "move picked models"> ui mousemode right "rotate selected
> models"> view matrix models
> #9,0.47843,-0.20219,-0.85453,324.65,0.80053,-0.29954,0.51907,362.01,-0.36091,-0.93241,0.01855,355.02>
> select #700-1000Nothing selected
> select #9:700-10001362 atoms, 1385 bonds, 175 residues, 1 model selected
> hide #!1 models> select clear> select #9/A:6065 atoms, 4 bonds, 1 residue, 1
> model selected
> select #9:600-10002157 atoms, 2199 bonds, 275 residues, 1 model selected
> select #9:604-10002123 atoms, 2164 bonds, 271 residues, 1 model selected
> select #9/A:5847 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:1-5844566 atoms, 4638 bonds, 584 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc
> (#1) using 4566 atoms
average map value = 0.009351, steps = 92
shifted from previous position = 4.38
rotated from previous position = 3.89 degrees
atoms outside contour = 2341, contour level = 0.0084977
Position of AlphaFold Q9QZE5 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.45889906 -0.18486325 -0.86904386 327.45356541
0.79055463 -0.36145506 0.49434160 364.85244362
-0.40550589 -0.91387954 -0.01972689 357.01911347
Axis -0.79351902 -0.26119917 0.54963856
Axis point 0.00000000 298.56869237 168.18761450
Rotation angle (degrees) 117.46078746
Shift along axis -158.90831637
> show #!1 models> ui mousemode right "rotate selected models"> view matrix
> models
> #9,0.27309,-0.67152,-0.68882,331.87,0.59697,-0.44319,0.66874,366.4,-0.75435,-0.59384,0.27985,356.44>
> view matrix models
> #9,0.8063,-0.1175,-0.57972,329.92,0.17462,-0.88911,0.42307,366.75,-0.56515,-0.44235,-0.69637,348.17>
> view matrix models
> #9,0.75803,-0.21289,-0.61649,330.2,0.39103,-0.60816,0.69082,367.31,-0.522,-0.76473,-0.37776,352.97>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.75803,-0.21289,-0.61649,354.81,0.39103,-0.60816,0.69082,381.91,-0.522,-0.76473,-0.37776,346.1>
> view matrix models
> #9,0.75803,-0.21289,-0.61649,354.95,0.39103,-0.60816,0.69082,384.47,-0.522,-0.76473,-0.37776,355.72>
> select #9:604-10002123 atoms, 2164 bonds, 271 residues, 1 model selected
> fitmap sel inMap #1Fit molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc
> (#1) using 2123 atoms
average map value = 0.006782, steps = 112
shifted from previous position = 1.97
rotated from previous position = 52.8 degrees
atoms outside contour = 1633, contour level = 0.0084977
Position of AlphaFold Q9QZE5 (#9) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.15078311 -0.84758859 -0.50878093 332.31596289
0.16314294 -0.48627331 0.85844199 387.32606835
-0.97501222 -0.21244257 0.06495629 366.55082693
Axis -0.69331528 0.30184886 0.65437083
Axis point 0.00000000 362.68162268 221.17266955
Rotation angle (degrees) 129.43978685
Shift along axis 126.37436574
> view matrix models
> #9,0.15078,-0.84759,-0.50878,327.58,0.16314,-0.48627,0.85844,381.92,-0.97501,-0.21244,0.064956,363.32>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.54718,0.18399,-0.81654,318.8,0.83443,-0.043237,0.54942,377.76,0.065782,-0.98198,-0.17718,368.82>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.54718,0.18399,-0.81654,321.53,0.83443,-0.043237,0.54942,375.98,0.065782,-0.98198,-0.17718,369.73>
> view matrix models
> #9,0.54718,0.18399,-0.81654,329.13,0.83443,-0.043237,0.54942,373.65,0.065782,-0.98198,-0.17718,370.98>
> view matrix models
> #9,0.54718,0.18399,-0.81654,326.81,0.83443,-0.043237,0.54942,371.45,0.065782,-0.98198,-0.17718,357.23>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.76141,-0.019108,-0.64799,329.95,0.60429,0.38283,0.69877,369.21,0.23472,-0.92362,0.30303,360.89>
> view matrix models
> #9,0.72763,-0.47084,-0.49887,334.18,0.56532,-0.00033507,0.82487,372.77,-0.38855,-0.88222,0.26593,359.09>
> view matrix models
> #9,0.53548,-0.47674,-0.69712,332.3,0.83644,0.41349,0.35972,366.81,0.11676,-0.77572,0.62018,362.1>
> view matrix models
> #9,0.55976,-0.55016,-0.61967,333.46,0.74824,0.014216,0.66328,371.77,-0.3561,-0.83494,0.41961,360.03>
> view matrix models
> #9,0.0083414,-0.40427,-0.9146,329.07,0.92123,-0.35263,0.16427,370.78,-0.38893,-0.84393,0.36948,359.63>
> select #9:200-5843015 atoms, 3063 bonds, 385 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 3015 atoms
average map value = 0.008169, steps = 140
shifted from previous position = 9.02
rotated from previous position = 13.4 degrees
atoms outside contour = 1695, contour level = 0.0084977
> ui mousemode right "translate selected models"> view matrix models
> #9,0.0083414,-0.40427,-0.9146,333.28,0.92123,-0.35263,0.16427,381.87,-0.38893,-0.84393,0.36948,365.25>
> select #9:100-5843782 atoms, 3840 bonds, 485 residues, 1 model selected
> select #9:1-5844566 atoms, 4638 bonds, 584 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4566 atoms
average map value = 0.007329, steps = 144
shifted from previous position = 12.3
rotated from previous position = 12.3 degrees
atoms outside contour = 2829, contour level = 0.0084977
> view matrix models
> #9,0.0083414,-0.40427,-0.9146,337.17,0.92123,-0.35263,0.16427,385.88,-0.38893,-0.84393,0.36948,365.25>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.20778,-0.49673,-0.84267,341.14,0.74791,-0.47455,0.46415,385.68,-0.63045,-0.72667,0.27291,360.36>
> view matrix models
> #9,0.23996,-0.52672,-0.81546,341.97,0.70114,-0.48694,0.52085,385.34,-0.67143,-0.69674,0.25246,359.43>
> view matrix models
> #9,0.25585,-0.4691,-0.84527,341.57,0.62735,-0.58469,0.51437,385.12,-0.73551,-0.66188,0.1447,357.76>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.25585,-0.4691,-0.84527,337.8,0.62735,-0.58469,0.51437,382.88,-0.73551,-0.66188,0.1447,357.91>
> view matrix models
> #9,0.25585,-0.4691,-0.84527,339.82,0.62735,-0.58469,0.51437,387.09,-0.73551,-0.66188,0.1447,364>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4566 atoms
average map value = 0.008131, steps = 152
shifted from previous position = 13.4
rotated from previous position = 38 degrees
atoms outside contour = 2572, contour level = 0.0084977
> select #9:604-10002123 atoms, 2164 bonds, 271 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006367, steps = 68
shifted from previous position = 11.5
rotated from previous position = 16.1 degrees
atoms outside contour = 1630, contour level = 0.0084977
> view matrix models
> #9,0.25585,-0.4691,-0.84527,337.41,0.62735,-0.58469,0.51437,389.41,-0.73551,-0.66188,0.1447,361.76>
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.37394,-0.55141,-0.74574,340.64,0.50685,-0.55188,0.66222,389.38,-0.77671,-0.6256,0.07311,360.15>
> view matrix models
> #9,0.50566,-0.50901,-0.69657,342.02,0.42662,-0.55425,0.71471,389.15,-0.74987,-0.65857,-0.063104,359.35>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.50566,-0.50901,-0.69657,337.55,0.42662,-0.55425,0.71471,394.21,-0.74987,-0.65857,-0.063104,358.41>
> view matrix models
> #9,0.50566,-0.50901,-0.69657,332.42,0.42662,-0.55425,0.71471,391.34,-0.74987,-0.65857,-0.063104,366.24>
> view matrix models
> #9,0.50566,-0.50901,-0.69657,331.23,0.42662,-0.55425,0.71471,391.93,-0.74987,-0.65857,-0.063104,365.89>
> view matrix models
> #9,0.50566,-0.50901,-0.69657,327.26,0.42662,-0.55425,0.71471,391.64,-0.74987,-0.65857,-0.063104,369.02>
> view matrix models
> #9,0.50566,-0.50901,-0.69657,335.89,0.42662,-0.55425,0.71471,386.47,-0.74987,-0.65857,-0.063104,367.12>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 92
shifted from previous position = 2.19
rotated from previous position = 27.9 degrees
atoms outside contour = 1633, contour level = 0.0084977
> select #9:1-5844566 atoms, 4638 bonds, 584 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4566 atoms
average map value = 0.008365, steps = 116
shifted from previous position = 8.23
rotated from previous position = 5.89 degrees
atoms outside contour = 2673, contour level = 0.0084977
> view matrix models
> #9,0.50566,-0.50901,-0.69657,339.01,0.42662,-0.55425,0.71471,386.18,-0.74987,-0.65857,-0.063104,369>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.22416,-0.41869,-0.88003,332.38,0.40267,-0.78253,0.47487,384.8,-0.88747,-0.46081,-0.006816,366.29>
> view matrix models
> #9,0.24958,-0.44213,-0.86153,333.19,0.32071,-0.80173,0.50435,384.73,-0.9137,-0.40218,-0.0583,364.53>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.24958,-0.44213,-0.86153,333.63,0.32071,-0.80173,0.50435,390.91,-0.9137,-0.40218,-0.0583,360.75>
> view matrix models
> #9,0.24958,-0.44213,-0.86153,336.43,0.32071,-0.80173,0.50435,393.51,-0.9137,-0.40218,-0.0583,360.3>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.31985,-0.55665,-0.7667,339.96,0.27095,-0.72168,0.637,394.23,-0.9079,-0.41148,-0.080006,360.12>
> view matrix models
> #9,0.43339,-0.40851,-0.8033,338.69,0.3922,-0.71703,0.57623,394.33,-0.81139,-0.56479,-0.15054,361.7>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.43339,-0.40851,-0.8033,346.01,0.3922,-0.71703,0.57623,392.04,-0.81139,-0.56479,-0.15054,363.41>
> view matrix models
> #9,0.43339,-0.40851,-0.8033,335.77,0.3922,-0.71703,0.57623,392.97,-0.81139,-0.56479,-0.15054,363.27>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.37526,-0.44115,-0.81521,335.42,0.6563,-0.49461,0.56976,392.72,-0.65456,-0.74883,0.10392,370.98>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4566 atoms
average map value = 0.00813, steps = 76
shifted from previous position = 1.91
rotated from previous position = 7.21 degrees
atoms outside contour = 2567, contour level = 0.0084977
> view matrix models
> #9,0.2927,-0.47966,-0.8272,335.05,0.66586,-0.51862,0.53634,392.59,-0.68627,-0.70778,0.16759,371.17>
> show #3 models> hide #3 models> show #3 models> hide #!1 models> select
> #9:1-2091643 atoms, 1668 bonds, 209 residues, 1 model selected
> select #9:1-2081635 atoms, 1660 bonds, 208 residues, 1 model selected
> select #9:1-2071624 atoms, 1649 bonds, 207 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 1624 atoms
average map value = 0.008311, steps = 68
shifted from previous position = 13.5
rotated from previous position = 13.2 degrees
atoms outside contour = 930, contour level = 0.0084977
> show #!1 models> view matrix models
> #9,0.35607,-0.49822,-0.79056,336.8,0.55476,-0.56809,0.60788,393.08,-0.75197,-0.65502,0.074109,367.89>
> view matrix models
> #9,0.14729,-0.48794,-0.86036,332.65,0.48246,-0.72391,0.49315,392.3,-0.86345,-0.48772,0.12879,365>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 1624 atoms
average map value = 0.01134, steps = 76
shifted from previous position = 5.66
rotated from previous position = 32 degrees
atoms outside contour = 679, contour level = 0.0084977
> select #9:207-5842950 atoms, 2996 bonds, 378 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2950 atoms
average map value = 0.008193, steps = 124
shifted from previous position = 2.41
rotated from previous position = 15.8 degrees
atoms outside contour = 1654, contour level = 0.0084977
> hide #3 models> show #3 models> hide #3 models> show #4 models> hide #4
> models> show #5 models> select #9:604-10002123 atoms, 2164 bonds, 271
> residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006678, steps = 252
shifted from previous position = 22.8
rotated from previous position = 49.8 degrees
atoms outside contour = 1532, contour level = 0.0084977
> view matrix models
> #9,0.39618,-0.42708,-0.8128,335.98,0.61508,-0.5338,0.58029,392.99,-0.6817,-0.72983,0.051211,369.42>
> view matrix models
> #9,0.53629,-0.34548,-0.77009,337.47,0.63827,-0.431,0.63784,393.01,-0.55227,-0.8336,-0.010633,371.25>
> view matrix models
> #9,0.89018,-0.24614,-0.3834,350.05,0.24658,-0.44732,0.85971,393.92,-0.38312,-0.85983,-0.3375,365.58>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.89018,-0.24614,-0.3834,333.92,0.24658,-0.44732,0.85971,407.27,-0.38312,-0.85983,-0.3375,369.07>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006524, steps = 152
shifted from previous position = 21.2
rotated from previous position = 21.5 degrees
atoms outside contour = 1547, contour level = 0.0084977
> view matrix models
> #9,0.89018,-0.24614,-0.3834,332.42,0.24658,-0.44732,0.85971,419.6,-0.38312,-0.85983,-0.3375,374.46>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006524, steps = 84
shifted from previous position = 13.5
rotated from previous position = 0.0285 degrees
atoms outside contour = 1545, contour level = 0.0084977
> view matrix models
> #9,0.89018,-0.24614,-0.3834,333.86,0.24658,-0.44732,0.85971,420.55,-0.38312,-0.85983,-0.3375,377.8>
> view matrix models
> #9,0.89018,-0.24614,-0.3834,325.62,0.24658,-0.44732,0.85971,416.49,-0.38312,-0.85983,-0.3375,373.58>
> view matrix models
> #9,0.89018,-0.24614,-0.3834,319.54,0.24658,-0.44732,0.85971,419.01,-0.38312,-0.85983,-0.3375,374.13>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.91854,-0.22913,0.32216,337.12,-0.39532,-0.5259,0.7531,414.21,-0.0031295,-0.81911,-0.57363,369.55>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.91854,-0.22913,0.32216,335.77,-0.39532,-0.5259,0.7531,425.61,-0.0031295,-0.81911,-0.57363,376.01>
> view matrix models
> #9,0.91854,-0.22913,0.32216,343.46,-0.39532,-0.5259,0.7531,420.62,-0.0031295,-0.81911,-0.57363,379.5>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 132
shifted from previous position = 15.9
rotated from previous position = 55.5 degrees
atoms outside contour = 1631, contour level = 0.0084977
> view matrix models
> #9,0.91854,-0.22913,0.32216,341.75,-0.39532,-0.5259,0.7531,415.68,-0.0031295,-0.81911,-0.57363,376.32>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 72
shifted from previous position = 6.12
rotated from previous position = 0.0154 degrees
atoms outside contour = 1631, contour level = 0.0084977
> view matrix models
> #9,0.91854,-0.22913,0.32216,341.47,-0.39532,-0.5259,0.7531,410.17,-0.0031295,-0.81911,-0.57363,373.68>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 100
shifted from previous position = 6.12
rotated from previous position = 0.0323 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.91854,-0.22913,0.32216,341.43,-0.39532,-0.5259,0.7531,407.42,-0.0031295,-0.81911,-0.57363,369.93>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 68
shifted from previous position = 4.65
rotated from previous position = 0.0387 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.91854,-0.22913,0.32216,343.31,-0.39532,-0.5259,0.7531,403.91,-0.0031295,-0.81911,-0.57363,365.44>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 80
shifted from previous position = 6.01
rotated from previous position = 0.0278 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.91854,-0.22913,0.32216,344.72,-0.39532,-0.5259,0.7531,402.05,-0.0031295,-0.81911,-0.57363,363.13>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 68
shifted from previous position = 3.25
rotated from previous position = 0.056 degrees
atoms outside contour = 1632, contour level = 0.0084977
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.92735,-0.26644,0.26275,343.88,-0.36008,-0.44427,0.82034,402.72,-0.10184,-0.85535,-0.50794,364.63>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 84
shifted from previous position = 1.14
rotated from previous position = 7.3 degrees
atoms outside contour = 1631, contour level = 0.0084977
> view matrix models
> #9,0.97653,-0.15522,0.14932,339.6,-0.20792,-0.4985,0.84159,405.33,-0.056194,-0.85288,-0.51907,364.67>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 76
shifted from previous position = 6.06
rotated from previous position = 9.62 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.99388,-0.080233,0.075903,336.64,-0.10681,-0.52344,0.84534,406.58,-0.028093,-0.84828,-0.52881,364.55>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 56
shifted from previous position = 3.86
rotated from previous position = 6.17 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.99952,0.022525,-0.021198,332.52,0.030046,-0.54429,0.83836,407.73,0.0073465,-0.83859,-0.54471,364.24>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 60
shifted from previous position = 5.15
rotated from previous position = 8.19 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.99035,-0.035866,-0.13386,330.63,0.11068,-0.37661,0.91974,407.45,-0.083402,-0.92568,-0.36901,369.54>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 76
shifted from previous position = 1.82
rotated from previous position = 13.1 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.94532,-0.16382,-0.28201,328.87,0.25469,-0.16932,0.95209,405.63,-0.20372,-0.97185,-0.11834,375.75>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006677, steps = 240
shifted from previous position = 15
rotated from previous position = 38.8 degrees
atoms outside contour = 1532, contour level = 0.0084977
> view matrix models
> #9,0.94236,-0.32127,-0.093519,337.1,0.060473,-0.11136,0.99194,404.36,-0.3291,-0.94042,-0.085515,375.25>
> view matrix models
> #9,0.93747,-0.33175,-0.10527,337.01,0.042417,-0.1913,0.98061,405.75,-0.34546,-0.92377,-0.16527,372.78>
> view matrix models
> #9,0.95322,-0.29687,-0.056938,337.54,-0.071279,-0.4038,0.91207,408.15,-0.29375,-0.86534,-0.40607,365.67>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.95322,-0.29687,-0.056938,329.08,-0.071279,-0.4038,0.91207,419.73,-0.29375,-0.86534,-0.40607,375.26>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006877, steps = 428
shifted from previous position = 11.8
rotated from previous position = 55.7 degrees
atoms outside contour = 1494, contour level = 0.0084977
> view matrix models
> #9,0.95322,-0.29687,-0.056938,327.92,-0.071279,-0.4038,0.91207,433.19,-0.29375,-0.86534,-0.40607,379.22>
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.51667,0.50061,0.69458,326.51,-0.2772,-0.66975,0.68891,434.44,0.81007,-0.54848,-0.20727,375.84>
> view matrix models
> #9,0.01178,0.71085,0.70325,321.44,-0.4121,-0.63734,0.65113,432.68,0.91106,-0.29748,0.28543,381.81>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.01178,0.71085,0.70325,341.14,-0.4121,-0.63734,0.65113,445.68,0.91106,-0.29748,0.28543,394.39>
> view matrix models
> #9,0.01178,0.71085,0.70325,342.19,-0.4121,-0.63734,0.65113,443.06,0.91106,-0.29748,0.28543,362.02>
> view matrix models
> #9,0.01178,0.71085,0.70325,349.39,-0.4121,-0.63734,0.65113,450.8,0.91106,-0.29748,0.28543,367.93>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 96
shifted from previous position = 23.4
rotated from previous position = 40.4 degrees
atoms outside contour = 1633, contour level = 0.0084977
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.052452,0.77204,0.63341,345.79,-0.42817,-0.55564,0.7127,449.9,0.90218,-0.30859,0.30141,368.66>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 88
shifted from previous position = 2.07
rotated from previous position = 5.98 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.10222,0.78283,0.61379,345,-0.43696,-0.51897,0.73467,449.4,0.89365,-0.3433,0.28902,369.35>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 68
shifted from previous position = 2.02
rotated from previous position = 3.19 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.17612,0.78168,0.5983,344.65,-0.4452,-0.47883,0.75665,448.79,0.87794,-0.39962,0.26368,370.33>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 72
shifted from previous position = 2.82
rotated from previous position = 4.45 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.21221,0.80166,0.55885,343.08,-0.44612,-0.42933,0.78527,448.09,0.86945,-0.41595,0.26653,370.87>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 104
shifted from previous position = 1.57
rotated from previous position = 3.33 degrees
atoms outside contour = 1631, contour level = 0.0084977
> view matrix models
> #9,0.21629,0.84535,0.48848,340.04,-0.44009,-0.36219,0.82167,447.07,0.87152,-0.39269,0.29369,370.89>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 72
shifted from previous position = 0.633
rotated from previous position = 4.83 degrees
atoms outside contour = 1635, contour level = 0.0084977
> view matrix models
> #9,0.25189,0.85883,0.44605,338.6,-0.439,-0.30936,0.84355,446.1,0.86245,-0.4083,0.29911,371.47>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 60
shifted from previous position = 1.67
rotated from previous position = 3.32 degrees
atoms outside contour = 1634, contour level = 0.0084977
> view matrix models
> #9,0.31454,0.86461,0.3918,337.1,-0.43453,-0.23582,0.86924,444.63,0.84394,-0.44366,0.30153,372.54>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 84
shifted from previous position = 2.69
rotated from previous position = 4.91 degrees
atoms outside contour = 1631, contour level = 0.0084977
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 64
shifted from previous position = 0.0389
rotated from previous position = 0.0388 degrees
atoms outside contour = 1633, contour level = 0.0084977
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 48
shifted from previous position = 0.0547
rotated from previous position = 0.0663 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.34767,0.86197,0.36897,336.63,-0.4519,-0.19075,0.87143,443.37,0.82153,-0.46971,0.32321,373.82>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 52
shifted from previous position = 1.86
rotated from previous position = 3.06 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.41831,0.85506,0.30641,335.33,-0.48722,-0.073476,0.87018,439.92,0.76657,-0.5133,0.38587,376.6>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 72
shifted from previous position = 4.35
rotated from previous position = 7.34 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.47673,0.83487,0.27516,335.21,-0.50535,0.0041705,0.8629,437.46,0.71927,-0.55043,0.42389,378.55>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 72
shifted from previous position = 3.29
rotated from previous position = 5.17 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.54586,0.80222,0.24182,335.45,-0.51991,0.097964,0.84859,434.37,0.65706,-0.58893,0.47055,380.72>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 56
shifted from previous position = 4.03
rotated from previous position = 6.21 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.58422,0.78548,0.20423,335.02,-0.52195,0.17093,0.83567,432.01,0.62149,-0.59481,0.50984,381.82>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 48
shifted from previous position = 2.44
rotated from previous position = 4.39 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.66003,0.72339,0.20263,336.73,-0.48903,0.20898,0.84686,431.34,0.57027,-0.65805,0.4917,382.95>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 88
shifted from previous position = 3.58
rotated from previous position = 5.57 degrees
atoms outside contour = 1630, contour level = 0.0084977
> view matrix models
> #9,0.69668,0.6908,0.1935,337.39,-0.48527,0.25515,0.83631,429.92,0.52835,-0.67654,0.51298,383.87>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 68
shifted from previous position = 2.15
rotated from previous position = 3.52 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.7674,0.61318,0.18737,339.25,-0.46018,0.32324,0.82689,428.1,0.44647,-0.72079,0.53022,385.2>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 112
shifted from previous position = 4.07
rotated from previous position = 6.43 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.83471,0.5055,0.21848,342.65,-0.39663,0.27661,0.87532,430.54,0.38204,-0.81729,0.43138,384.71>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 72
shifted from previous position = 5.02
rotated from previous position = 8.94 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.87367,0.4305,0.22666,344.72,-0.35999,0.25864,0.89639,431.63,0.32728,-0.86474,0.38094,384.3>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 108
shifted from previous position = 3.14
rotated from previous position = 5.31 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.89969,0.36941,0.23257,346.41,-0.33154,0.2317,0.91455,432.86,0.28395,-0.89992,0.33093,383.62>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 68
shifted from previous position = 2.64
rotated from previous position = 4.48 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.93128,0.28224,0.23034,348.53,-0.2932,0.20542,0.93372,434.19,0.21622,-0.93709,0.27405,382.59>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 104
shifted from previous position = 3.54
rotated from previous position = 5.73 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.94139,0.30383,0.14656,345.85,-0.21345,0.20008,0.95625,435.47,0.26121,-0.93148,0.2532,382.21>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 112
shifted from previous position = 2.1
rotated from previous position = 5.33 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.96161,0.25045,0.11219,346.23,-0.18303,0.28069,0.94219,433.5,0.20448,-0.92655,0.31575,383.43>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 104
shifted from previous position = 3.38
rotated from previous position = 5.6 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.98255,0.17574,0.060951,346.55,-0.12928,0.40957,0.90307,430.14,0.13375,-0.89519,0.42514,385.22>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 60
shifted from previous position = 5.04
rotated from previous position = 8.87 degrees
atoms outside contour = 1635, contour level = 0.0084977
> view matrix models
> #9,0.99365,0.095442,0.059664,348.19,-0.087313,0.31908,0.9437,433.46,0.071031,-0.94291,0.32539,382.74>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 72
shifted from previous position = 4.31
rotated from previous position = 7.49 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.99146,0.12345,-0.042143,344.69,0.0017896,0.31016,0.95068,434.92,0.13044,-0.94263,0.30729,382.93>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 112
shifted from previous position = 2.48
rotated from previous position = 6.2 degrees
atoms outside contour = 1631, contour level = 0.0084977
> ui mousemode right "translate selected models"> view matrix models
> #9,0.99146,0.12345,-0.042143,342.65,0.0017896,0.31016,0.95068,433.45,0.13044,-0.94263,0.30729,381.49>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 88
shifted from previous position = 2.9
rotated from previous position = 0.0475 degrees
atoms outside contour = 1634, contour level = 0.0084977
> view matrix models
> #9,0.99146,0.12345,-0.042143,339.45,0.0017896,0.31016,0.95068,435.85,0.13044,-0.94263,0.30729,382.38>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 108
shifted from previous position = 4.1
rotated from previous position = 0.0423 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.99146,0.12345,-0.042143,339.85,0.0017896,0.31016,0.95068,435.55,0.13044,-0.94263,0.30729,382.27>
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.97798,0.15207,-0.14291,336.02,0.09135,0.30376,0.94836,436.57,0.18762,-0.94054,0.28318,382.1>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.97798,0.15207,-0.14291,333.58,0.09135,0.30376,0.94836,435.4,0.18762,-0.94054,0.28318,380.77>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 68
shifted from previous position = 2.59
rotated from previous position = 6.2 degrees
atoms outside contour = 1633, contour level = 0.0084977
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.98965,-0.0080958,-0.14328,336.82,0.13841,0.31741,0.93813,435.32,0.037883,-0.94825,0.31525,380.29>
> view matrix models
> #9,0.99548,0.0093203,-0.09456,338.1,0.090332,0.21583,0.97224,437.87,0.02947,-0.97639,0.21401,377.51>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 112
shifted from previous position = 5.63
rotated from previous position = 10.2 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.99058,-0.068844,-0.11833,338.69,0.13205,0.2523,0.9586,437.29,-0.036138,-0.9652,0.25902,377.93>
> view matrix models
> #9,0.98606,-0.13199,-0.10131,340.32,0.12681,0.20197,0.97115,438.54,-0.10772,-0.97046,0.2159,375.74>
> ui mousemode right "translate selected models"> view matrix models
> #9,0.98606,-0.13199,-0.10131,339.76,0.12681,0.20197,0.97115,440.24,-0.10772,-0.97046,0.2159,376.78>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 60
shifted from previous position = 5.36
rotated from previous position = 8.16 degrees
atoms outside contour = 1633, contour level = 0.0084977
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.94936,-0.27174,-0.15772,339.76,0.20035,0.13689,0.97011,442.23,-0.24203,-0.95258,0.1844,373.72>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 96
shifted from previous position = 6.44
rotated from previous position = 9.34 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.92398,-0.33277,-0.18846,339.37,0.23189,0.095634,0.96803,443.23,-0.30411,-0.93814,0.16553,372.06>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 80
shifted from previous position = 3.04
rotated from previous position = 4.53 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.8957,-0.38747,-0.21815,338.86,0.25872,0.055099,0.96438,444.09,-0.36165,-0.92023,0.1496,370.48>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 68
shifted from previous position = 2.83
rotated from previous position = 4.21 degrees
atoms outside contour = 1630, contour level = 0.0084977
> view matrix models
> #9,0.82815,-0.48586,-0.27947,337.42,0.31227,-0.014117,0.94989,445.38,-0.46546,-0.87392,0.14003,368.07>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 56
shifted from previous position = 5.42
rotated from previous position = 8.03 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,336.17,0.34333,-0.064777,0.93698,446.1,-0.53311,-0.83477,0.13763,366.52>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 88
shifted from previous position = 3.6
rotated from previous position = 5.47 degrees
atoms outside contour = 1633, contour level = 0.0084977
> ui mousemode right "translate selected models"> view matrix models
> #9,0.77325,-0.54677,-0.32114,336.73,0.34333,-0.064777,0.93698,442.16,-0.53311,-0.83477,0.13763,365.74>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 56
shifted from previous position = 4.06
rotated from previous position = 0.00419 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,337.22,0.34333,-0.064777,0.93698,440.84,-0.53311,-0.83477,0.13763,365.56>
> ui mousemode right "translate selected models"> fitmap sel inMap #1
> moveWholeMolecules falseFit molecule AlphaFold Q9QZE5 (#9) to map
> postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 88
shifted from previous position = 1.41
rotated from previous position = 0.0229 degrees
atoms outside contour = 1634, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,335.31,0.34333,-0.064777,0.93698,438.09,-0.53311,-0.83477,0.13763,365.41>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 48
shifted from previous position = 3.35
rotated from previous position = 0.0167 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,334.05,0.34333,-0.064777,0.93698,435.82,-0.53311,-0.83477,0.13763,365.27>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 48
shifted from previous position = 2.6
rotated from previous position = 0.014 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,332.56,0.34333,-0.064777,0.93698,431.78,-0.53311,-0.83477,0.13763,364.96>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 104
shifted from previous position = 4.32
rotated from previous position = 0.0647 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,331.95,0.34333,-0.064777,0.93698,428.43,-0.53311,-0.83477,0.13763,364.64>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 72
shifted from previous position = 3.43
rotated from previous position = 0.0132 degrees
atoms outside contour = 1631, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,331.76,0.34333,-0.064777,0.93698,426.64,-0.53311,-0.83477,0.13763,364.47>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 84
shifted from previous position = 1.8
rotated from previous position = 0.0296 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,331.81,0.34333,-0.064777,0.93698,423.53,-0.53311,-0.83477,0.13763,364.13>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 84
shifted from previous position = 3.12
rotated from previous position = 0.0356 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,332.96,0.34333,-0.064777,0.93698,421.78,-0.53311,-0.83477,0.13763,363.84>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 84
shifted from previous position = 2.11
rotated from previous position = 0.0418 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,334.11,0.34333,-0.064777,0.93698,419.59,-0.53311,-0.83477,0.13763,363.51>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 68
shifted from previous position = 2.49
rotated from previous position = 0.0764 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,334.99,0.34333,-0.064777,0.93698,419.05,-0.53311,-0.83477,0.13763,364.92>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 64
shifted from previous position = 1.74
rotated from previous position = 0.0445 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,336.11,0.34333,-0.064777,0.93698,417.5,-0.53311,-0.83477,0.13763,366.08>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 44
shifted from previous position = 2.24
rotated from previous position = 0.0309 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,336.99,0.34333,-0.064777,0.93698,415.8,-0.53311,-0.83477,0.13763,367.35>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 64
shifted from previous position = 2.31
rotated from previous position = 0.0358 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,340.17,0.34333,-0.064777,0.93698,412.98,-0.53311,-0.83477,0.13763,369.45>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 52
shifted from previous position = 4.76
rotated from previous position = 0.0468 degrees
atoms outside contour = 1631, contour level = 0.0084977
> view matrix models
> #9,0.77325,-0.54677,-0.32114,340.95,0.34333,-0.064777,0.93698,412.06,-0.53311,-0.83477,0.13763,371.98>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 88
shifted from previous position = 2.78
rotated from previous position = 0.0444 degrees
atoms outside contour = 1633, contour level = 0.0084977
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.7178,-0.55951,-0.41439,338.12,0.3933,-0.16528,0.90443,413.67,-0.57453,-0.81218,0.10141,370.13>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 72
shifted from previous position = 3.9
rotated from previous position = 6.92 degrees
atoms outside contour = 1631, contour level = 0.0084977
> view matrix models
> #9,0.73481,-0.51747,-0.4385,337,0.41632,-0.1663,0.89388,413.71,-0.53548,-0.83939,0.09324,370.89>
> view matrix models
> #9,0.67825,-0.52005,-0.51915,334.29,0.45761,-0.25385,0.85215,414.67,-0.57494,-0.81554,0.065812,369.28>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 64
shifted from previous position = 3.87
rotated from previous position = 7.06 degrees
atoms outside contour = 1634, contour level = 0.0084977
> ui mousemode right "translate selected models"> view matrix models
> #9,0.67825,-0.52005,-0.51915,335,0.45761,-0.25385,0.85215,411.58,-0.57494,-0.81554,0.065812,369.68>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 88
shifted from previous position = 3.22
rotated from previous position = 0.0832 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.67825,-0.52005,-0.51915,336.13,0.45761,-0.25385,0.85215,410.05,-0.57494,-0.81554,0.065812,369.97>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 100
shifted from previous position = 1.92
rotated from previous position = 0.025 degrees
atoms outside contour = 1634, contour level = 0.0084977
> view matrix models
> #9,0.67825,-0.52005,-0.51915,337.5,0.45761,-0.25385,0.85215,407.2,-0.57494,-0.81554,0.065812,370.42>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 84
shifted from previous position = 3.2
rotated from previous position = 0.0183 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.67825,-0.52005,-0.51915,338.19,0.45761,-0.25385,0.85215,405.44,-0.57494,-0.81554,0.065812,370.68>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 88
shifted from previous position = 1.9
rotated from previous position = 0.0472 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.67825,-0.52005,-0.51915,339.32,0.45761,-0.25385,0.85215,403.47,-0.57494,-0.81554,0.065812,371.01>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 84
shifted from previous position = 2.31
rotated from previous position = 0.00501 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.67825,-0.52005,-0.51915,341.08,0.45761,-0.25385,0.85215,402.27,-0.57494,-0.81554,0.065812,371.34>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 44
shifted from previous position = 2.15
rotated from previous position = 0.0538 degrees
atoms outside contour = 1630, contour level = 0.0084977
> ui mousemode right "rotate selected models"> view matrix models
> #9,0.68238,-0.51479,-0.51898,341.04,0.43744,-0.28125,0.85414,402.55,-0.58566,-0.80987,0.033274,370.31>
> view matrix models
> #9,0.65688,-0.50421,-0.5606,339.52,0.46738,-0.31114,0.8275,402.82,-0.59166,-0.80558,0.031274,370.11>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 104
shifted from previous position = 2.24
rotated from previous position = 3.61 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.63653,-0.50347,-0.58425,338.66,0.479,-0.33565,0.81111,402.98,-0.60447,-0.79615,0.027511,369.69>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 72
shifted from previous position = 0.981
rotated from previous position = 1.93 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.54609,-0.4734,-0.69114,334.3,0.54331,-0.42784,0.72234,403.14,-0.63765,-0.76996,0.023556,368.72>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 100
shifted from previous position = 4.27
rotated from previous position = 8.41 degrees
atoms outside contour = 1630, contour level = 0.0084977
> view matrix models
> #9,0.53268,-0.49064,-0.68958,334.45,0.55227,-0.41589,0.72252,403.06,-0.64128,-0.76571,0.049429,369.26>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 44
shifted from previous position = 0.527
rotated from previous position = 1.47 degrees
atoms outside contour = 1633, contour level = 0.0084977
> ui mousemode right "translate selected models"> view matrix models
> #9,0.53268,-0.49064,-0.68958,335.38,0.55227,-0.41589,0.72252,401.67,-0.64128,-0.76571,0.049429,369.88>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 52
shifted from previous position = 1.78
rotated from previous position = 0.0462 degrees
atoms outside contour = 1632, contour level = 0.0084977
> view matrix models
> #9,0.53268,-0.49064,-0.68958,337.03,0.55227,-0.41589,0.72252,398.25,-0.64128,-0.76571,0.049429,371.22>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 72
shifted from previous position = 4
rotated from previous position = 0.0539 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.53268,-0.49064,-0.68958,336.5,0.55227,-0.41589,0.72252,396.14,-0.64128,-0.76571,0.049429,371.91>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006781, steps = 48
shifted from previous position = 2.28
rotated from previous position = 0.0375 degrees
atoms outside contour = 1633, contour level = 0.0084977
> view matrix models
> #9,0.53268,-0.49064,-0.68958,336.5,0.55227,-0.41589,0.72252,394.77,-0.64128,-0.76571,0.049429,372.12>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 52
shifted from previous position = 1.4
rotated from previous position = 0.0123 degrees
atoms outside contour = 1633, contour level = 0.0084977
> ui mousemode right "translate selected models"> ui mousemode right "rotate
> selected models"> view matrix models
> #9,0.48168,-0.52169,-0.70415,336.01,0.54192,-0.45414,0.70716,394.9,-0.6887,-0.72222,0.063968,371.16>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.006782, steps = 84
shifted from previous position = 2.18
rotated from previous position = 4.06 degrees
atoms outside contour = 1633, contour level = 0.0084977
> select #9:1-5844566 atoms, 4638 bonds, 584 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 4566 atoms
average map value = 0.008702, steps = 84
shifted from previous position = 7.03
rotated from previous position = 12.9 degrees
atoms outside contour = 2382, contour level = 0.0084977
> select clear> hide #5 models> hide #!1 models> select #9:517-584535 atoms,
> 543 bonds, 68 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 535 atoms
average map value = 0.007748, steps = 80
shifted from previous position = 1.92
rotated from previous position = 4.63 degrees
atoms outside contour = 310, contour level = 0.0084977
> show #!1 models> show #5 models> select clear> volume #1 level 0.00753> show
> #!2 models> show #3 models> hide #!2 models> show #4 models> show #8 models>
> show #7 models> show #6 models> hide #9 models> hide #8 models> show #8
> models> hide #7 models> hide #6 models> hide #3 models> hide #4 models> hide
> #5 models> select #8:1-1781453 atoms, 1472 bonds, 178 residues, 1 model
> selected
> fitmap sel inMap #1Fit molecule AlphaFold Q5XJY5 (#8) to map postprocess.mrc
> (#1) using 1453 atoms
average map value = 0.008626, steps = 80
shifted from previous position = 1.02
rotated from previous position = 3.47 degrees
atoms outside contour = 690, contour level = 0.0075295
Position of AlphaFold Q5XJY5 (#8) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.15504099 0.95631904 0.24782288 253.82646300
-0.90175689 0.03454077 0.43086129 302.50191978
0.40348086 -0.29027715 0.86772252 330.45240550
Axis -0.36071731 -0.07786096 -0.92941954
Axis point 212.05516318 81.20858689 0.00000000
Rotation angle (degrees) 88.35812850
Shift along axis -422.24161336
> volume #1 level 0.01043> volume #1 level 0.009742> show #!2 models> hide #!2
> models> show #3 models> show #4 models> show #5 models> show #6 models> show
> #7 models> show #9 models> show #10 models> select clear> show #!2 models>
> volume #2 level 0.09192> volume #2 level 0.2169> hide #!2 models> ui tool
> show AlphaFoldFetching compressed Q9CRA5 UniProt info from
> https://www.uniprot.org/uniprot/Q9CRA5.xml
> alphafold match Q9CRA5Fetching compressed AlphaFold Q9CRA5 from
> https://alphafold.ebi.ac.uk/files/AF-Q9CRA5-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: Q9CRA5 (UniProt Q9CRA5)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q9CRA5 | Q9CRA5 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #112367 atoms, 2398 bonds, 298 residues, 1 model selected
> ui mousemode right "translate selected models"> view matrix models
> #11,1,0,0,286.27,0,1,0,282.99,0,0,1,272.4> view matrix models
> #11,1,0,0,288.58,0,1,0,364.1,0,0,1,265.21> view matrix models
> #11,1,0,0,297.99,0,1,0,368.21,0,0,1,317.05> ui mousemode right "rotate
> selected models"> view matrix models
> #11,0.99397,-0.020497,0.10769,298.11,-0.032135,0.88472,0.46502,368.63,-0.1048,-0.46568,0.87873,314.67>
> hide #3 models> hide #4 models> hide #5 models> hide #6 models> hide #7
> models> hide #8 models> hide #9 models> hide #10 models> view matrix models
> #11,0.84844,-0.32207,0.42002,296.59,-0.5206,-0.651,0.55243,360.31,0.095516,-0.68737,-0.72,312.88>
> view matrix models
> #11,0.81812,-0.34541,0.45975,296.3,-0.56853,-0.60586,0.55651,359.9,0.086316,-0.71668,-0.69204,312.78>
> view matrix models
> #11,0.58772,-0.41319,0.6956,294.19,-0.80874,-0.27569,0.51955,357.93,-0.022902,-0.86791,-0.49619,311.71>
> ui mousemode right "translate selected models"> view matrix models
> #11,0.58772,-0.41319,0.6956,310.63,-0.80874,-0.27569,0.51955,351.47,-0.022902,-0.86791,-0.49619,304.59>
> view matrix models
> #11,0.58772,-0.41319,0.6956,310.03,-0.80874,-0.27569,0.51955,346.98,-0.022902,-0.86791,-0.49619,304.94>
> select #11:57-10001954 atoms, 1985 bonds, 242 residues, 1 model selected
> ui tool show "Fit in Map"> fitmap sel inMap #1Fit molecule AlphaFold Q9CRA5
> (#11) to map postprocess.mrc (#1) using 1954 atoms
average map value = 0.008773, steps = 60
shifted from previous position = 2.39
rotated from previous position = 17.6 degrees
atoms outside contour = 1138, contour level = 0.0097424
Position of AlphaFold Q9CRA5 (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64865054 -0.27425736 0.70995449 310.01926151
-0.71703282 -0.53296917 0.44923022 345.45914188
0.25517916 -0.80045410 -0.54236227 303.67555190
Axis -0.89159019 0.32446052 -0.31589919
Axis point 0.00000000 279.93960156 -1.69675172
Rotation angle (degrees) 135.50735744
Shift along axis -260.25314202
> show #3 models> show #4 models> show #5 models> show #6 models> show #7
> models> show #8 models> show #9 models> show #10 models> show #!2 models>
> volume #2 level 0.2032> volume #1 level 0.01362> volume #2 level 0.1792>
> select clear> hide #3 models> hide #4 models> hide #5 models> hide #6
> models> hide #7 models> hide #8 models> hide #9 models> hide #10 models>
> volume #1 level 0.01196> volume #2 level 0.1039> volume #2 level 0.1552>
> hide #!2 models> hide #11 models> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/warpV1_erase/relion/PostProcess/job062/alphafold_copi.cxs[Errno
> 13] Permission denied: '/fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/warpV1_erase/relion/PostProcess/job062/alphafold_copi.cxs.13524.tmp'
> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/warpV1_erase/relion/PostProcess/copi_alphafold.cxs[Errno
> 13] Permission denied: '/fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/warpV1_erase/relion/PostProcess/copi_alphafold.cxs.13524.tmp'
> save /fs/pool/pool-briggs/zke/alphafold_copi_gt.cxs includeMaps true——— End
> of log from Sun Nov 5 03:35:04 2023 ———opened ChimeraX session
> show #3 models> show #4 models> show #5 models> show #6 models> show #7
> models> show #8 models> show #9 models> show #!2 models> hide #!2 models>
> volume #1 level 0.009804> show #10 models> show #11 models> show #!2 models>
> hide #!2 models> select #9:98-196760 atoms, 769 bonds, 99 residues, 1 model
> selected
> select #9:98-198772 atoms, 781 bonds, 101 residues, 1 model selected
> select #9:98-12086059 atoms, 6162 bonds, 777 residues, 1 model selected
> select #9:98-208864 atoms, 875 bonds, 111 residues, 1 model selected
> select #9:98-207853 atoms, 864 bonds, 110 residues, 1 model selected
> ui tool show "Fit in Map"> fitmap sel inMap #1 moveWholeMolecules falseFit
> molecule AlphaFold Q9QZE5 (#9) to map postprocess.mrc (#1) using 853 atoms
average map value = 0.01232, steps = 64
shifted from previous position = 6.32
rotated from previous position = 18.5 degrees
atoms outside contour = 344, contour level = 0.0098043
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 853 atoms
average map value = 0.01232, steps = 44
shifted from previous position = 0.0596
rotated from previous position = 0.14 degrees
atoms outside contour = 345, contour level = 0.0098043
> select #9:200-222193 atoms, 196 bonds, 23 residues, 1 model selected
> select #9:206-222136 atoms, 137 bonds, 17 residues, 1 model selected
> select #9:207-222128 atoms, 129 bonds, 16 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q9QZE5
> (#9) to map postprocess.mrc (#1) using 128 atoms
average map value = 0.0125, steps = 104
shifted from previous position = 8.69
rotated from previous position = 12 degrees
atoms outside contour = 52, contour level = 0.0098043
> select #9:2078 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"> select #9:2068 atoms, 7
> bonds, 1 residue, 1 model selected
> select #9:2059 atoms, 8 bonds, 1 residue, 1 model selected
> select #9:2008 atoms, 7 bonds, 1 residue, 1 model selected
> select #9:1984 atoms, 3 bonds, 1 residue, 1 model selected
> select #9:1998 atoms, 7 bonds, 1 residue, 1 model selected
> select #9:2008 atoms, 7 bonds, 1 residue, 1 model selected
> select #9:20112 atoms, 12 bonds, 1 residue, 1 model selected
> select #9:20210 atoms, 10 bonds, 1 residue, 1 model selected
> select #9:2037 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:20210 atoms, 10 bonds, 1 residue, 1 model selected
> 1Unknown command: 1
> select #9:20112 atoms, 12 bonds, 1 residue, 1 model selected
> select #9:20210 atoms, 10 bonds, 1 residue, 1 model selected
> select #9:2037 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:20210 atoms, 10 bonds, 1 residue, 1 model selected
> select #9:20112 atoms, 12 bonds, 1 residue, 1 model selected
> select #9:20411 atoms, 10 bonds, 1 residue, 1 model selected
> select #9:2037 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:2059 atoms, 8 bonds, 1 residue, 1 model selected
> hide #3 models> hide #4 models> hide #5 models> hide #6 models> hide #7
> models> hide #11 models> hide #10 models> hide #8 models> select #9:20411
> atoms, 10 bonds, 1 residue, 1 model selected
> select #9:2037 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:1998 atoms, 7 bonds, 1 residue, 1 model selected
> select #9:2008 atoms, 7 bonds, 1 residue, 1 model selected
> select #9:2008 atoms, 7 bonds, 1 residue, 1 model selected
> select #9:20112 atoms, 12 bonds, 1 residue, 1 model selected
> select #9:20210 atoms, 10 bonds, 1 residue, 1 model selected
> select #9:2037 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:2059 atoms, 8 bonds, 1 residue, 1 model selected
> select #9:20411 atoms, 10 bonds, 1 residue, 1 model selected
> select #9:2037 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:20210 atoms, 10 bonds, 1 residue, 1 model selected
> select #9:2037 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:20411 atoms, 10 bonds, 1 residue, 1 model selected
> select #9:2037 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:2059 atoms, 8 bonds, 1 residue, 1 model selected
> select #9:2068 atoms, 7 bonds, 1 residue, 1 model selected
> select #9:2078 atoms, 7 bonds, 1 residue, 1 model selected
> select clear> select #9/A:6057 atoms, 6 bonds, 1 residue, 1 model selected
> select #9:584-604157 atoms, 159 bonds, 21 residues, 1 model selected
> select #9:590-604112 atoms, 113 bonds, 15 residues, 1 model selected
> select #9:588-604130 atoms, 131 bonds, 17 residues, 1 model selected
> select #9:586-604143 atoms, 144 bonds, 19 residues, 1 model selected
> select #9:585-604150 atoms, 152 bonds, 20 residues, 1 model selected
> select #9:584-604157 atoms, 159 bonds, 21 residues, 1 model selected
> delete sel> hide #!9 models> show #8 models> select #9:257-10004654 atoms,
> 4733 bonds, 1 pseudobond, 597 residues, 2 models selected
> select #8\:257-1000Expected an objects specifier or a keyword
> select #8:257-10002014 atoms, 2054 bonds, 255 residues, 1 model selected
> ui mousemode right "translate selected atoms"> fitmap sel inMap #1
> moveWholeMolecules falseFit molecule AlphaFold Q5XJY5 (#8) to map
> postprocess.mrc (#1) using 2014 atoms
average map value = 0.006316, steps = 60
shifted from previous position = 7.18
rotated from previous position = 6.19 degrees
atoms outside contour = 1480, contour level = 0.0098043
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q5XJY5
> (#8) to map postprocess.mrc (#1) using 2014 atoms
average map value = 0.006563, steps = 148
shifted from previous position = 19.3
rotated from previous position = 20.9 degrees
atoms outside contour = 1472, contour level = 0.0098043
> select add #84014 atoms, 4083 bonds, 511 residues, 1 model selected
> ui mousemode right "rotate selected models"> view matrix models
> #8,-0.65575,-0.45666,0.60121,239.54,0.70208,-0.076013,0.70803,346.55,-0.27763,0.88639,0.37046,305.61>
> view matrix models
> #8,-0.41192,-0.5627,0.71672,247.03,0.89918,-0.12358,0.41976,349.78,-0.14763,0.81737,0.55688,310.53>
> view matrix models
> #8,0.043275,-0.70295,0.70992,259.25,0.97747,0.17673,0.11541,348.75,-0.20659,0.68893,0.69476,310.36>
> view matrix models
> #8,-0.55786,-0.70229,0.44225,241.71,0.82871,-0.5003,0.25087,347.91,0.045081,0.50645,0.86109,318.64>
> view matrix models
> #8,-0.67786,-0.63134,0.37673,237.91,0.73318,-0.61845,0.2828,346.01,0.054444,0.4679,0.8821,319.15>
> ui mousemode right "translate selected models"> view matrix models
> #8,-0.67786,-0.63134,0.37673,251.48,0.73318,-0.61845,0.2828,366.41,0.054444,0.4679,0.8821,310.61>
> view matrix models
> #8,-0.67786,-0.63134,0.37673,254.38,0.73318,-0.61845,0.2828,374.81,0.054444,0.4679,0.8821,310.23>
> view matrix models
> #8,-0.67786,-0.63134,0.37673,264.5,0.73318,-0.61845,0.2828,373.94,0.054444,0.4679,0.8821,312.95>
> select #8:257-10002014 atoms, 2054 bonds, 255 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q5XJY5
> (#8) to map postprocess.mrc (#1) using 2014 atoms
average map value = 0.007698, steps = 100
shifted from previous position = 18.4
rotated from previous position = 35.6 degrees
atoms outside contour = 1372, contour level = 0.0098043
> view matrix models
> #8,-0.67786,-0.63134,0.37673,241.27,0.73318,-0.61845,0.2828,379.02,0.054444,0.4679,0.8821,275.08>
> view matrix models
> #8,-0.67786,-0.63134,0.37673,236.54,0.73318,-0.61845,0.2828,370.7,0.054444,0.4679,0.8821,277.28>
> view matrix models
> #8,-0.67786,-0.63134,0.37673,237.48,0.73318,-0.61845,0.2828,372,0.054444,0.4679,0.8821,282.61>
> view matrix models
> #8,-0.67786,-0.63134,0.37673,228.93,0.73318,-0.61845,0.2828,361.57,0.054444,0.4679,0.8821,272.74>
> view matrix models
> #8,-0.67786,-0.63134,0.37673,224.08,0.73318,-0.61845,0.2828,375.92,0.054444,0.4679,0.8821,277.88>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q5XJY5
> (#8) to map postprocess.mrc (#1) using 2014 atoms
average map value = 0.006786, steps = 148
shifted from previous position = 20.6
rotated from previous position = 27.6 degrees
atoms outside contour = 1529, contour level = 0.0098043
> view matrix models
> #8,-0.67786,-0.63134,0.37673,220.78,0.73318,-0.61845,0.2828,377.23,0.054444,0.4679,0.8821,296.19>
> fitmap sel inMap #1 moveWholeMolecules falseFit molecule AlphaFold Q5XJY5
> (#8) to map postprocess.mrc (#1) using 2014 atoms
average map value = 0.006638, steps = 104
shifted from previous position = 13.8
rotated from previous position = 12.7 degrees
atoms outside contour = 1535, contour level = 0.0098043
> view matrix models
> #8,-0.67786,-0.63134,0.37673,220.41,0.73318,-0.61845,0.2828,367.14,0.054444,0.4679,0.8821,309.5>
> ui mousemode right "rotate selected models"> view matrix models
> #8,-0.60234,-0.16822,0.78031,220.15,-0.17007,-0.92805,-0.33135,351.59,0.77991,-0.33229,0.5304,325.75>
> view matrix models
> #8,-0.56665,-0.21292,0.79597,220.93,-0.31574,-0.83618,-0.44845,348.69,0.76106,-0.50543,0.4066,326.01>
> view matrix models
> #8,-0.80177,-0.30588,0.51343,217.02,0.098336,-0.91491,-0.3915,356.65,0.58949,-0.26341,0.76362,321.78>
> open 5nzr5nzr title:
The structure of the COPI coat leaf [more info...]
| Chain information for 5nzr #12
---
Chain | Description | UniProt
A | Coatomer subunit alpha | COPA_MOUSE 1-1224
B | Coatomer subunit beta | COPB_MOUSE 16-968
C | Coatomer subunit beta' | COPB2_MOUSE 1-905
D | Coatomer subunit delta | COPD_MOUSE 1-511
F M R | ADP-ribosylation factor 1 | ARF1_YEAST 1-181
G K | Coatomer subunit gamma-1 | COPG1_MOUSE 1-874
L Z | Coatomer subunit zeta-1 | COPZ1_MOUSE 1-177
> hide #8 models
> select add #12
20984 atoms, 21006 bonds, 7 pseudobonds, 5001 residues, 3 models selected
> rainbow sel & #!12
> hide sel & #!12 atoms
> show sel & #!12 cartoons
> view matrix models
> #8,-0.64994,0.65231,0.38997,-81.046,-0.44881,-0.74353,0.49572,377.96,0.61331,0.14717,0.77601,199.42,#12,0.52179,-0.81339,-0.25717,178.56,0.84178,0.44205,0.30983,-62.075,-0.13833,-0.37814,0.91535,69.76
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.64994,0.65231,0.38997,141.42,-0.44881,-0.74353,0.49572,557.2,0.61331,0.14717,0.77601,304.75,#12,0.52179,-0.81339,-0.25717,401.02,0.84178,0.44205,0.30983,117.16,-0.13833,-0.37814,0.91535,175.1
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.38397,-0.58767,-0.71219,403.83,0.75014,0.2512,-0.61171,192.35,0.53839,-0.76911,0.34438,528.33,#12,0.12195,0.77873,-0.61539,297.65,-0.99234,0.083426,-0.091086,407.27,-0.019592,0.62179,0.78294,58.888
> view matrix models
> #8,0.44702,-0.57148,-0.68817,450.81,0.39074,0.81679,-0.42447,20.948,0.80467,-0.079146,0.58843,362.7,#12,-0.53693,0.83623,-0.11145,304.96,-0.78106,-0.54268,-0.30895,483.41,-0.31883,-0.078831,0.94453,156.08
> view matrix models
> #8,0.54098,-0.32184,-0.77702,369.6,0.15438,0.94619,-0.28442,-15.762,0.82675,0.033909,0.56155,326.3,#12,-0.73424,0.65186,-0.18968,357.49,-0.55923,-0.73914,-0.37542,490.02,-0.38492,-0.16957,0.90724,178.39
> view matrix models
> #8,0.4776,-0.51082,-0.71482,430.93,0.33258,0.85817,-0.39106,8.8775,0.8132,-0.050961,0.57975,353.57,#12,-0.59368,0.79417,-0.12976,318.28,-0.72993,-0.59934,-0.32862,486.79,-0.33875,-0.10038,0.93551,161.86
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.4776,-0.51082,-0.71482,482.75,0.33258,0.85817,-0.39106,39.498,0.8132,-0.050961,0.57975,377.3,#12,-0.59368,0.79417,-0.12976,370.1,-0.72993,-0.59934,-0.32862,517.41,-0.33875,-0.10038,0.93551,185.59
> view matrix models
> #8,0.4776,-0.51082,-0.71482,473.46,0.33258,0.85817,-0.39106,77.071,0.8132,-0.050961,0.57975,460.12,#12,-0.59368,0.79417,-0.12976,360.82,-0.72993,-0.59934,-0.32862,554.98,-0.33875,-0.10038,0.93551,268.42
> view matrix models
> #8,0.4776,-0.51082,-0.71482,415.29,0.33258,0.85817,-0.39106,47.406,0.8132,-0.050961,0.57975,495.54,#12,-0.59368,0.79417,-0.12976,302.64,-0.72993,-0.59934,-0.32862,525.32,-0.33875,-0.10038,0.93551,303.83
> view matrix models
> #8,0.4776,-0.51082,-0.71482,415.6,0.33258,0.85817,-0.39106,48.007,0.8132,-0.050961,0.57975,495.11,#12,-0.59368,0.79417,-0.12976,302.95,-0.72993,-0.59934,-0.32862,525.92,-0.33875,-0.10038,0.93551,303.41
> view matrix models
> #8,0.4776,-0.51082,-0.71482,419.97,0.33258,0.85817,-0.39106,44.047,0.8132,-0.050961,0.57975,508.07,#12,-0.59368,0.79417,-0.12976,307.33,-0.72993,-0.59934,-0.32862,521.96,-0.33875,-0.10038,0.93551,316.36
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.29304,-0.92622,-0.23718,592.8,0.49296,0.35892,-0.79257,157.89,0.81922,0.11534,0.56176,455.55,#12,-0.073413,0.96907,0.2356,187.3,-0.91195,0.030392,-0.40917,476.63,-0.40368,-0.24489,0.88152,346.85
> view matrix models
> #8,0.39675,-0.37422,-0.83818,358.81,0.45925,0.87155,-0.17173,73.623,0.79478,-0.3168,0.51765,580.67,#12,-0.63398,0.70954,-0.3076,342.32,-0.72297,-0.68499,-0.08998,503.78,-0.27455,0.16534,0.94725,276.48
> view matrix models
> #8,0.50375,-0.66794,-0.5478,489.38,0.5286,0.73991,-0.41608,88.71,0.68324,-0.079968,0.7258,526.68,#12,-0.48084,0.87511,0.054582,264.06,-0.86376,-0.46207,-0.20102,505.65,-0.15069,-0.1438,0.97807,295.95
> view matrix models
> #8,0.1025,-0.67908,-0.72687,447.72,0.73567,0.54358,-0.4041,162.25,0.66953,-0.49332,0.5553,631.62,#12,-0.24766,0.91595,-0.31575,276.4,-0.96359,-0.26678,-0.018091,472.34,-0.10081,0.29977,0.94867,241.32
> view matrix models
> #8,0.685,-0.70374,-0.18846,553.89,0.65744,0.70857,-0.25632,124.94,0.31392,0.051678,0.94804,491.25,#12,-0.43071,0.78501,0.44526,224.12,-0.87545,-0.48328,0.0051794,485.63,0.21925,-0.38757,0.89539,293.78
> view matrix models
> #8,0.75433,-0.6511,-0.083978,554.39,0.60264,0.73751,-0.30482,107.09,0.2604,0.17933,0.9487,449.23,#12,-0.44876,0.70275,0.55205,223.51,-0.86526,-0.49615,-0.071779,494.92,0.22346,-0.50988,0.83072,315.27
> fitmap sel inMap #1
Fit molecules AlphaFold Q5XJY5 (#8), 5nzr (#12) to map postprocess.mrc (#1)
using 20984 atoms
average map value = 0.00986, steps = 348
shifted from previous position = 33.8
rotated from previous position = 35.7 degrees
atoms outside contour = 11489, contour level = 0.0098043
Position of AlphaFold Q5XJY5 (#8) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.49299499 -0.60059429 -0.62947792 453.02472673
0.62412801 0.74820379 -0.22506737 108.04034281
0.60615194 -0.28191772 0.74370843 551.83093680
Axis -0.03265990 -0.70985575 0.70358947
Axis point -190.29422483 0.00000000 888.35117527
Rotation angle (degrees) 60.49802227
Shift along axis 296.77363624
Position of 5nzr (#12) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
-0.53474921 0.84440971 -0.03186735 278.17462040
-0.84482079 -0.53504839 -0.00102956 482.54311095
-0.01791995 0.02637164 0.99949158 224.70041209
Axis 0.01621843 -0.00825529 -0.99983439
Axis point 273.18809601 162.79475561 0.00000000
Rotation angle (degrees) 122.35428873
Shift along axis -224.13517875
> select clear
> show #8 models
> hide #8 models
> show #!9 models
> hide #!9 models
> show #10 models
> hide #10 models
> show #6 models
> hide #6 models
> show #5 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> select #5:257-1000
5433 atoms, 5510 bonds, 697 residues, 1 model selected
> select #5:50-100
415 atoms, 424 bonds, 51 residues, 1 model selected
> select #5:678-1000
2123 atoms, 2157 bonds, 276 residues, 1 model selected
> select #5:673-1000
2166 atoms, 2201 bonds, 281 residues, 1 model selected
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 2166 atoms
average map value = 0.006375, steps = 144
shifted from previous position = 6.2
rotated from previous position = 29 degrees
atoms outside contour = 1554, contour level = 0.0098043
> undo
> ui mousemode right "translate selected atoms"
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.007053, steps = 96
shifted from previous position = 18.7
rotated from previous position = 20.8 degrees
atoms outside contour = 1515, contour level = 0.0098043
> fitmap sel inMap #1 moveWholeMolecules false
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 2123 atoms
average map value = 0.008288, steps = 120
shifted from previous position = 5.52
rotated from previous position = 36.8 degrees
atoms outside contour = 1297, contour level = 0.0098043
> show #!12 models
> volume #1 level 0.007653
> hide #!12 models
> show #4 models
> show #3 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> select clear
[Repeated 2 time(s)]Drag select of 160 residues
> select add #8
4014 atoms, 4083 bonds, 511 residues, 1 model selected
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.52203,0.85231,0.032475,68.046,-0.46112,0.25,0.85139,238.43,0.71753,-0.45943,0.52352,599.04
> view matrix models
> #8,0.52016,0.85303,0.042083,68.629,-0.48056,0.25159,0.8401,234.03,0.70604,-0.45721,0.5408,598.69
> view matrix models
> #8,0.051357,0.99444,0.091954,-34.655,-0.5072,-0.053346,0.86018,329.69,0.8603,-0.090815,0.50164,498.72
> view matrix models
> #8,-0.30688,0.94053,0.14568,-60.294,-0.90559,-0.33565,0.25931,298.59,0.29279,-0.05235,0.95474,459.54
> view matrix models
> #8,-0.31349,0.94827,-0.050019,-85.39,-0.91245,-0.28622,0.29243,285.6,0.26299,0.13731,0.95498,395.14
> view matrix models
> #8,-0.39059,0.91742,-0.076076,-88.957,-0.91913,-0.39326,-0.023448,283.68,-0.051429,0.060765,0.99683,381.36
> view matrix models
> #8,-0.36375,0.9173,-0.16202,-94.81,-0.92881,-0.37037,-0.011636,276.39,-0.070681,0.14625,0.98672,350.41
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.36375,0.9173,-0.16202,-96.715,-0.92881,-0.37037,-0.011636,304.42,-0.070681,0.14625,0.98672,364.98
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.13102,0.98728,0.090013,-23.655,-0.95349,0.10063,0.28411,183.99,0.27144,-0.12305,0.95456,493.69
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.13102,0.98728,0.090013,-36.779,-0.95349,0.10063,0.28411,181.38,0.27144,-0.12305,0.95456,500.49
> select #8:673-1000
Nothing selected
> select #8:1-255
1991 atoms, 2019 bonds, 255 residues, 1 model selected
> ui tool show "Fit in Map"
> fitmap sel inMap #1
Fit molecule AlphaFold Q5XJY5 (#8) to map postprocess.mrc (#1) using 1991
atoms
average map value = 0.006643, steps = 256
shifted from previous position = 15.1
rotated from previous position = 47 degrees
atoms outside contour = 1304, contour level = 0.0076533
Position of AlphaFold Q5XJY5 (#8) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.62548770 0.77964233 0.03038068 -69.32003114
-0.77483337 -0.62526057 0.09317979 432.54139912
0.09164275 0.03474284 0.99518569 432.15915881
Axis -0.03753707 -0.03935179 -0.99852011
Axis point 56.58688874 228.36184294 0.00000000
Rotation angle (degrees) 128.88661905
Shift along axis -445.93881773
> view matrix models
> #8,-0.62549,0.77964,0.030381,-56.649,-0.77483,-0.62526,0.09318,422.08,0.091643,0.034743,0.99519,440.99
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.22073,0.97526,0.012319,-5.7316,-0.85987,0.18862,0.47439,193.79,0.46033,-0.1153,0.88023,526.17
> view matrix models
> #8,0.15542,0.98522,-0.072084,-27.163,-0.86472,0.17096,0.47226,198.51,0.4776,-0.011065,0.87851,495.15
> view matrix models
> #8,0.26671,0.96245,0.050607,8.856,-0.87241,0.21877,0.43708,178.34,0.4096,-0.16072,0.898,535.69
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.26671,0.96245,0.050607,7.313,-0.87241,0.21877,0.43708,169.87,0.4096,-0.16072,0.898,525
> view matrix models
> #8,0.26671,0.96245,0.050607,-10.046,-0.87241,0.21877,0.43708,167.9,0.4096,-0.16072,0.898,531.38
> view matrix models
> #8,0.26671,0.96245,0.050607,-11.003,-0.87241,0.21877,0.43708,173.12,0.4096,-0.16072,0.898,531.71
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> view matrix models
> #8,-0.10602,0.99339,-0.044085,-82.1,-0.98768,-0.10007,0.12027,223.73,0.11506,0.056293,0.99176,432.96
> view matrix models
> #8,0.052591,0.99338,-0.10211,-66.953,-0.99323,0.062639,0.097836,168.7,0.10358,0.096275,0.98995,418.47
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.052591,0.99338,-0.10211,-66.631,-0.99323,0.062639,0.097836,178.27,0.10358,0.096275,0.98995,414.29
> view matrix models
> #8,0.052591,0.99338,-0.10211,-68.517,-0.99323,0.062639,0.097836,176.92,0.10358,0.096275,0.98995,415.64
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.030369,0.96092,-0.27516,-88.694,-0.97222,0.03552,0.23135,203.23,0.23208,0.27454,0.93315,370.08
> view matrix models
> #8,0.030946,0.98758,-0.15403,-75.383,-0.98929,0.052261,0.13632,185.03,0.14268,0.14817,0.97862,403.19
> view matrix models
> #8,0.040371,0.9904,-0.13218,-72.571,-0.99117,0.056413,0.11997,181.64,0.12627,0.12617,0.98394,408.55
> view matrix models
> #8,0.30426,0.95155,0.044526,-4.6598,-0.92561,0.28428,0.24988,132.46,0.22511,-0.11724,0.96725,497.63
> fitmap sel inMap #1
Fit molecule AlphaFold Q5XJY5 (#8) to map postprocess.mrc (#1) using 1991
atoms
average map value = 0.006936, steps = 372
shifted from previous position = 4.52
rotated from previous position = 23.4 degrees
atoms outside contour = 1277, contour level = 0.0076533
Position of AlphaFold Q5XJY5 (#8) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04305036 0.99254206 0.11404797 -52.98885446
-0.90935144 -0.08620824 0.40699890 271.42760552
0.41379540 -0.08618823 0.90628084 502.96547353
Axis -0.24814055 -0.15081394 -0.95691244
Axis point -0.77179557 179.84860224 0.00000000
Rotation angle (degrees) 96.40115017
Shift along axis -509.08030191
> select #8:255-1000
2027 atoms, 2067 bonds, 257 residues, 1 model selected
> delete sel
> select #8:180-1000
525 atoms, 533 bonds, 75 residues, 1 model selected
> select up
556 atoms, 564 bonds, 79 residues, 1 model selected
> select down
525 atoms, 533 bonds, 75 residues, 1 model selected
> delete sel
> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/alphafold_copi_gt2.cxs
> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/alphafold_copi_gt2.cxs includeMaps true
> select add #3
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> color #3 blue
> select subtract #3
Nothing selected
> select add #4
7214 atoms, 7373 bonds, 905 residues, 1 model selected
> color #4 cyan
> select clear
> select add #5
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> color #5 #005500ff
> select subtract #5
Nothing selected
> select add #6
1457 atoms, 1483 bonds, 181 residues, 1 model selected
> color #6 #ff557fff
> select add #7
2914 atoms, 2966 bonds, 362 residues, 2 models selected
> select subtract #6
1457 atoms, 1483 bonds, 181 residues, 1 model selected
> color #7 #ffaaffff
> select clear
> color #7 #ff557fff
> select add #8
1462 atoms, 1481 bonds, 179 residues, 1 model selected
> color #8 #aa5500ff
> select subtract #8
Nothing selected
> select add #9
6673 atoms, 6786 bonds, 1 pseudobond, 853 residues, 2 models selected
> select add #8
8135 atoms, 8267 bonds, 1 pseudobond, 1032 residues, 3 models selected
> select subtract #9
1462 atoms, 1481 bonds, 179 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #9
6673 atoms, 6786 bonds, 1 pseudobond, 853 residues, 2 models selected
> select add #8
8135 atoms, 8267 bonds, 1 pseudobond, 1032 residues, 3 models selected
> select subtract #8
6673 atoms, 6786 bonds, 1 pseudobond, 853 residues, 2 models selected
> color #9 #55ff00ff
> select subtract #9
Nothing selected
> select add #10
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> color #10 yellow
> color #10 #ffff7fff
> color #10 yellow
> color #9 lime
> select subtract #10
Nothing selected
> select add #11
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> color #11 #aa00ffff
> show #!2 models
> hide #!2 models
> select clear
> close #12
> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/alphafold_copi_gt3.cxs includeMaps true
> ui tool show AlphaFold
> alphafold match P84078
1 AlphaFold model found using UniProt identifier: P84078 (UniProt P84078)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
P84078 | P84078 | 100.0 | 100.0
Opened 1 AlphaFold model
> select add #121457 atoms, 1483 bonds, 181 residues, 1 model selected
> view matrix models
> #12,0.99732,0.03037,-0.066609,0.14664,-0.041627,0.98373,-0.17474,1.1913,0.060218,0.17704,0.98236,-1.382>
> ui mousemode right "translate selected models"> view matrix models
> #12,0.99732,0.03037,-0.066609,192.14,-0.041627,0.98373,-0.17474,369.59,0.060218,0.17704,0.98236,287.78>
> view matrix models
> #12,0.99732,0.03037,-0.066609,244.52,-0.041627,0.98373,-0.17474,330.85,0.060218,0.17704,0.98236,312>
> view matrix models
> #12,0.99732,0.03037,-0.066609,244.99,-0.041627,0.98373,-0.17474,337.04,0.060218,0.17704,0.98236,281.29>
> color #12 #ff5500ff> color #12 #ff557fff> ui mousemode right "rotate
> selected models"> view matrix models
> #12,0.96921,-0.057544,-0.23943,246.84,-0.16396,0.57464,-0.80181,344.51,0.18372,0.81638,0.54751,278.51>
> view matrix models
> #12,-0.66037,0.0084873,-0.7509,246.84,0.10956,0.99033,-0.085153,336.65,0.74291,-0.1385,-0.65491,295.68>
> view matrix models
> #12,-0.81274,0.36614,-0.45321,241.48,0.50848,0.8255,-0.24496,339.8,0.28444,-0.42953,-0.85709,298.83>
> view matrix models
> #12,-0.711,0.49496,-0.49949,240.78,0.70072,0.55818,-0.44432,343.79,0.058885,-0.66592,-0.7437,299.87>
> view matrix models
> #12,-0.69871,0.42186,-0.57778,241.96,0.65547,0.70109,-0.28076,341.39,0.28664,-0.57489,-0.76638,299.57>
> ui mousemode right "translate selected models"> view matrix models
> #12,-0.69871,0.42186,-0.57778,246.79,0.65547,0.70109,-0.28076,352.02,0.28664,-0.57489,-0.76638,288.94>
> ui mousemode right "rotate selected models"> view matrix models
> #12,-0.59293,0.10513,-0.79836,251.22,0.64323,0.6583,-0.39103,353.09,0.48445,-0.74538,-0.45795,288.83>
> view matrix models
> #12,-0.68781,0.25488,-0.67967,248.96,0.69867,-0.021515,-0.71512,361.36,-0.19689,-0.96673,-0.16328,287.83>
> view matrix models
> #12,-0.70244,0.38024,-0.60167,247.31,0.48017,-0.37083,-0.79494,364.65,-0.52538,-0.84729,0.077904,284.68>
> view matrix models
> #12,-0.76601,0.36378,-0.53,246.9,0.54444,-0.071237,-0.83577,362.32,-0.34179,-0.92876,-0.14349,287.13>
> ui mousemode right "rotate selected models"> view matrix models
> #12,-0.84687,0.36676,-0.38509,245.82,0.45782,0.13437,-0.87883,360.6,-0.27058,-0.92056,-0.28171,288.05>
> view matrix models
> #12,-0.76349,0.20858,-0.6112,248.81,0.6457,0.26411,-0.71646,358.71,0.011989,-0.94167,-0.33633,289.05>
> ui mousemode right "translate selected models"> fitmap sel inMap #1Fit
> molecule AlphaFold P84078 (#12) to map postprocess.mrc (#1) using 1457 atoms
average map value = 0.006393, steps = 76
shifted from previous position = 8.87
rotated from previous position = 15.9 degrees
atoms outside contour = 1045, contour level = 0.0076533
Position of AlphaFold P84078 (#12) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.74110472 0.25780732 -0.61991868 250.25747317
0.64078173 -0.00400708 -0.76771265 351.24260378
-0.20040600 -0.96618804 -0.16222856 290.85088224
Axis -0.32985322 -0.69720285 0.63647862
Axis point -0.08358810 0.00000000 328.20413989
Rotation angle (degrees) 162.49109040
Shift along axis -142.31520995
> ui mousemode right "rotate selected models"> view matrix models
> #12,-0.86938,0.31454,-0.3811,248.02,0.49119,0.46609,-0.73586,346.57,-0.053833,-0.82694,-0.55971,292.37>
> view matrix models
> #12,-0.79921,0.37642,-0.46858,248.13,0.59483,0.38348,-0.70648,347.29,-0.086243,-0.84336,-0.53039,292.28>
> ui mousemode right "translate selected models"> view matrix models
> #12,-0.79921,0.37642,-0.46858,247.25,0.59483,0.38348,-0.70648,350.41,-0.086243,-0.84336,-0.53039,291.7>
> view matrix models
> #12,-0.79921,0.37642,-0.46858,244.11,0.59483,0.38348,-0.70648,350.21,-0.086243,-0.84336,-0.53039,292.13>
> ui mousemode right "rotate selected models"> view matrix models
> #12,-0.95386,0.24463,-0.17409,243.16,0.25188,0.33633,-0.90743,351.35,-0.16343,-0.90941,-0.38243,291.66>
> view matrix models
> #12,-0.79001,-0.13282,-0.59854,249.53,0.55952,0.24291,-0.79242,351.96,0.25064,-0.96091,-0.11759,291.11>
> view matrix models
> #12,-0.67783,0.13357,-0.72298,248.11,0.73388,0.06354,-0.67631,353.12,-0.044396,-0.989,-0.14109,291.03>
> select clear> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/alphafold_copi_gt4.cxs> save
> /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/alphafold_copi_gt4.cxs includeMaps true> ui
> tool show "Color Zone"> select add #39810 atoms, 10032 bonds, 1233 residues,
> 1 model selected
> select add #417024 atoms, 17405 bonds, 2138 residues, 2 models selected
> select add #524525 atoms, 25024 bonds, 3091 residues, 3 models selected
> select add #625982 atoms, 26507 bonds, 3272 residues, 4 models selected
> select add #727439 atoms, 27990 bonds, 3453 residues, 5 models selected
> select add #934112 atoms, 34776 bonds, 1 pseudobond, 4306 residues, 7 models
> selected
> select add #1136479 atoms, 37174 bonds, 1 pseudobond, 4604 residues, 8
> models selected
> select add #1237936 atoms, 38657 bonds, 1 pseudobond, 4785 residues, 9
> models selected
> select add #839398 atoms, 40138 bonds, 1 pseudobond, 4964 residues, 10
> models selected
> select add #1040818 atoms, 41579 bonds, 1 pseudobond, 5141 residues, 11
> models selected
> color zone #1 near sel distance 5> hide #3 models> hide #4 models> hide #5
> models> hide #6 models> hide #7 models> hide #8 models> hide #!9 models>
> hide #10 models> hide #11 models> hide #12 models> color zone #1 near sel
> distance 300[Repeated 1 time(s)]> color zone #1 near sel distance 160.89>
> color zone #1 near sel distance 162.01> color zone #1 near sel distance
> 23.73> view matrix models
> #3,0.9148,0.37497,0.15015,272.72,-0.20072,0.74462,-0.6366,357.54,-0.35051,0.55222,0.75644,352.79,#4,-0.17501,-0.17837,-0.96827,300.32,-0.011019,-0.98304,0.18308,289.64,-0.98451,0.04271,0.17007,350.81,#5,0.046501,-0.73948,0.67157,285.03,-0.16587,0.65725,0.73519,314.42,-0.98505,-0.14558,-0.092095,347.46,#6,0.13817,0.035476,0.98977,236.96,-0.7229,-0.6795,0.12527,313.55,0.67699,-0.73282,-0.068242,291.07,#7,-0.82079,-0.53173,0.20873,354.89,-0.51806,0.53897,-0.66417,308.12,0.24066,-0.65328,-0.71785,333.36,#8,-0.04305,0.99254,0.11405,-52.989,-0.90935,-0.086208,0.407,271.43,0.4138,-0.086188,0.90628,502.97,#10,0.17048,-0.93854,-0.30012,342.77,-0.36432,0.22296,-0.90419,353.65,0.91554,0.26349,-0.30392,330.16,#9,0.48168,-0.52169,-0.70415,336.01,0.54192,-0.45414,0.70716,394.9,-0.6887,-0.72222,0.063968,371.16,#11,0.64865,-0.27426,0.70995,310.02,-0.71703,-0.53297,0.44923,345.46,0.25518,-0.80045,-0.54236,303.68,#12,-0.67783,0.13357,-0.72298,248.11,0.73388,0.06354,-0.67631,353.12,-0.044396,-0.989,-0.14109,291.03[Repeated
> 3 time(s)]> color single #1> color zone #1 near sel distance 4.8> color zone
> #1 near sel distance 4> color zone #1 near sel distance 3.17> ui tool show
> "Volume Viewer"> volume #1 level 0.009138> color zone #1 near sel distance
> 3.17> color zone #1 near sel distance 3.1> color zone #1 near sel distance
> 3> color zone #1 near sel distance 3.5> color zone #1 near sel distance 3>
> color zone #1 near sel distance 5> color zone #1 near sel distance
> 4[Repeated 1 time(s)]> color zone #1 near sel distance 3> color zone #1 near
> sel distance 3.5[Repeated 1 time(s)]> save
> /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/alphafold_copi_gt_colored.cxs includeMaps
> true——— End of log from Sun Nov 5 21:56:53 2023 ———opened ChimeraX session
> hide #!1 models> show #!1 models> show #3 models> hide #3 models> select add
> #240818 atoms, 41579 bonds, 1 pseudobond, 5141 residues, 13 models selected
> select subtract #240818 atoms, 41579 bonds, 1 pseudobond, 5141 residues, 11
> models selected
> select add #140818 atoms, 41579 bonds, 1 pseudobond, 5141 residues, 13
> models selected
> select subtract #140818 atoms, 41579 bonds, 1 pseudobond, 5141 residues, 11
> models selected
> select add #240818 atoms, 41579 bonds, 1 pseudobond, 5141 residues, 13
> models selected
> select subtract #240818 atoms, 41579 bonds, 1 pseudobond, 5141 residues, 11
> models selected
> select add #240818 atoms, 41579 bonds, 1 pseudobond, 5141 residues, 13
> models selected
> show #!2 models> hide #!2 models> select subtract #240818 atoms, 41579
> bonds, 1 pseudobond, 5141 residues, 11 models selected
> show #6 models> hide #6 models> show #6 models> hide #6 models> show #5 models> hide #5 models> show #6 models> hide #6 models> show #7 models> hide #7 models> show #7 models> show #6 models> hide #6 models> hide #7 models> show #8 models> hide #8 models> show #10 models> hide #10 models> show #10 models> hide #10 models> hide #!1 models> show #4 models> show #3 models> hide #3 models> show #3 models> hide #3 models> hide #4 models> show #4 models> show #7 models> hide #7 models> show #8 models> hide #8 models> show #!9 models> hide #!9 models> show #!9 models> hide #!9 models> show #10 models> hide #10 models> show #11 models> hide #11 models> show #12 models> hide #12 models> hide #4 models> show #3 models> show #4 models> show #5 models> show #!1 models> hide #4 models> hide #5 models> hide #!1 models> show #!1 models> hide #3 models> show #4 models> hide #4 models> show #4 models> hide #4 models> show #4 models> hide #4 models> show #5 models> hide #5 models> show #6 models> hide #6 models> show #7 models> hide #7 models> show #8 models> log metadata #6The model has no metadata> log chains #6 | Chain information for AlphaFold P84078 #6
---
Chain | Description | UniProt
A | ADP-ribosylation factor 1 | ARF1_MOUSE
> log metadata #6
The model has no metadata
> log chains #6
Chain information for AlphaFold P84078 #6
---
Chain | Description | UniProt
A | ADP-ribosylation factor 1 | ARF1_MOUSE
> show #11 models
> hide #8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #3 models
> select subtract #3
31008 atoms, 31547 bonds, 1 pseudobond, 3908 residues, 10 models selected
> select subtract #4
23794 atoms, 24174 bonds, 1 pseudobond, 3003 residues, 9 models selected
> select subtract #5
16293 atoms, 16555 bonds, 1 pseudobond, 2050 residues, 8 models selected
> select subtract #6
14836 atoms, 15072 bonds, 1 pseudobond, 1869 residues, 7 models selected
> select subtract #7
13379 atoms, 13589 bonds, 1 pseudobond, 1688 residues, 6 models selected
> select subtract #8
11917 atoms, 12108 bonds, 1 pseudobond, 1509 residues, 5 models selected
> select subtract #9
5244 atoms, 5322 bonds, 656 residues, 3 models selected
> select subtract #10
3824 atoms, 3881 bonds, 479 residues, 2 models selected
> select subtract #11
1457 atoms, 1483 bonds, 181 residues, 1 model selected
> select subtract #12
Nothing selected
> show #4 models
> hide #4 models
> show #4 models
> show #!1 models
> hide #!1 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #12 models
> hide #12 models
> show #10 models
> hide #10 models
> show #8 models
> hide #8 models
> show #10 models
> hide #4 models
> show #5 models
> hide #5 models
> show #5 models
> show #3,5,10-11 atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #3 models
> show #3 models
> hide #5 models
> hide #3 models
> hide #10 models
> show #3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #3 models
> show #8 models
> hide #8 models
> show #4 models
> show #4,11 atoms
> show #!1 models
> show #3 models
> show #10 models
> hide #!1 models
> hide #3-4,10-11 atoms
> select add #11
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> color sel byhetero
> show sel atoms
> select subtract #11
Nothing selected
> show #5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> select add #10
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> select add #3
11230 atoms, 11473 bonds, 1410 residues, 2 models selected
> select add #4
18444 atoms, 18846 bonds, 2315 residues, 3 models selected
> show sel atoms
> color sel byhetero
> select subtract #3
8634 atoms, 8814 bonds, 1082 residues, 2 models selected
> select subtract #4
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> select subtract #10
Nothing selected
> hide #!1 models
> hide #!9 models
> show #!9 models
> show #!1 models
> volume #1 style mesh
> volume #1 style surface
> volume #1 color #b1b1b17f
> volume #1 color #afafaf7f
> volume #1 level 0.0118
> volume #1 level 0.008577
> volume #1 level 0.0104
> volume #2 level 0.1605
> volume #1 level 0.008436
> volume #1 level 0.01026
> volume #1 level 0.007033
> volume #1 level 0.007875
> volume #1 level 0.01068
> volume #1 level 0.008857
> volume #1 level 0.007174
> volume #1 level 0.009839
> ui tool show "Side View"
> volume #1 level 0.009278
> hide #11 models
> hide #!9 models
> hide #10 models
> hide #5 models
> hide #4 models
Drag select of 1422 atoms, 289 residues, 1232 bonds
> ui tool show "Fit in Map"
> show #!1 models
> fitmap sel inMap #1
Fit molecule acop F8WHL2 (#3) to map postprocess.mrc (#1) using 2365 atoms
average map value = 0.008396, steps = 64
shifted from previous position = 0.487
rotated from previous position = 1.71 degrees
atoms outside contour = 1428, contour level = 0.0092781
Position of acop F8WHL2 (#3) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.91219836 0.37649899 0.16168688 273.02716587
-0.20531480 0.76147730 -0.61481553 358.66813907
-0.35459832 0.52763701 0.77191917 352.72945796
Axis 0.82659436 0.37354588 -0.42095753
Axis point 0.00000000 -548.32199304 667.79519136
Rotation angle (degrees) 43.71407343
Shift along axis 211.17759714
> fitmap sel inMap #1
Fit molecule acop F8WHL2 (#3) to map postprocess.mrc (#1) using 2365 atoms
average map value = 0.008396, steps = 44
shifted from previous position = 0.0602
rotated from previous position = 0.122 degrees
atoms outside contour = 1426, contour level = 0.0092781
Position of acop F8WHL2 (#3) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.91165951 0.37825395 0.16062650 273.02136836
-0.20726890 0.76074469 -0.61506675 358.63406864
-0.35484718 0.52743858 0.77194041 352.76062362
Axis 0.82585192 0.37260651 -0.42324106
Axis point 0.00000000 -547.86166392 669.09704534
Rotation angle (degrees) 43.76587675
Shift along axis 209.80183211
> fitmap sel inMap #1
Fit molecule acop F8WHL2 (#3) to map postprocess.mrc (#1) using 2365 atoms
average map value = 0.008396, steps = 48
shifted from previous position = 0.008
rotated from previous position = 0.0126 degrees
atoms outside contour = 1425, contour level = 0.0092781
Position of acop F8WHL2 (#3) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.91157168 0.37844088 0.16068466 273.02809909
-0.20736646 0.76067368 -0.61512169 358.62890418
-0.35501579 0.52740690 0.77188453 352.75435033
Axis 0.82573495 0.37271004 -0.42337811
Axis point 0.00000000 -547.84692199 669.07342633
Rotation angle (degrees) 43.77476898
Shift along axis 209.76496906
> fitmap sel inMap #1
Fit molecule acop F8WHL2 (#3) to map postprocess.mrc (#1) using 2365 atoms
average map value = 0.008396, steps = 40
shifted from previous position = 0.0437
rotated from previous position = 0.0783 degrees
atoms outside contour = 1426, contour level = 0.0092781
Position of acop F8WHL2 (#3) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.91189991 0.37734607 0.16139540 273.02985270
-0.20623049 0.76130412 -0.61472353 358.67292985
-0.35483449 0.52728168 0.77205343 352.73949104
Axis 0.82605985 0.37341055 -0.42212519
Axis point 0.00000000 -548.53424760 668.55477028
Rotation angle (degrees) 43.72805759
Shift along axis 210.57103104
> fitmap sel inMap #1
Fit molecule acop F8WHL2 (#3) to map postprocess.mrc (#1) using 2365 atoms
average map value = 0.008396, steps = 44
shifted from previous position = 0.0362
rotated from previous position = 0.059 degrees
atoms outside contour = 1428, contour level = 0.0092781
Position of acop F8WHL2 (#3) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.91166197 0.37815506 0.16084521 273.02714315
-0.20706981 0.76081322 -0.61504904 358.63509873
-0.35495707 0.52741064 0.77190898 352.75166197
Axis 0.82584358 0.37285518 -0.42303830
Axis point 0.00000000 -547.96751807 668.91182334
Rotation angle (degrees) 43.76423830
Shift along axis 209.96920099
> select clear
> show #11 models
> volume #1 level 0.006975
> volume #1 level 0.006399
> show #!9 models
> show #10 models
> show #4 models
> show #5 models
> volume #1 level 0.009134
> volume #1 level 0.01172
> show #8 models
> volume #1 level 0.008702
> volume #1 level 0.006543
> volume #1 style image region 0,0,121,243,243,121 step 1 showOutlineBox true
> volume #1 region 0,0,0,243,243,243 step 1
> volume #1 style surface region 0,0,0,243,243,243 step 1
> volume #1 style image colorMode opaque8 orthoplanes xyz positionPlanes
> 121,121,121 imageMode orthoplanes
> select clear
[Repeated 2 time(s)]Drag select of 1 atoms
> volume #1 region 0,0,121,243,243,121 step 1 colorMode auto8 imageMode "full
> region"
> volume #1 level -0.001441,0 level 0.008572,0.8 level 0.03099,1
> volume #1 level -0.002945,0 level 0.008572,0.8 level 0.03099,1
> view orient
> volume #2 level 0.07496
> volume #2 level 0.06071
> volume #2 level 0.07496
> volume #1 region 0,0,0,243,243,243 step 1
> volume #1 style surface region 0,0,0,243,243,243 step 1
> volume #1 level 0.005561
> volume #1 level 0.006964
> volume #1 level 0.00963
> ui tool show "Side View"
> volume #1 level 0.007183
> volume #1 level 0.006895
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> hide #3 models
> volume #1 level 0.005456
> volume #2 level 0.1391
> volume #2 level 0.1017
> volume #2 level 0.107
> volume #1 level 0.004161
> volume #2 level 0.08921
> volume #1 level 0.007039
> volume #2 level 0.07139
> show #3 models
> show #6 models
> select add #4
7215 atoms, 7373 bonds, 906 residues, 2 models selected
> select subtract #4
1 atom, 1 residue, 1 model selected
> show #7 models
> volume #2 level 0.1088
> volume #1 level 0.008479
> volume #1 level 0.007615
> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/alphafold_copi_colored_RT.cxs
——— End of log from Mon Nov 6 14:26:30 2023 ———
opened ChimeraX session
> view matrix models
> #5,0.046501,-0.73948,0.67157,279.15,-0.16587,0.65725,0.73519,333.32,-0.98505,-0.14558,-0.092095,332.17
> undo
> select add #5
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select subtract #5
Nothing selected
> view orient
> ui tool show "Side View"
[Repeated 1 time(s)]
> open "/fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/Golph3_ Q9CRA5.pdb"
Golph3_ Q9CRA5.pdb title:
Alphafold monomer V2.0 prediction for golgi phosphoprotein 3 (Q9CRA5) [more
info...]
Chain information for Golph3_ Q9CRA5.pdb #13
---
Chain | Description | UniProt
A | golgi phosphoprotein 3 | GOLP3_MOUSE
> color #13 #aa00ffff
> select add #13
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> view matrix models #13,1,0,0,276.76,0,1,0,332.9,0,0,1,0
> view orient
> view matrix models #13,1,0,0,355.84,0,1,0,382.85,0,0,1,275.03
> view orient
> hide #!1 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #!9 models
> hide #10 models
> view matrix models #13,1,0,0,268.7,0,1,0,322.92,0,0,1,275.03
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.97373,0.15944,-0.16259,268.4,0.044839,0.56579,0.82333,324.28,0.22326,-0.80899,0.54377,274.73
> view matrix models
> #13,0.32122,0.91528,-0.24308,262.8,0.6686,-0.037407,0.74268,329.55,0.67067,-0.40108,-0.62397,277.87
> select subtract #13
Nothing selected
> select add #11
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> hide sel atoms
> select add #13
4734 atoms, 4796 bonds, 596 residues, 2 models selected
> select subtract #11
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> view matrix models
> #13,0.16284,0.95393,-0.25201,261.15,-0.28856,0.2903,0.91239,320.3,0.94351,-0.075856,0.32253,283.56
> view matrix models
> #13,-0.78377,0.61861,-0.055017,250.68,-0.31405,-0.31835,0.89444,318.7,0.5358,0.71831,0.44379,281.11
> view matrix models
> #13,-0.5019,0.83478,-0.22636,253.8,-0.70387,-0.24212,0.66779,314.17,0.50265,0.49449,0.7091,280.86
> view matrix models
> #13,0.065166,-0.9415,0.33066,257.36,-0.3304,0.29232,0.89743,319.82,-0.94159,-0.16773,-0.29202,261.72
> view matrix models
> #13,0.012373,0.97222,-0.23374,259.61,-0.60886,0.19276,0.76951,316.33,0.79318,0.1328,0.59433,282.97
> view matrix models
> #13,-0.59761,-0.48095,-0.64152,249.08,-0.74685,0.042854,0.66361,314.3,-0.29167,0.8757,-0.38481,270.73
> view matrix models
> #13,-0.15915,-0.98598,0.050164,254.24,-0.69624,0.14812,0.70236,315.15,-0.69994,0.076857,-0.71005,263.93
> view matrix models
> #13,-0.66249,-0.74742,-0.049687,249.11,-0.69396,0.58743,0.41634,315.48,-0.282,0.31031,-0.90785,268.5
> view matrix models
> #13,-0.55091,-0.8161,0.17456,250.65,-0.5615,0.5172,0.64592,317.26,-0.61742,0.25783,-0.74318,265.13
> view matrix models
> #13,-0.93688,0.069665,-0.34263,247.24,-0.088586,0.90068,0.42535,322.68,0.33824,0.42886,-0.83766,275.58
> view matrix models
> #13,-0.43282,-0.17251,-0.88482,250.98,-0.83401,0.44921,0.32038,313.47,0.3422,0.87661,-0.3383,277.66
> view matrix models
> #13,-0.057092,0.66385,-0.74569,257.1,-0.6289,0.55617,0.54328,316.39,0.77539,0.49998,0.38574,283.11
> view matrix models
> #13,0.61602,-0.32904,0.71571,265.43,-0.73709,0.079722,0.67107,314.5,-0.27787,-0.94095,-0.19342,267.45
> view matrix models
> #13,0.69392,0.13166,0.70791,267.23,-0.72004,0.12232,0.68306,314.8,0.0033426,-0.98372,0.17968,271.2
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.69392,0.13166,0.70791,301.65,-0.72004,0.12232,0.68306,347.24,0.0033426,-0.98372,0.17968,308.86
> view matrix models
> #13,0.69392,0.13166,0.70791,309.76,-0.72004,0.12232,0.68306,353.07,0.0033426,-0.98372,0.17968,297.95
> view matrix models
> #13,0.69392,0.13166,0.70791,305.93,-0.72004,0.12232,0.68306,351.19,0.0033426,-0.98372,0.17968,303.08
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.11747,-0.64077,0.75869,298.2,-0.61649,0.55189,0.56157,352.95,-0.77855,-0.53369,-0.3302,294.5
> view matrix models
> #13,0.1885,-0.97807,0.088577,296.79,-0.84088,-0.11415,0.52904,349.05,-0.50733,-0.17421,-0.84396,297.06
> view matrix models
> #13,0.59014,-0.11275,0.79939,304.49,-0.72863,-0.50075,0.46728,349.31,0.34761,-0.85822,-0.37766,305.84
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.59014,-0.11275,0.79939,308.27,-0.72863,-0.50075,0.46728,345.91,0.34761,-0.85822,-0.37766,300.91
> ui tool show "Fit in Map"
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 76
shifted from previous position = 3.41
rotated from previous position = 10.8 degrees
atoms outside contour = 1145, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64614882 -0.25313043 0.72001159 309.96620079
-0.70221101 -0.56674711 0.43092622 345.46001007
0.29898395 -0.78404254 -0.54395395 303.52015626
Axis -0.89203727 0.30912099 -0.32971763
Axis point 0.00000000 273.71750205 -0.02590981
Rotation angle (degrees) 137.07755023
Shift along axis -269.78841019
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.008089, steps = 44
shifted from previous position = 0.0456
rotated from previous position = 0.0682 degrees
atoms outside contour = 1141, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64651584 -0.25217749 0.72001651 309.93070193
-0.70151346 -0.56742773 0.43116659 345.48458153
0.29982682 -0.78385731 -0.54375692 303.52703002
Axis -0.89215987 0.30853416 -0.32993550
Axis point 0.00000000 273.57083787 -0.00990298
Rotation angle (degrees) 137.08245403
Shift along axis -270.05828434
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.008089, steps = 44
shifted from previous position = 0.0194
rotated from previous position = 0.0463 degrees
atoms outside contour = 1142, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64604103 -0.25275846 0.72023895 309.94363828
-0.70206406 -0.56707846 0.43072970 345.49036416
0.29956141 -0.78392294 -0.54380858 303.51714131
Axis -0.89201211 0.30893561 -0.32995938
Axis point 0.00000000 273.66219930 -0.04201137
Rotation angle (degrees) 137.08990962
Shift along axis -269.88752898
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 44
shifted from previous position = 0.0418
rotated from previous position = 0.0504 degrees
atoms outside contour = 1143, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64636118 -0.25319855 0.71979699 309.93048754
-0.70211612 -0.56670327 0.43113844 345.45300114
0.29874768 -0.78405222 -0.54406978 303.52367429
Axis -0.89210135 0.30910265 -0.32956142
Axis point 0.00000000 273.71820034 0.01220992
Rotation angle (degrees) 137.07164569
Shift along axis -269.73866191
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 44
shifted from previous position = 0.0257
rotated from previous position = 0.0502 degrees
atoms outside contour = 1141, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64652691 -0.25247006 0.71990403 309.92686216
-0.70167034 -0.56717519 0.43124359 345.47615271
0.29943561 -0.78394590 -0.54384478 303.51593635
Axis -0.89215765 0.30869599 -0.32979010
Axis point 0.00000000 273.61712486 -0.00837966
Rotation angle (degrees) 137.07506047
Shift along axis -269.95306990
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.008089, steps = 60
shifted from previous position = 0.0226
rotated from previous position = 0.0373 degrees
atoms outside contour = 1142, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64611264 -0.25289852 0.72012554 309.94576635
-0.70211941 -0.56690516 0.43086759 345.48140307
0.29927711 -0.78400311 -0.54384955 303.52003959
Axis -0.89202854 0.30901133 -0.32984403
Axis point 0.00000000 273.69093966 -0.03799504
Rotation angle (degrees) 137.08132893
Shift along axis -269.83707582
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 44
shifted from previous position = 0.0335
rotated from previous position = 0.0327 degrees
atoms outside contour = 1142, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64640789 -0.25311440 0.71978464 309.92928487
-0.70205233 -0.56674684 0.43118505 345.45377982
0.29879653 -0.78404790 -0.54404919 303.52341629
Axis -0.89211568 0.30905194 -0.32957020
Axis point 0.00000000 273.70689544 0.01206002
Rotation angle (degrees) 137.07064729
Shift along axis -269.76188543
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 44
shifted from previous position = 0.00803
rotated from previous position = 0.0272 degrees
atoms outside contour = 1144, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64651368 -0.25270084 0.71983495 309.92467471
-0.70180692 -0.56697645 0.43128268 345.45873947
0.29914397 -0.78401530 -0.54390523 303.52203189
Axis -0.89214924 0.30882890 -0.32968840
Axis point 0.00000000 273.65121371 -0.00046679
Rotation angle (degrees) 137.06980045
Shift along axis -269.87911520
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 36
shifted from previous position = 0.0382
rotated from previous position = 0.0185 degrees
atoms outside contour = 1143, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64630410 -0.25291434 0.71994815 309.96058094
-0.70202489 -0.56686202 0.43107830 345.44892887
0.29908538 -0.78402920 -0.54391741 303.51941258
Axis -0.89208498 0.30898119 -0.32971961
Axis point 0.00000000 273.68044455 -0.01876412
Rotation angle (degrees) 137.07431483
Shift along axis -269.85025963
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 40
shifted from previous position = 0.011
rotated from previous position = 0.0289 degrees
atoms outside contour = 1144, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64629761 -0.25253292 0.72008785 309.96423516
-0.70183762 -0.56713436 0.43102502 345.45952995
0.29953856 -0.78395519 -0.54377469 303.52011382
Axis -0.89208737 0.30878422 -0.32989760
Axis point 0.00000000 273.62558016 -0.03473124
Rotation angle (degrees) 137.08004063
Shift along axis -269.97328544
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 40
shifted from previous position = 0.0105
rotated from previous position = 0.0439 degrees
atoms outside contour = 1145, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64606725 -0.25321007 0.72005678 309.97169872
-0.70226344 -0.56678527 0.43079057 345.46213640
0.29903707 -0.78398923 -0.54400158 303.51790237
Axis -0.89201641 0.30915603 -0.32974122
Axis point 0.00000000 273.71811066 -0.02066242
Rotation angle (degrees) 137.08459098
Shift along axis -269.78050527
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.60865,-0.30325,0.7332,309.49,-0.75282,-0.51259,0.41293,344.99,0.25061,-0.8033,-0.54029,302.96
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess.mrc (#1) using 2367
atoms
average map value = 0.00809, steps = 52
shifted from previous position = 0.584
rotated from previous position = 4.55 degrees
atoms outside contour = 1145, contour level = 0.007615
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.64612560 -0.25328407 0.71997839 309.97378268
-0.70229521 -0.56665464 0.43091061 345.45261473
0.29883630 -0.78405975 -0.54401026 303.51809865
Axis -0.89202933 0.30920186 -0.32966328
Axis point 0.00000000 273.73630342 -0.02211936
Rotation angle (degrees) 137.07700574
Shift along axis -269.74988755
> close #11
> select subtract #13
Nothing selected
> show #13 atoms
> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/CopZ1_P61924.pdb
CopZ1_P61924.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit ζ-1 (P61924) [more
info...]
Chain information for CopZ1_P61924.pdb #11
---
Chain | Description | UniProt
A | coatomer subunit ζ-1 | COPZ1_MOUSE
> select add #11
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> hide #13 models
> show #10 models
> color #11 yellow
> view orient
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,412.97,0,1,0,362.45,0,0,1,0
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.28196,-0.95943,0,404.1,0.95943,0.28196,0,362.86,0,0,1,0
> select subtract #11
Nothing selected
> select add #10
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> hide sel atoms
> select subtract #10
Nothing selected
> select add #11
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> view matrix models
> #11,0.033721,-0.99943,0,402.7,0.99943,0.033721,0,361.63,0,0,1,0
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.033721,-0.99943,0,342.47,0.99943,0.033721,0,336.17,0,0,1,0
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.033721,-0.99943,0,192.3,0.99943,0.033721,0,291.19,0,0,1,246.14
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.51418,0.84644,0.13844,201.18,0.23149,-0.018464,0.97266,293.63,0.82585,0.53217,-0.18645,245.33
> view matrix models
> #11,-0.81006,-0.32615,-0.48726,188.99,-0.42602,0.89837,0.10693,290.12,0.40287,0.2942,-0.86669,237.53
> view matrix models
> #11,0.33494,-0.93767,-0.092694,193.46,-0.049436,0.080753,-0.99551,280.02,0.94094,0.33801,-0.019308,245.85
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.33494,-0.93767,-0.092694,180.24,-0.049436,0.080753,-0.99551,304.01,0.94094,0.33801,-0.019308,252.33
> view matrix models
> #11,0.33494,-0.93767,-0.092694,182.45,-0.049436,0.080753,-0.99551,302.85,0.94094,0.33801,-0.019308,249.69
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.58303,-0.77258,-0.25137,183.53,-0.12599,0.21968,-0.9674,303.46,0.80262,0.5957,0.030739,250.84
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.58303,-0.77258,-0.25137,394.78,-0.12599,0.21968,-0.9674,292.48,0.80262,0.5957,0.030739,322.66
> view matrix models
> #11,0.58303,-0.77258,-0.25137,342.1,-0.12599,0.21968,-0.9674,297.41,0.80262,0.5957,0.030739,334.03
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.09807,-0.60668,0.78887,347.56,0.87809,-0.32029,-0.35548,303.05,0.46833,0.72757,0.50131,336.29
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.09807,-0.60668,0.78887,290.43,0.87809,-0.32029,-0.35548,305.55,0.46833,0.72757,0.50131,310.6
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.51411,-0.43145,-0.74131,278.55,-0.57073,0.81725,-0.079829,307.03,0.64028,0.38205,-0.6664,301.81
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.51411,-0.43145,-0.74131,336.74,-0.57073,0.81725,-0.079829,305.08,0.64028,0.38205,-0.6664,335.87
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.5611,-0.75996,-0.32808,337.34,-0.52848,0.63395,-0.56463,301.06,0.63709,-0.14343,-0.75733,332.26
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.5611,-0.75996,-0.32808,344.5,-0.52848,0.63395,-0.56463,300.61,0.63709,-0.14343,-0.75733,333.65
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009085, steps = 96
shifted from previous position = 14.2
rotated from previous position = 39.8 degrees
atoms outside contour = 596, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.65612108 -0.66306754 -0.36034228 358.45599666
0.03304888 0.45178776 -0.89151310 302.54901226
0.75393163 -0.59684945 -0.27451383 333.03309009
Axis 0.21883981 -0.82754522 0.51698941
Axis point 141.38063663 0.00000000 344.83519421
Rotation angle (degrees) 137.68233649
Shift along axis 0.24603705
> view matrix models
> #11,-0.65612,-0.66307,-0.36034,337.95,0.033049,0.45179,-0.89151,304.28,0.75393,-0.59685,-0.27451,334.97
> view matrix models
> #11,-0.65612,-0.66307,-0.36034,344.16,0.033049,0.45179,-0.89151,302.51,0.75393,-0.59685,-0.27451,317.7
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.48065,-0.76499,0.42867,349.56,0.22057,0.36766,0.90343,314.63,-0.84872,0.52879,-0.0079814,318.33
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.48065,-0.76499,0.42867,359.28,0.22057,0.36766,0.90343,330.7,-0.84872,0.52879,-0.0079814,345.5
> view matrix models
> #11,-0.48065,-0.76499,0.42867,339.68,0.22057,0.36766,0.90343,398.75,-0.84872,0.52879,-0.0079814,358.46
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.78957,0.55823,-0.25489,341.34,-0.49154,-0.82396,-0.28192,380.83,-0.36739,-0.097305,0.92496,363.23
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.78957,0.55823,-0.25489,332.99,-0.49154,-0.82396,-0.28192,351.76,-0.36739,-0.097305,0.92496,331.06
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.027563,-0.78417,0.61993,334.61,0.56547,-0.52364,-0.63722,356.14,0.82431,0.33299,0.45786,336.08
> view matrix models
> #11,-0.088637,-0.99326,-0.074688,328.59,-0.18898,0.090391,-0.97781,353.87,0.97797,-0.072556,-0.19571,330.21
> view matrix models
> #11,-0.048357,-0.63332,-0.77238,326.28,-0.98685,0.14969,-0.060953,356.44,0.15422,0.75928,-0.63223,328.24
> view matrix models
> #11,0.18852,-0.98175,0.024952,330.61,-0.9579,-0.18943,-0.21575,353.63,0.21654,0.016772,-0.97613,322.04
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.18852,-0.98175,0.024952,349.2,-0.9579,-0.18943,-0.21575,381.13,0.21654,0.016772,-0.97613,329.2
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.30887,-0.57468,0.75786,353.97,0.69524,-0.68017,-0.23242,386,0.64903,0.4551,0.60962,344.1
> view matrix models
> #11,-0.33862,-0.4259,0.83902,355.22,0.68583,-0.7222,-0.089802,386.65,0.64418,0.54502,0.53665,344.12
> view matrix models
> #11,-0.051493,-0.83384,0.54961,352.34,0.13696,-0.55103,-0.82317,380.25,0.98924,0.032886,0.14258,340.24
> view matrix models
> #11,-0.35337,-0.87827,-0.32215,344.97,-0.57225,0.47536,-0.66825,383.8,0.74004,-0.051788,-0.67057,333.27
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.35337,-0.87827,-0.32215,338.22,-0.57225,0.47536,-0.66825,359.87,0.74004,-0.051788,-0.67057,318.59
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.45947,-0.83498,-0.30283,338.09,-0.55681,0.53641,-0.63422,360.51,0.69199,-0.12278,-0.71138,317.69
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.008332, steps = 264
shifted from previous position = 16.8
rotated from previous position = 45.1 degrees
atoms outside contour = 725, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.14490497 -0.94257009 -0.30093885 343.98346956
0.02593039 0.30042689 -0.95345231 351.04735013
0.98910574 -0.14596344 -0.01909214 332.12049846
Axis 0.44762189 -0.71512095 0.53687677
Axis point 154.78387367 0.00000000 433.32854122
Rotation angle (degrees) 115.58090126
Shift along axis 81.24099907
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.00833, steps = 48
shifted from previous position = 0.0196
rotated from previous position = 0.0437 degrees
atoms outside contour = 726, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.14442177 -0.94279172 -0.30047651 343.99752907
0.02557187 0.30000257 -0.95359559 351.05991620
0.98918575 -0.14540371 -0.01921796 332.11826612
Axis 0.44801956 -0.71492170 0.53681042
Axis point 154.93427764 0.00000000 433.34103574
Rotation angle (degrees) 115.58302704
Shift along axis 81.42181454
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.008331, steps = 44
shifted from previous position = 0.012
rotated from previous position = 0.0327 degrees
atoms outside contour = 725, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.14462707 -0.94264711 -0.30083126 343.98854183
0.02599114 0.30030370 -0.95348946 351.05362745
0.98914482 -0.14571934 -0.01893157 332.12042077
Axis 0.44774036 -0.71502316 0.53690824
Axis point 154.81133413 0.00000000 433.38296097
Rotation angle (degrees) 115.57088802
Shift along axis 81.32426712
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.008335, steps = 44
shifted from previous position = 0.0501
rotated from previous position = 0.0741 degrees
atoms outside contour = 723, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.14450379 -0.94228707 -0.30201614 343.95309313
0.02651760 0.30142228 -0.95312194 351.02230471
0.98914887 -0.14573847 -0.01856947 332.12020104
Axis 0.44733595 -0.71537819 0.53677239
Axis point 154.49156924 0.00000000 433.39712225
Rotation angle (degrees) 115.51995899
Shift along axis 81.02183476
> view matrix models
> #11,0.29089,-0.90988,-0.29582,346.23,-0.40311,0.16385,-0.90036,348.56,0.86769,0.38115,-0.31912,332.6
> view matrix models
> #11,0.273,-0.90949,-0.31353,346.03,-0.42413,0.17875,-0.88779,348.62,0.86348,0.37534,-0.33694,332.43
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.273,-0.90949,-0.31353,347.03,-0.42413,0.17875,-0.88779,350.28,0.86348,0.37534,-0.33694,332.97
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009324, steps = 76
shifted from previous position = 5.69
rotated from previous position = 7.45 degrees
atoms outside contour = 645, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.17020150 -0.93893062 -0.29906646 342.80776470
-0.36434641 0.22202517 -0.90440949 353.66700232
0.91557804 0.26289564 -0.30430698 330.14035254
Axis 0.65581946 -0.68241583 0.32281492
Axis point 206.51500646 0.00000000 375.79548709
Rotation angle (degrees) 117.13187954
Shift along axis 90.04627202
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009324, steps = 36
shifted from previous position = 0.0443
rotated from previous position = 0.0688 degrees
atoms outside contour = 650, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.17048591 -0.93853525 -0.30014354 342.77320402
-0.36432041 0.22297922 -0.90418522 353.65274953
0.91553547 0.26349926 -0.30391273 330.16427787
Axis 0.65572471 -0.68267652 0.32245600
Axis point 206.25290908 0.00000000 375.82290352
Rotation angle (degrees) 117.07933445
Shift along axis 89.79788555
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009324, steps = 44
shifted from previous position = 0.0458
rotated from previous position = 0.0533 degrees
atoms outside contour = 645, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.17019889 -0.93884863 -0.29932524 342.80974553
-0.36430887 0.22228606 -0.90436053 353.66515969
0.91559346 0.26296800 -0.30419804 330.13951983
Axis 0.65576329 -0.68249775 0.32275583
Axis point 206.45362062 0.00000000 375.80586237
Rotation angle (degrees) 117.12005919
Shift along axis 89.98082632
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009324, steps = 44
shifted from previous position = 0.0414
rotated from previous position = 0.0377 degrees
atoms outside contour = 648, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.17027087 -0.93865053 -0.29990503 342.77744890
-0.36418996 0.22285573 -0.90426822 353.65417232
0.91562739 0.26319294 -0.30390126 330.16355955
Axis 0.65566088 -0.68265831 0.32262429
Axis point 206.28107658 0.00000000 375.83806717
Rotation angle (degrees) 117.08985859
Shift along axis 89.83958784
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009323, steps = 48
shifted from previous position = 0.0164
rotated from previous position = 0.0444 degrees
atoms outside contour = 647, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.17044548 -0.93839188 -0.30061441 342.76603098
-0.36428585 0.22345574 -0.90408150 353.64712017
0.91555675 0.26360618 -0.30375586 330.17288534
Axis 0.65561495 -0.68283669 0.32234004
Axis point 206.13215060 0.00000000 375.83357392
Rotation angle (degrees) 117.06025783
Shift along axis 89.66724627
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009324, steps = 44
shifted from previous position = 0.0659
rotated from previous position = 0.116 degrees
atoms outside contour = 647, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.16986193 -0.93907605 -0.29880280 342.81616751
-0.36417863 0.22192805 -0.90450090 353.67028609
0.91570785 0.26245786 -0.30429430 330.13715823
Axis 0.65570493 -0.68242396 0.32303033
Axis point 206.54140774 -0.00000000 375.81317869
Rotation angle (degrees) 117.14552928
Shift along axis 90.07748914
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009324, steps = 48
shifted from previous position = 0.0575
rotated from previous position = 0.0788 degrees
atoms outside contour = 648, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.17029394 -0.93861252 -0.30001088 342.77150957
-0.36419912 0.22294769 -0.90424186 353.65200714
0.91561945 0.26325060 -0.30387521 330.16831641
Axis 0.65565190 -0.68268564 0.32258472
Axis point 206.25375182 0.00000000 375.83811054
Rotation angle (degrees) 117.08531880
Shift along axis 89.81289917
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess.mrc (#1) using 1420
atoms
average map value = 0.009324, steps = 60
shifted from previous position = 0.0508
rotated from previous position = 0.056 degrees
atoms outside contour = 645, contour level = 0.007615
Position of CopZ1_P61924.pdb (#11) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.17018568 -0.93891614 -0.29912093 342.80979355
-0.36427807 0.22210233 -0.90441807 353.66731607
0.91560817 0.26288220 -0.30422792 330.13797895
Axis 0.65579022 -0.68243579 0.32283212
Axis point 206.49577920 0.00000000 375.80926708
Rotation angle (degrees) 117.12736020
Shift along axis 90.03522412
> close #10
> show sel atoms
> select subtract #11
Nothing selected
> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/CopZ2_Q9CTG7.pdb
CopZ2_Q9CTG7.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit ζ (Q9CTG7) [more
info...]
Chain information for CopZ2_Q9CTG7.pdb #10
---
Chain | Description | UniProt
A | coatomer subunit ζ | Q9CTG7_MOUSE
> color #10 yellow
> color #10 #ffe415ff
> select add #10
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> select add #11
2883 atoms, 2927 bonds, 362 residues, 2 models selected
> view orient
> select subtract #11
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> view matrix models #10,1,0,0,381.07,0,1,0,383.04,0,0,1,0
> view orient
> view matrix models #10,1,0,0,374.85,0,1,0,378.42,0,0,1,0
> select subtract #10
Nothing selected
> select add #11
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> hide sel atoms
> select add #10
2883 atoms, 2927 bonds, 362 residues, 2 models selected
> select subtract #11
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> view matrix models #10,1,0,0,287.93,0,1,0,328.63,0,0,1,0
> view matrix models #10,1,0,0,343.95,0,1,0,332.78,0,0,1,0
> view matrix models #10,1,0,0,442.15,0,1,0,335.46,0,0,1,301.19
> view matrix models #10,1,0,0,352.81,0,1,0,346.86,0,0,1,274.44
> view matrix models #10,1,0,0,352.92,0,1,0,347.76,0,0,1,274.36
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.049529,-0.98686,-0.15383,367.71,0.92397,-0.013207,0.38223,361.26,-0.37924,-0.16106,0.91117,276.98
> view matrix models
> #10,0.24183,0.79508,0.5562,349,0.27062,0.49521,-0.82555,347.26,-0.93182,0.35016,-0.09541,264.17
> view matrix models
> #10,-0.88773,0.42149,0.18513,354.56,-0.46024,-0.8036,-0.37738,370.13,-0.01029,-0.42022,0.90737,279.24
> view matrix models
> #10,0.5523,0.81779,0.16183,344.72,-0.71469,0.36455,0.59692,362.94,0.42916,-0.44534,0.78581,277.29
> view matrix models
> #10,0.82717,-0.023948,-0.56144,349.45,0.41989,0.69033,0.58918,355.09,0.37347,-0.7231,0.58108,279.56
> fitmap #10 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#10) to map postprocess.mrc (#1) using 1463
atoms
average map value = 0.006114, steps = 140
shifted from previous position = 23.5
rotated from previous position = 38.2 degrees
atoms outside contour = 1092, contour level = 0.007615
Position of CopZ2_Q9CTG7.pdb (#10) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.88402019 -0.44961589 -0.12788222 332.64950901
0.37717743 0.52448779 0.76331498 348.95649289
-0.27612588 -0.72302014 0.63324276 291.78912770
Axis -0.87059401 0.08683105 0.48427929
Axis point 0.00000000 548.10741163 -129.13457334
Rotation angle (degrees) 58.60901243
Shift along axis -117.99497945
> view matrix models
> #10,-0.26989,-0.4414,-0.85576,330.49,0.71571,-0.6865,0.12838,359.06,-0.64414,-0.57783,0.50119,289.98
> view matrix models
> #10,-0.51279,0.85245,-0.10185,319.91,-0.65826,-0.46656,-0.59078,354.84,-0.55112,-0.2359,0.80038,287.47
> view matrix models
> #10,0.54499,0.69903,0.46297,323.03,-0.80542,0.58993,0.057372,346.3,-0.23302,-0.40415,0.88451,289.37
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.54499,0.69903,0.46297,343.94,-0.80542,0.58993,0.057372,355.86,-0.23302,-0.40415,0.88451,294.19
> view matrix models
> #10,0.54499,0.69903,0.46297,341.13,-0.80542,0.58993,0.057372,354.09,-0.23302,-0.40415,0.88451,293.59
> fitmap #10 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#10) to map postprocess.mrc (#1) using 1463
atoms
average map value = 0.006546, steps = 212
shifted from previous position = 30.4
rotated from previous position = 20.4 degrees
atoms outside contour = 1021, contour level = 0.007615
Position of CopZ2_Q9CTG7.pdb (#10) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.73669002 0.63643510 0.22855680 312.27083288
-0.67533922 0.67507429 0.29697081 348.51516327
0.03470983 -0.37312879 0.92713006 296.97660948
Axis -0.45102704 0.13047348 -0.88292201
Axis point 583.20033603 4.03637851 0.00000000
Rotation angle (degrees) 47.97558826
Shift along axis -357.57779045
> view matrix models
> #10,0.73669,0.63644,0.22856,383.16,-0.67534,0.67507,0.29697,346.7,0.03471,-0.37313,0.92713,317.35
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.8917,-0.024931,-0.45195,391.69,-0.25601,0.85121,0.45815,344.32,0.37328,0.52423,-0.76541,291.43
> view matrix models
> #10,-0.97734,-0.20479,-0.053647,397.39,-0.20905,0.89367,0.39706,343.14,-0.033368,0.39927,-0.91623,293.17
> view matrix models
> #10,-0.97068,-0.24034,0.0048746,398.29,-0.20106,0.82284,0.53151,345.09,-0.13175,0.51494,-0.84704,292.48
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.97068,-0.24034,0.0048746,348.48,-0.20106,0.82284,0.53151,350.59,-0.13175,0.51494,-0.84704,277.67
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.97068,-0.24034,0.0048746,337.99,-0.20106,0.82284,0.53151,341.33,-0.13175,0.51494,-0.84704,377.83
> view matrix models
> #10,-0.97068,-0.24034,0.0048746,336.87,-0.20106,0.82284,0.53151,331.98,-0.13175,0.51494,-0.84704,365.23
> view matrix models
> #10,-0.97068,-0.24034,0.0048746,341.4,-0.20106,0.82284,0.53151,354.03,-0.13175,0.51494,-0.84704,372.18
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.73008,-0.61764,-0.29242,343.37,-0.66372,0.53902,0.5186,359.11,-0.16269,0.5727,-0.80346,371.84
> view matrix models
> #10,-0.71629,-0.64127,-0.27513,343.78,-0.64312,0.45368,0.6169,360.93,-0.27078,0.61882,-0.73739,372.07
> view matrix models
> #10,-0.69961,-0.66511,-0.2611,344.15,-0.60849,0.36304,0.70565,362.7,-0.37454,0.65256,-0.6587,372.55
> view matrix models
> #10,-0.74234,-0.5056,-0.43965,340.8,-0.49638,0.85574,-0.14598,349.3,0.45004,0.10987,-0.88623,375.45
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.74234,-0.5056,-0.43965,345.65,-0.49638,0.85574,-0.14598,353.04,0.45004,0.10987,-0.88623,327.68
> fitmap #10 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#10) to map postprocess.mrc (#1) using 1463
atoms
average map value = 0.007804, steps = 112
shifted from previous position = 6.03
rotated from previous position = 23.2 degrees
atoms outside contour = 796, contour level = 0.007615
Position of CopZ2_Q9CTG7.pdb (#10) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.85055957 -0.31374086 -0.42203688 342.67631914
-0.44282855 0.86016552 0.25301816 354.86177316
0.28363943 0.40209699 -0.87055541 331.35797852
Axis 0.20346164 -0.96310161 -0.17617790
Axis point 181.91062897 0.00000000 173.60700899
Rotation angle (degrees) 158.50893683
Shift along axis -330.42441065
> show #!1 models
> hide #!1 models
> select subtract #10
Nothing selected
> select add #10
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> view matrix models
> #10,-0.85056,-0.31374,-0.42204,333.72,-0.44283,0.86017,0.25302,310.44,0.28364,0.4021,-0.87056,315.16
> view matrix models
> #10,-0.85056,-0.31374,-0.42204,336.02,-0.44283,0.86017,0.25302,319.56,0.28364,0.4021,-0.87056,312.93
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.67283,-0.69984,-0.23984,341.99,-0.66918,0.71396,-0.20605,318.66,0.31544,0.021855,-0.94869,317.26
> view matrix models
> #10,-0.73416,0.48102,0.4792,332.08,0.52731,0.84854,-0.043894,314.45,-0.42773,0.22046,-0.87661,317.47
> view matrix models
> #10,-0.76341,0.50277,-0.4055,325.08,0.44947,0.86436,0.22552,316.55,0.46388,-0.010097,-0.88584,317.71
> view matrix models
> #10,-0.87394,0.32299,-0.36318,328.12,0.39525,0.90716,-0.14434,313.31,0.28284,-0.26969,-0.92047,321.43
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.87394,0.32299,-0.36318,341.44,0.39525,0.90716,-0.14434,354.81,0.28284,-0.26969,-0.92047,330.58
> fitmap #10 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#10) to map postprocess.mrc (#1) using 1463
atoms
average map value = 0.009525, steps = 80
shifted from previous position = 1.71
rotated from previous position = 9.08 degrees
atoms outside contour = 688, contour level = 0.007615
Position of CopZ2_Q9CTG7.pdb (#10) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.82108011 0.27510216 -0.50014626 341.74342227
0.40712094 0.89639270 -0.17530741 354.41739312
0.40010001 -0.34756144 -0.84801006 329.40214578
Axis -0.18601212 -0.97214979 0.14256325
Axis point 88.87915642 0.00000000 225.35054236
Rotation angle (degrees) 152.41795576
Shift along axis -361.15457305
> fitmap #10 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#10) to map postprocess.mrc (#1) using 1463
atoms
average map value = 0.009525, steps = 40
shifted from previous position = 0.041
rotated from previous position = 0.0584 degrees
atoms outside contour = 688, contour level = 0.007615
Position of CopZ2_Q9CTG7.pdb (#10) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.82147696 0.27547367 -0.49928938 341.77800489
0.40709792 0.89642205 -0.17521079 354.42904198
0.39930805 -0.34719129 -0.84853481 329.39090309
Axis -0.18606033 -0.97216447 0.14240015
Axis point 88.99506313 0.00000000 225.24288376
Rotation angle (degrees) 152.47321208
Shift along axis -361.24933356
> fitmap #10 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#10) to map postprocess.mrc (#1) using 1463
atoms
average map value = 0.009525, steps = 28
shifted from previous position = 0.0496
rotated from previous position = 0.0357 degrees
atoms outside contour = 687, contour level = 0.007615
Position of CopZ2_Q9CTG7.pdb (#10) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.82127964 0.27516259 -0.49978528 341.73563276
0.40703624 0.89642670 -0.17533027 354.41459269
0.39977654 -0.34742590 -0.84821813 329.40793045
Axis -0.18598478 -0.97216185 0.14251664
Axis point 88.92474209 0.00000000 225.31390781
Rotation angle (degrees) 152.44108053
Shift along axis -361.15986104
> select subtract #10
Nothing selected
> select add #10
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> select add #11
2883 atoms, 2927 bonds, 362 residues, 2 models selected
> select subtract #11
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> select subtract #10
Nothing selected
> show #!1 models
> hide #10 models
> hide #11 models
> show #11 models
> show #10 models
> select add #10
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> select add #11
2883 atoms, 2927 bonds, 362 residues, 2 models selected
> show sel atoms
> select subtract #10
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> select subtract #11
Nothing selected
> hide #10 models
> hide #11 models
> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/CopBprime_O55029.pdb
CopBprime_O55029.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit β' (O55029) [more
info...]
Chain information for CopBprime_O55029.pdb #14
---
Chain | Description | UniProt
A | coatomer subunit β' | COPB2_MOUSE
> color #14 cyan
> view orient
> show #4 models
> select add #14
7214 atoms, 7373 bonds, 905 residues, 1 model selected
> view matrix models #14,1,0,0,228.73,0,1,0,248.76,0,0,1,0
> view matrix models #14,1,0,0,235.96,0,1,0,297.18,0,0,1,356.32
> hide #!1 models
> view matrix models #14,1,0,0,301.49,0,1,0,292.72,0,0,1,337.83
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.21105,0.30599,-0.92835,315.42,-0.013511,-0.94873,-0.31578,302.41,-0.97738,0.079188,-0.19609,356.54
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.21105,0.30599,-0.92835,308.04,-0.013511,-0.94873,-0.31578,302.09,-0.97738,0.079188,-0.19609,359.62
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.074611,0.028571,-0.9968,308.5,-0.41122,-0.90976,-0.056856,291.17,-0.90848,0.41415,-0.056129,356.57
> view matrix models
> #14,0.18837,-0.019388,-0.98191,309.45,-0.35781,-0.93244,-0.050231,291.62,-0.9146,0.3608,-0.18258,359.7
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.18837,-0.019388,-0.98191,300.67,-0.35781,-0.93244,-0.050231,285.78,-0.9146,0.3608,-0.18258,358.06
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.13765,0.068029,-0.98814,300.17,-0.0062466,-0.99756,-0.069548,290.26,-0.99046,0.015746,-0.13689,356.43
> view matrix models
> #14,0.086001,-0.061835,-0.99437,299.88,0.12356,-0.9897,0.072231,288.18,-0.9886,-0.12908,-0.077476,355.12
> fitmap #14 inMap #1
Fit molecule CopBprime_O55029.pdb (#14) to map postprocess.mrc (#1) using 7214
atoms
average map value = 0.008523, steps = 108
shifted from previous position = 4.16
rotated from previous position = 18.4 degrees
atoms outside contour = 3124, contour level = 0.007615
Position of CopBprime_O55029.pdb (#14) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.17477003 -0.17847582 -0.96829841 300.34041736
-0.01134919 -0.98300368 0.18323471 289.60827762
-0.98454387 0.04301334 0.16977402 350.79324012
Axis -0.64097385 0.07426053 0.76396197
Axis point 287.19131626 140.76950562 0.00000000
Rotation angle (degrees) 173.72033654
Shift along axis 96.98880360
> fitmap #14 inMap #1
Fit molecule CopBprime_O55029.pdb (#14) to map postprocess.mrc (#1) using 7214
atoms
average map value = 0.008523, steps = 48
shifted from previous position = 0.0108
rotated from previous position = 0.0055 degrees
atoms outside contour = 3124, contour level = 0.007615
Position of CopBprime_O55029.pdb (#14) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.17471715 -0.17850967 -0.96830171 300.34609995
-0.01127211 -0.98300107 0.18325345 289.59931761
-0.98455414 0.04293233 0.16973497 350.79135670
Axis -0.64099264 0.07424175 0.76394803
Axis point 287.19342385 140.77805503 0.00000000
Rotation angle (degrees) 173.71603635
Shift along axis 96.96708375
> fitmap #14 inMap #1
Fit molecule CopBprime_O55029.pdb (#14) to map postprocess.mrc (#1) using 7214
atoms
average map value = 0.008522, steps = 44
shifted from previous position = 0.0494
rotated from previous position = 0.0198 degrees
atoms outside contour = 3123, contour level = 0.007615
Position of CopBprime_O55029.pdb (#14) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.17494710 -0.17852356 -0.96825763 300.31865683
-0.01101722 -0.98300764 0.18323372 289.63800088
-0.98451619 0.04272372 0.17000751 350.80696897
Axis -0.64089853 0.07415902 0.76403502
Axis point 287.13230492 140.83588199 0.00000000
Rotation angle (degrees) 173.70661595
Shift along axis 97.03429488
> show sel atoms
> close #4
> select subtract #14
Nothing selected
> hide #14 models
> show #3 models
> hide #3 atoms
> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/CopA-F8WHL2.pdb
QXcbConnection: XCB error: 3 (BadWindow), sequence: 30554, resource id:
16942318, major code: 40 (TranslateCoords), minor code: 0
> view orient
> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/CopA-F8WHL2.pdb
QXcbConnection: XCB error: 3 (BadWindow), sequence: 32143, resource id:
16942568, major code: 40 (TranslateCoords), minor code: 0
> hide #3 models
> open "/fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/CopB_ Q9JIF7.pdb"
CopB_ Q9JIF7.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit β (Q9JIF7) [more
info...]
Chain information for CopB_ Q9JIF7.pdb #4
---
Chain | Description | UniProt
A | coatomer subunit β | COPB_MOUSE
> color #4 #005500ff
> view orient
> show #5 models
> select add #5
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select add #4
15002 atoms, 15238 bonds, 1906 residues, 2 models selected
> view orient
> select subtract #5
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> show #!1 models
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,283.85,0,1,0,328.89,0,0,1,0
> view matrix models #4,1,0,0,347.13,0,1,0,311.6,0,0,1,341.24
> view orient
> hide #!1 models
> view orient
> view matrix models #4,1,0,0,289.86,0,1,0,314.18,0,0,1,310.57
> select subtract #4
Nothing selected
> select add #5
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> hide sel atoms
> select add #4
15002 atoms, 15238 bonds, 1906 residues, 2 models selected
> select subtract #5
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.28068,-0.70115,0.65544,293.98,-0.1319,0.70459,0.69724,311.51,-0.9507,0.10925,-0.29025,322.36
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.28068,-0.70115,0.65544,299.54,-0.1319,0.70459,0.69724,319.17,-0.9507,0.10925,-0.29025,324.3
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.65201,-0.54033,0.53191,295.35,-0.25785,0.5017,0.82572,319.53,-0.71301,-0.67553,0.18779,322.32
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.65201,-0.54033,0.53191,291.14,-0.25785,0.5017,0.82572,325.2,-0.71301,-0.67553,0.18779,351.76
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.4548,-0.87158,0.18304,294.92,-0.12085,0.14322,0.98228,324.51,-0.88236,-0.46886,-0.040194,353.38
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.4548,-0.87158,0.18304,276.95,-0.12085,0.14322,0.98228,324.55,-0.88236,-0.46886,-0.040194,336.28
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.069656,-0.65121,0.7557,275.62,-0.1579,0.75518,0.63621,325.22,-0.98499,-0.075011,-0.15543,336.47
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.006862, steps = 92
shifted from previous position = 13.5
rotated from previous position = 14.7 degrees
atoms outside contour = 4266, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.02361329 -0.71170813 0.70207831 283.50221234
0.07555118 0.69899545 0.71112403 323.06318360
-0.99686229 0.06983482 0.03726481 346.61824676
Axis -0.32400626 0.85837621 0.39775650
Axis point 312.61014964 -0.00000000 -97.23838407
Rotation angle (degrees) 98.26064659
Shift along axis 323.32291623
> view matrix models
> #4,-0.039282,-0.61847,0.78483,282.87,-0.17399,0.77767,0.60412,324.69,-0.98396,-0.11282,-0.13815,348.02
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.039282,-0.61847,0.78483,282.43,-0.17399,0.77767,0.60412,325.87,-0.98396,-0.11282,-0.13815,349.87
> view matrix models
> #4,-0.039282,-0.61847,0.78483,283.43,-0.17399,0.77767,0.60412,316.45,-0.98396,-0.11282,-0.13815,352.4
> view matrix models
> #4,-0.039282,-0.61847,0.78483,280.48,-0.17399,0.77767,0.60412,321.91,-0.98396,-0.11282,-0.13815,349.33
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.007081, steps = 76
shifted from previous position = 5.23
rotated from previous position = 9.83 degrees
atoms outside contour = 4196, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.01660204 -0.71696194 0.69691459 284.11343250
-0.07144030 0.69607980 0.71440128 317.58202257
-0.99730670 -0.03792727 -0.06277633 348.65007309
Axis -0.38326875 0.86310970 0.32885668
Axis point 335.00417014 0.00000000 -72.91250391
Rotation angle (degrees) 101.04905018
Shift along axis 279.87223028
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.007082, steps = 48
shifted from previous position = 0.0612
rotated from previous position = 0.0384 degrees
atoms outside contour = 4200, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.01692030 -0.71693318 0.69693652 284.05349358
-0.07202636 0.69609938 0.71432336 317.59170809
-0.99725920 -0.03811123 -0.06341630 348.64710676
Axis -0.38335861 0.86317737 0.32857419
Axis point 334.96570898 0.00000000 -72.72373614
Rotation angle (degrees) 101.07644974
Shift along axis 279.80006421
> view matrix models
> #4,-0.01692,-0.71693,0.69694,284.45,-0.072026,0.6961,0.71432,329.79,-0.99726,-0.038111,-0.063416,351.11
> view matrix models
> #4,-0.01692,-0.71693,0.69694,284.34,-0.072026,0.6961,0.71432,325.54,-0.99726,-0.038111,-0.063416,349.71
> view matrix models
> #4,-0.01692,-0.71693,0.69694,284.37,-0.072026,0.6961,0.71432,329.68,-0.99726,-0.038111,-0.063416,352.5
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.007082, steps = 100
shifted from previous position = 12.7
rotated from previous position = 0.0636 degrees
atoms outside contour = 4200, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.01691113 -0.71768668 0.69616079 284.06387498
-0.07179888 0.69533455 0.71509075 317.57056123
-0.99727576 -0.03789058 -0.06328799 348.63805779
Axis -0.38366119 0.86284462 0.32909459
Axis point 334.98821277 0.00000000 -72.89333153
Rotation angle (degrees) 101.09476358
Shift along axis 279.76466456
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.007082, steps = 48
shifted from previous position = 0.0664
rotated from previous position = 0.0489 degrees
atoms outside contour = 4201, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.01688880 -0.71709481 0.69677098 284.11645596
-0.07170364 0.69594474 0.71450647 317.57357730
-0.99728299 -0.03789386 -0.06317198 348.67352273
Axis -0.38333652 0.86309472 0.32881698
Axis point 334.99021187 0.00000000 -72.82036243
Rotation angle (degrees) 101.07291229
Shift along axis 279.83364008
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.007082, steps = 60
shifted from previous position = 0.0629
rotated from previous position = 0.0223 degrees
atoms outside contour = 4198, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.01680257 -0.71727840 0.69658407 284.06435287
-0.07198223 0.69574245 0.71467545 317.58085384
-0.99726437 -0.03813329 -0.06332156 348.64131381
Axis -0.38355477 0.86301288 0.32877729
Axis point 335.01079253 0.00000000 -72.81676274
Rotation angle (degrees) 101.08066674
Shift along axis 279.74747890
> ui mousemode right "translate selected models"
> select subtract #4
Nothing selected
> select add #4
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> show #!1 models
> fitmap #5 inMap #1
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 7501 atoms
average map value = 0.008654, steps = 64
shifted from previous position = 0.23
rotated from previous position = 0.455 degrees
atoms outside contour = 3206, contour level = 0.007615
Position of bcop Q9JIF7 (#5) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.04829043 -0.74196257 0.66869990 284.94471830
-0.15903620 0.65522873 0.73850036 314.23275652
-0.98609102 -0.14200999 -0.08635763 347.42829540
Axis -0.44854959 0.84298361 0.29695436
Axis point 360.97684873 0.00000000 -73.52227939
Rotation angle (degrees) 101.03562095
Shift along axis 240.25157323
> fitmap #5 inMap #1
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 7501 atoms
average map value = 0.008654, steps = 48
shifted from previous position = 0.00691
rotated from previous position = 0.0175 degrees
atoms outside contour = 3205, contour level = 0.007615
Position of bcop Q9JIF7 (#5) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.04856677 -0.74202042 0.66861569 284.94379926
-0.15895151 0.65513306 0.73860346 314.23632504
-0.98609110 -0.14214906 -0.08612757 347.43381820
Axis -0.44865466 0.84290638 0.29701486
Axis point 361.04538475 0.00000000 -73.60071018
Rotation angle (degrees) 101.02363291
Shift along axis 240.22344619
> fitmap #5 inMap #1
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 7501 atoms
average map value = 0.008653, steps = 60
shifted from previous position = 0.0131
rotated from previous position = 0.0259 degrees
atoms outside contour = 3204, contour level = 0.007615
Position of bcop Q9JIF7 (#5) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.04830079 -0.74187618 0.66879500 284.95295438
-0.15868386 0.65537318 0.73844797 314.24162957
-0.98614727 -0.14179460 -0.08606873 347.42930560
Axis -0.44839342 0.84302357 0.29707675
Axis point 360.94600410 0.00000000 -73.58702601
Rotation angle (degrees) 101.02267014
Shift along axis 240.35523879
> fitmap #5 inMap #1
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 7501 atoms
average map value = 0.008654, steps = 48
shifted from previous position = 0.0104
rotated from previous position = 0.0215 degrees
atoms outside contour = 3203, contour level = 0.007615
Position of bcop Q9JIF7 (#5) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.04855166 -0.74197520 0.66866697 284.94626243
-0.15889800 0.65519312 0.73856169 314.23609417
-0.98610047 -0.14210824 -0.08608766 347.43200387
Axis -0.44860881 0.84293018 0.29701658
Axis point 361.03389089 0.00000000 -73.60342354
Rotation angle (degrees) 101.02115594
Shift along axis 240.24274795
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.016803,-0.71728,0.69658,281.97,-0.071982,0.69574,0.71468,327.09,-0.99726,-0.038133,-0.063322,352.85
> view matrix models
> #4,-0.016803,-0.71728,0.69658,282.46,-0.071982,0.69574,0.71468,326.46,-0.99726,-0.038133,-0.063322,350.63
> view matrix models
> #4,-0.016803,-0.71728,0.69658,281.96,-0.071982,0.69574,0.71468,327.54,-0.99726,-0.038133,-0.063322,352.56
> view matrix models
> #4,-0.016803,-0.71728,0.69658,281.99,-0.071982,0.69574,0.71468,327.35,-0.99726,-0.038133,-0.063322,352.52
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.15215,-0.74422,0.65037,281.51,-0.032738,0.65387,0.75589,327.03,-0.98782,-0.1363,0.075122,351.92
> fitmap #5 inMap #1
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 7501 atoms
average map value = 0.008653, steps = 64
shifted from previous position = 0.0477
rotated from previous position = 0.0377 degrees
atoms outside contour = 3204, contour level = 0.007615
Position of bcop Q9JIF7 (#5) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.04852805 -0.74175367 0.66891442 284.99078272
-0.15835458 0.65551970 0.73838860 314.23634123
-0.98618904 -0.14175822 -0.08564899 347.43060192
Axis -0.44830940 0.84303938 0.29715871
Axis point 360.98503593 0.00000000 -73.69172233
Rotation angle (degrees) 100.99951138
Shift along axis 240.39159212
> fitmap #5 inMap #1
Fit molecule bcop Q9JIF7 (#5) to map postprocess.mrc (#1) using 7501 atoms
average map value = 0.008654, steps = 48
shifted from previous position = 0.0556
rotated from previous position = 0.0475 degrees
atoms outside contour = 3201, contour level = 0.007615
Position of bcop Q9JIF7 (#5) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
0.04863342 -0.74201839 0.66861309 284.93974625
-0.15904224 0.65511159 0.73860297 314.22958632
-0.98607319 -0.14225851 -0.08615195 347.43227410
Axis -0.44870924 0.84289419 0.29696700
Axis point 361.06707546 0.00000000 -73.59260335
Rotation angle (degrees) 101.02302588
Shift along axis 240.18311442
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.006862, steps = 88
shifted from previous position = 6.32
rotated from previous position = 12.5 degrees
atoms outside contour = 4265, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.02375568 -0.71180544 0.70197485 283.50658347
0.07563230 0.69888106 0.71122782 323.06929077
-0.99685276 0.06998767 0.03723309 346.61881962
Axis -0.32398834 0.85833729 0.39785507
Axis point 312.57973963 0.00000000 -97.24580641
Rotation angle (degrees) 98.26899806
Shift along axis 323.35364799
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.006862, steps = 44
shifted from previous position = 0.00175
rotated from previous position = 0.00181 degrees
atoms outside contour = 4266, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.02377180 -0.71182364 0.70195584 283.50748601
0.07562490 0.69886199 0.71124735 323.07085740
-0.99685293 0.06999297 0.03721839 346.61918331
Axis -0.32399671 0.85833092 0.39786199
Axis point 312.57975706 0.00000000 -97.24599552
Rotation angle (degrees) 98.27044239
Shift along axis 323.35280925
> hide #!1 models
> select subtract #4
Nothing selected
> select add #4
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> view matrix models
> #4,0.037432,-0.68363,0.72887,282.99,-0.02112,0.72867,0.68453,323.62,-0.99908,-0.041017,0.012837,347.04
> view matrix models
> #4,-0.013914,-0.70418,0.70988,283.4,-0.03586,0.70985,0.70344,323.63,-0.99926,-0.015669,-0.035129,347.26
> view matrix models
> #4,-0.010473,-0.70137,0.71272,283.36,0.10431,0.7081,0.69836,322.98,-0.99449,0.08166,0.065747,346.41
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.010473,-0.70137,0.71272,286.39,0.10431,0.7081,0.69836,317.88,-0.99449,0.08166,0.065747,343.25
> view matrix models
> #4,-0.010473,-0.70137,0.71272,285.35,0.10431,0.7081,0.69836,327.55,-0.99449,0.08166,0.065747,343.29
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.10478,-0.55074,0.82807,283.76,-0.14287,0.81568,0.56058,329.27,-0.98418,-0.17704,0.0067812,344.22
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.006862, steps = 80
shifted from previous position = 6.78
rotated from previous position = 18.4 degrees
atoms outside contour = 4263, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.02384645 -0.71201247 0.70176177 283.52234822
0.07529000 0.69868878 0.71145302 323.10748618
-0.99687650 0.06980127 0.03694617 346.63245742
Axis -0.32420988 0.85827759 0.39780339
Axis point 312.64515312 0.00000000 -97.23309937
Rotation angle (degrees) 98.28549839
Shift along axis 323.28673342
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.006863, steps = 60
shifted from previous position = 0.0417
rotated from previous position = 0.0158 degrees
atoms outside contour = 4262, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.02361562 -0.71191785 0.70186556 283.49898678
0.07534867 0.69879696 0.71134055 323.07473827
-0.99687756 0.06968338 0.03713954 346.61902368
Axis -0.32419993 0.85829698 0.39776966
Axis point 312.65585505 0.00000000 -97.25491070
Rotation angle (degrees) 98.27008644
Shift along axis 323.25824990
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.006862, steps = 44
shifted from previous position = 0.0162
rotated from previous position = 0.0265 degrees
atoms outside contour = 4265, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.02351289 -0.71164250 0.70214820 283.50337203
0.07557556 0.69906733 0.71105077 323.05904795
-0.99686282 0.06978411 0.03734569 346.61866410
Axis -0.32398886 0.85839585 0.39772827
Axis point 312.62223016 0.00000000 -97.24838705
Rotation angle (degrees) 98.25331819
Shift along axis 323.32065465
> ui mousemode right "rotate selected models"
> select subtract #4
Nothing selected
> hide #4 models
> hide #5 models
> show #5 models
> show #4 models
> hide #5 models
> ui mousemode right select
Drag select of 5 residues
Drag select of 274 residues
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 2115
atoms
average map value = 0.008315, steps = 68
shifted from previous position = 2.03
rotated from previous position = 4.73 degrees
atoms outside contour = 923, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.10579048 -0.70730759 0.69894516 282.96553278
0.07896248 0.69469453 0.71495765 324.74299380
-0.99124835 0.13082616 -0.01764130 345.12798806
Axis -0.29901705 0.86521045 0.40249183
Axis point 295.29571959 0.00000000 -81.09648469
Rotation angle (degrees) 102.37848859
Shift along axis 335.27071250
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 2115
atoms
average map value = 0.008315, steps = 40
shifted from previous position = 0.00564
rotated from previous position = 0.0106 degrees
atoms outside contour = 921, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.10571287 -0.70737352 0.69889019 282.97073069
0.07909744 0.69461975 0.71501538 324.74730754
-0.99124587 0.13086675 -0.01747882 345.12460712
Axis -0.29902027 0.86516498 0.40258719
Axis point 295.29640717 0.00000000 -81.15126842
Rotation angle (degrees) 102.37364024
Shift along axis 335.28875858
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 2115
atoms
average map value = 0.008316, steps = 40
shifted from previous position = 0.0453
rotated from previous position = 0.0245 degrees
atoms outside contour = 923, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.10592320 -0.70735006 0.69888209 282.93834319
0.07872769 0.69466415 0.71501305 324.71829023
-0.99125286 0.13075784 -0.01789301 345.13557589
Axis -0.29909432 0.86522081 0.40241214
Axis point 295.29572978 0.00000000 -81.02182809
Rotation angle (degrees) 102.39065520
Shift along axis 335.21451712
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 2115
atoms
average map value = 0.008315, steps = 44
shifted from previous position = 0.0476
rotated from previous position = 0.0219 degrees
atoms outside contour = 920, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.10568605 -0.70734140 0.69892675 282.97127380
0.07902633 0.69466562 0.71497868 324.74852806
-0.99125441 0.13079689 -0.01751787 345.12632225
Axis -0.29903611 0.86518479 0.40253283
Axis point 295.31018308 0.00000000 -81.13842742
Rotation angle (degrees) 102.37265369
Shift along axis 335.27353174
> show #!1 models
> hide #!1 models
> show #5 models
> hide #5 models
> show #5 models
> select add #4
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #5 models
Drag select of 507 residues
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 4000
atoms
average map value = 0.008277, steps = 72
shifted from previous position = 7.64
rotated from previous position = 16 degrees
atoms outside contour = 1925, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04641244 -0.73475835 0.67673928 284.67198897
-0.15304210 0.66424091 0.73168445 314.76006697
-0.98712917 -0.13752886 -0.08161992 347.30373745
Axis -0.44228138 0.84662536 0.29599439
Axis point 359.30312780 0.00000000 -73.42097611
Rotation angle (degrees) 100.68931043
Shift along axis 243.37869526
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 4000
atoms
average map value = 0.008278, steps = 44
shifted from previous position = 0.0309
rotated from previous position = 0.0374 degrees
atoms outside contour = 1923, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04632868 -0.73495241 0.67653426 284.65184512
-0.15360392 0.66396531 0.73181685 314.77209918
-0.98704584 -0.13782242 -0.08213094 347.29830464
Axis -0.44253516 0.84654949 0.29583203
Axis point 359.33832379 0.00000000 -73.32232922
Rotation angle (degrees) 100.71468633
Shift along axis 243.24367199
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 4000
atoms
average map value = 0.008278, steps = 44
shifted from previous position = 0.011
rotated from previous position = 0.0194 degrees
atoms outside contour = 1925, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04646218 -0.73509123 0.67637427 284.66420229
-0.15336806 0.66382787 0.73199098 314.77262106
-0.98707624 -0.13774410 -0.08189663 347.29963762
Axis -0.44257410 0.84646478 0.29601613
Axis point 359.36528756 0.00000000 -73.41896329
Rotation angle (degrees) 100.70796949
Shift along axis 243.26522574
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 4000
atoms
average map value = 0.008277, steps = 44
shifted from previous position = 0.0424
rotated from previous position = 0.0391 degrees
atoms outside contour = 1921, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04628338 -0.73469053 0.67682175 284.68851949
-0.15313190 0.66432115 0.73159280 314.80954549
-0.98712130 -0.13750359 -0.08175753 347.32087173
Axis -0.44222981 0.84667848 0.29591949
Axis point 359.29889691 0.00000000 -73.38479054
Rotation angle (degrees) 100.69474521
Shift along axis 243.42373270
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 4000
atoms
average map value = 0.008277, steps = 44
shifted from previous position = 0.0115
rotated from previous position = 0.0203 degrees
atoms outside contour = 1921, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04618245 -0.73461065 0.67691533 284.69347280
-0.15282529 0.66446533 0.73152598 314.80719942
-0.98717355 -0.13723344 -0.08158045 347.32596892
Axis -0.44204899 0.84673477 0.29602859
Axis point 359.24246153 0.00000000 -73.41107435
Rotation angle (degrees) 100.68832229
Shift along axis 243.52815631
> select add #4
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select subtract #4
Nothing selected
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #5 models
> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/alphafold_copi_colored_RT_2.cxs
——— End of log from Tue Nov 7 08:56:24 2023 ———
opened ChimeraX session
> show #13 models
> show #3 models
> select add #3
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> show sel atoms
> select subtract #3
Nothing selected
> hide #13 models
> show #13 models
> show #!1 models
> ui tool show "Side View"
> hide #!1 models
> show #!1 models
> hide #3 models
> show #11 models
> select add #11
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> select add #13
3787 atoms, 3839 bonds, 475 residues, 2 models selected
> view
> hide #!1 models
> view orient
> select subtract #11
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> select subtract #13
Nothing selected
> show #!1 models
> hide #11 models
> show #10 models
> show #11 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #11 models
> hide #10 models
> show #14 models
> select add #13
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> select add #14
9581 atoms, 9771 bonds, 1203 residues, 2 models selected
> hide #!1 models
> view orient
> select subtract #13
7214 atoms, 7373 bonds, 905 residues, 1 model selected
> select subtract #14
Nothing selected
> show #!1 models
> hide #!1 models
> hide #13 models
> show #4 models
> hide #14 models
> select add #4
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> view orient
> show #!1 models
> show #!2 models
> select subtract #4
Nothing selected
> hide #!1 models
> hide #!2 models
> ui mousemode right select
Drag select of 136 residues
> select add #4
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select subtract #4
Nothing selected
> ui mousemode right select
Drag select of 383 residues
> select #4/A:608
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 383 residues
> select up
3380 atoms, 3422 bonds, 427 residues, 1 model selected
> select down
3033 atoms, 383 residues, 1 model selected
> select up
3380 atoms, 3422 bonds, 427 residues, 1 model selected
> show #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.12931,-0.68543,0.71656,283.94,-0.23247,0.68153,0.69388,315.37,-0.96397,-0.2563,-0.071212,347.45
> ui tool show "Fit in Map"
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.007082, steps = 84
shifted from previous position = 3.21
rotated from previous position = 12.7 degrees
atoms outside contour = 4196, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.01686710 -0.71703128 0.69683688 284.06166900
-0.07196391 0.69599912 0.71442734 317.58765092
-0.99726461 -0.03809679 -0.06333986 348.64581860
Axis -0.38340310 0.86312684 0.32865502
Axis point 334.98003117 0.00000000 -72.76424387
Rotation angle (degrees) 101.07559198
Shift along axis 279.79249866
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 3380
atoms
average map value = 0.008192, steps = 76
shifted from previous position = 0.897
rotated from previous position = 6.5 degrees
atoms outside contour = 1610, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04832578 -0.75310177 0.65612677 284.99448632
-0.14577385 0.64454303 0.75054265 314.37538401
-0.98813693 -0.13191669 -0.07863450 347.54799047
Axis -0.44967374 0.83786547 0.30947535
Axis point 360.57332885 0.00000000 -77.77491042
Rotation angle (degrees) 101.12107188
Shift along axis 242.80727879
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 3380
atoms
average map value = 0.008192, steps = 48
shifted from previous position = 0.0193
rotated from previous position = 0.0344 degrees
atoms outside contour = 1611, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04835907 -0.75283920 0.65642558 285.00381271
-0.14534849 0.64489493 0.75032283 314.40058169
-0.98819796 -0.13169538 -0.07823752 347.55577869
Axis -0.44941378 0.83798324 0.30953408
Axis point 360.53354608 0.00000000 -77.83680326
Rotation angle (degrees) 101.09823628
Shift along axis 242.95813649
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 3380
atoms
average map value = 0.008192, steps = 44
shifted from previous position = 0.0441
rotated from previous position = 0.0661 degrees
atoms outside contour = 1614, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04819420 -0.75355540 0.65561542 284.97654024
-0.14565957 0.64405910 0.75098014 314.36156413
-0.98816021 -0.13168955 -0.07872264 347.53382883
Axis -0.44981266 0.83767585 0.30978660
Axis point 360.54300294 0.00000000 -77.83205172
Rotation angle (degrees) 101.14161651
Shift along axis 242.80835826
> view matrix models
> #4,0.14326,-0.70641,0.69315,284.18,-0.20842,0.66313,0.7189,314.8,-0.96749,-0.24746,-0.052234,347.57
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 3380
atoms
average map value = 0.008192, steps = 72
shifted from previous position = 2.9
rotated from previous position = 7.29 degrees
atoms outside contour = 1611, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04831351 -0.75332636 0.65586980 284.96451865
-0.14584994 0.64427774 0.75075561 314.38729611
-0.98812631 -0.13193021 -0.07874528 347.53736280
Axis -0.44980665 0.83776171 0.30956307
Axis point 360.57386656 0.00000000 -77.78776602
Rotation angle (degrees) 101.13241001
Shift along axis 242.78743656
> fitmap sel inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 3380
atoms
average map value = 0.008192, steps = 48
shifted from previous position = 0.0166
rotated from previous position = 0.012 degrees
atoms outside contour = 1612, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.04835771 -0.75341224 0.65576789 284.96244308
-0.14599671 0.64415306 0.75083406 314.36720535
-0.98810247 -0.13204857 -0.07884594 347.53130144
Axis -0.44991512 0.83771285 0.30953767
Axis point 360.59905243 0.00000000 -77.77460156
Rotation angle (degrees) 101.13769886
Shift along axis 242.71456482
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.007082, steps = 76
shifted from previous position = 3.8
rotated from previous position = 6.54 degrees
atoms outside contour = 4198, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.01696456 -0.71697328 0.69689419 284.10696210
-0.07179855 0.69606869 0.71437619 317.57979658
-0.99727487 -0.03791691 -0.06328615 348.65955561
Axis -0.38328441 0.86315904 0.32870887
Axis point 334.96615091 0.00000000 -72.77270692
Rotation angle (degrees) 101.07483838
Shift along axis 279.83559197
> fitmap #4 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#4) to map postprocess.mrc (#1) using 7501
atoms
average map value = 0.007082, steps = 60
shifted from previous position = 0.0455
rotated from previous position = 0.023 degrees
atoms outside contour = 4198, contour level = 0.007615
Position of CopB_ Q9JIF7.pdb (#4) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
-0.01683813 -0.71721297 0.69665058 284.06623356
-0.07197130 0.69581138 0.71460944 317.58211952
-0.99726456 -0.03810615 -0.06333491 348.64231772
Axis -0.38350654 0.86304514 0.32874887
Axis point 334.99916050 0.00000000 -72.80113275
Rotation angle (degrees) 101.08008266
Shift along axis 279.76221407
> show #!2 models
> select add #4
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #4 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> view orient
> show #3 models
> show #4 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> hide #10 models
> show #13 models
> show #14 models
> save /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/alphafold_copi_colored_RT_4.cxs
——— End of log from Tue Nov 7 12:35:14 2023 ———
opened ChimeraX session
> show #!2 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/COPI_golph_linkage1_postprocess.mrc"
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.508, step 1, values float32
> volume #15 level 0.4248
> select add #15
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,-73.73,0,1,0,34.966,0,0,1,96.96
> hide #!15 models
> show #!15 models
> hide #14 models
> hide #13 models
> hide #11 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #4 models
> hide #3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> view matrix models #15,1,0,0,-226.17,0,1,0,89.162,0,0,1,41.878
> view matrix models #15,1,0,0,-58.982,0,1,0,132.68,0,0,1,89.156
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.98223,0.0044902,-0.18765,-6.0444,0.0015777,0.99948,0.032175,123.88,0.18769,-0.031899,0.98171,59.539
> view matrix models
> #15,0.98052,0.015967,-0.19577,-5.9641,-0.016526,0.99986,-0.0012203,136.68,0.19572,0.0044318,0.98065,50.268
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.98052,0.015967,-0.19577,-6.7123,-0.016526,0.99986,-0.0012203,137.02,0.19572,0.0044318,0.98065,22.376
> volume #15 level 0.3841
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> color #15 #b2b2b26f models
> color #15 #b2b2b266 models
> color #15 #b2b2b2a7 models
> view matrix models
> #15,0.98052,0.015967,-0.19577,8.2659,-0.016526,0.99986,-0.0012203,135.59,0.19572,0.0044318,0.98065,26.362
> view matrix models
> #15,0.98052,0.015967,-0.19577,36.638,-0.016526,0.99986,-0.0012203,121.02,0.19572,0.0044318,0.98065,17.22
> view matrix models
> #15,0.98052,0.015967,-0.19577,53.856,-0.016526,0.99986,-0.0012203,135.88,0.19572,0.0044318,0.98065,28.038
> view matrix models
> #15,0.98052,0.015967,-0.19577,27.557,-0.016526,0.99986,-0.0012203,153.9,0.19572,0.0044318,0.98065,24.813
> show #3 models
> view matrix models
> #15,0.98052,0.015967,-0.19577,50.336,-0.016526,0.99986,-0.0012203,216.5,0.19572,0.0044318,0.98065,21.949
> view matrix models
> #15,0.98052,0.015967,-0.19577,58.964,-0.016526,0.99986,-0.0012203,209.14,0.19572,0.0044318,0.98065,23.112
> view matrix models
> #15,0.98052,0.015967,-0.19577,51.096,-0.016526,0.99986,-0.0012203,214.85,0.19572,0.0044318,0.98065,22.124
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.86137,0.40179,-0.31082,24.932,-0.45966,0.87696,-0.14023,375.33,0.21623,0.26366,0.94007,-27.258
> view matrix models
> #15,0.79215,0.50964,-0.3358,23.588,-0.56964,0.81491,-0.10698,403.94,0.21912,0.27603,0.93584,-29.425
> view matrix models
> #15,0.77613,0.58521,-0.23484,-15.943,-0.55601,0.8108,0.18292,324.84,0.29745,-0.011395,0.95467,10.116
> view matrix models
> #15,0.79154,0.55932,-0.2462,-10.745,-0.54262,0.82859,0.13787,330.05,0.28111,0.024466,0.95936,4.7514
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.79154,0.55932,-0.2462,6.5942,-0.54262,0.82859,0.13787,316.28,0.28111,0.024466,0.95936,5.2536
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.84779,0.51493,-0.12689,-27.897,-0.4968,0.85484,0.14978,297.43,0.1856,-0.063942,0.98054,39.557
> view matrix models
> #15,0.87354,0.48646,0.017035,-65.656,-0.48414,0.86468,0.13391,296.75,0.050414,-0.12523,0.99085,79.624
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.87354,0.48646,0.017035,-53.181,-0.48414,0.86468,0.13391,267.53,0.050414,-0.12523,0.99085,75.68
> color #15 #b2b2b2cd models
> view matrix models
> #15,0.87354,0.48646,0.017035,-36.081,-0.48414,0.86468,0.13391,288.3,0.050414,-0.12523,0.99085,77.008
> view matrix models
> #15,0.87354,0.48646,0.017035,-66.127,-0.48414,0.86468,0.13391,288.73,0.050414,-0.12523,0.99085,78.763
> color #15 #b2b2b2cc models
> view matrix models
> #15,0.87354,0.48646,0.017035,-83.691,-0.48414,0.86468,0.13391,287.23,0.050414,-0.12523,0.99085,72.864
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.81283,0.58249,-0.0015564,-86.063,-0.58225,0.81241,-0.031082,363.79,-0.016841,0.026171,0.99952,52.8
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.81283,0.58249,-0.0015564,-74.108,-0.58225,0.81241,-0.031082,372.83,-0.016841,0.026171,0.99952,44.774
> view matrix models
> #15,0.81283,0.58249,-0.0015564,-68.602,-0.58225,0.81241,-0.031082,387.08,-0.016841,0.026171,0.99952,60.564
> ui tool show "Fit in Map"
> fitmap #15 inMap #2
Fit map COPI_golph_linkage1_postprocess.mrc in map emdb 3720 using 80938
points
correlation = 0.3638, correlation about mean = 0.1594, overlap = 958.1
steps = 632, shift = 72.3, angle = 35.2 degrees
Position of COPI_golph_linkage1_postprocess.mrc (#15) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.24079995 -0.95955855 -0.14581762 250.87523828
0.83039920 0.28145928 -0.48085116 -67.76251124
0.50244656 -0.00529790 0.86459203 -280.59782339
Axis 0.24235349 -0.33037117 0.91220594
Axis point 245.94884364 110.49212662 0.00000000
Rotation angle (degrees) 78.84723205
Shift along axis -172.77573255
> select subtract #15
Nothing selected
> hide #3 models
> hide #!2 models
> show #!1 models
> show #3 models
> show #4 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #11 models
> show #13 models
> show #14 models
> hide #!1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/Linkage_1_fitting_Golph_AF_RT.cxs"
> show #!2 models
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #!9 models
> hide #11 models
> hide #13 models
> hide #14 models
> volume #15 level 0.3212
> volume #15 level 0.3724
> rename #3 CopA_F8WHL2
> rename #6 hArf1_P84078
> rename #7 hArf1_P84078
> show #8 models
> rename #8 CopD_Q5XJY5
> show #!9 models
> hide #!9 models
> rename #9 CopG_Q9QZE5
> hide #8 models
> rename #12 hArf1_P84078
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/Linkage_1_fitting_Golph_AF_RT.cxs"
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/References/emd_2986_2015_linkage1.map"
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 3.62, step 1, values float32
> select add #16
2 models selected
> view orient
> volume #2 level 0.1928
> volume #16 level 2.055
> view matrix models #16,1,0,0,278.66,0,1,0,276.94,0,0,1,316.22
> view matrix models #16,1,0,0,314.02,0,1,0,383.93,0,0,1,284.35
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.9211,0.23554,-0.30999,307.52,-0.039987,0.84925,0.52648,394.98,0.38727,-0.47254,0.79166,279.97
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.9211,0.23554,-0.30999,274.17,-0.039987,0.84925,0.52648,426.96,0.38727,-0.47254,0.79166,310.55
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.84705,0.4058,-0.34327,273.57,-0.22779,0.86068,0.45535,424.96,0.48023,-0.30751,0.82147,311.73
> view matrix models
> #16,0.094305,0.61913,-0.77961,262.59,0.22261,0.75015,0.62267,429.53,0.97034,-0.23227,-0.06708,293.82
> view matrix models
> #16,0.63479,0.41444,-0.65213,266.35,-0.45893,0.88122,0.1133,417,0.62163,0.22736,0.74959,311.47
> view matrix models
> #16,0.7821,0.62298,0.014788,281.56,-0.39044,0.47139,0.79079,431.14,0.48568,-0.62425,0.61191,306.63
> view matrix models
> #16,0.75419,0.57526,-0.31665,274.21,-0.54707,0.81716,0.18155,418.14,0.36319,0.036304,0.93101,314.42
> view matrix models
> #16,0.40768,0.6183,-0.67194,265.71,-0.51322,0.76379,0.39144,422.69,0.75525,0.18527,0.6287,309.11
> view matrix models
> #16,0.57225,0.76359,-0.2991,274.47,-0.5793,0.63455,0.51162,424.9,0.58046,-0.1195,0.80547,311.97
> fitmap #16 inMap #15
Fit map emd_2986_2015_linkage1.map in map COPI_golph_linkage1_postprocess.mrc
using 304384 points
correlation = 0.9442, correlation about mean = 0.3153, overlap = 4.02e+05
steps = 92, shift = 5.38, angle = 8.38 degrees
Position of emd_2986_2015_linkage1.map (#16) relative to
COPI_golph_linkage1_postprocess.mrc (#15) coordinates:
Matrix rotation and translation
0.99951007 -0.03108553 -0.00364675 217.45099910
0.03109278 0.99951461 0.00194671 217.65079361
0.00358447 -0.00205915 0.99999145 304.80668615
Axis -0.06386343 -0.11528365 0.99127753
Axis point -7856.22741698 7659.73186145 0.00000000
Rotation angle (degrees) 1.79724595
Shift along axis 263.16927579
> hide #!2 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> select subtract #16
Nothing selected
> hide #!16 models
> show #!16 models
> hide #!16 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/References/emd_3722_2017_linkage1.map"
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0843, step 1, values float32
> volume #17 level 0.03583
> select add #17
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #17,1,0,0,144.81,0,1,0,167.76,0,0,1,191.42
> view matrix models #17,1,0,0,98.86,0,1,0,202.13,0,0,1,156.34
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.41117,0.899,-0.15079,219.81,-0.69907,-0.20482,0.68509,449.79,0.58501,0.3871,0.71268,19.753
> view matrix models
> #17,-0.768,0.57205,0.28799,277.81,-0.015321,-0.46594,0.88468,338.08,0.64027,0.67502,0.36661,10.921
> view matrix models
> #17,-0.49445,0.8172,0.29616,178.99,0.30081,-0.15879,0.94037,211.97,0.81549,0.55406,-0.16731,86.496
> view matrix models
> #17,-0.51648,0.74901,-0.41502,310.27,-0.70967,-0.10318,0.69694,430.79,0.47919,0.65448,0.58483,10.006
> view matrix models
> #17,-0.41194,0.8427,-0.34665,262.01,-0.81675,-0.1728,0.55051,487.55,0.40401,0.50991,0.75946,23.231
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.41194,0.8427,-0.34665,-69.085,-0.81675,-0.1728,0.55051,318.09,0.40401,0.50991,0.75946,-135.89
> view matrix models
> #17,-0.41194,0.8427,-0.34665,250.19,-0.81675,-0.1728,0.55051,510.18,0.40401,0.50991,0.75946,-8.5576
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.70549,0.67986,-0.20018,312.46,-0.335,-0.070995,0.93954,337.88,0.62455,0.7299,0.27784,-13.944
> view matrix models
> #17,-0.48961,0.53476,-0.68871,377.62,-0.8124,0.0070959,0.58305,470.35,0.31668,0.84497,0.43097,-2.2417
> view matrix models
> #17,-0.50936,0.83183,-0.22048,250.28,-0.76322,-0.31832,0.56229,525.55,0.39754,0.45468,0.79701,-3.0074
> view matrix models
> #17,-0.67427,0.45577,-0.58106,409.9,-0.62558,0.065621,0.7774,392.97,0.39244,0.88768,0.24087,6.0427
> view matrix models
> #17,-0.72949,0.59011,-0.34584,357.25,-0.68333,-0.60655,0.4064,589.7,0.030051,0.53279,0.84571,43.644
> fitmap #17 inMap #15
Fit map emd_3722_2017_linkage1.map in map COPI_golph_linkage1_postprocess.mrc
using 723117 points
correlation = 0.9448, correlation about mean = 0.4448, overlap = 1.725e+04
steps = 80, shift = 5.27, angle = 4.21 degrees
Position of emd_3722_2017_linkage1.map (#17) relative to
COPI_golph_linkage1_postprocess.mrc (#15) coordinates:
Matrix rotation and translation
0.11586229 0.99297385 0.02405942 4.16632834
-0.99323203 0.11562620 0.01098721 377.48279546
0.00812812 -0.02516959 0.99965015 115.04537270
Axis -0.01820035 0.00801938 -0.99980220
Axis point 213.55721314 188.00836730 0.00000000
Rotation angle (degrees) 83.36353620
Shift along axis -112.07126543
> view matrix models
> #17,-0.66805,0.66076,-0.3422,336.84,-0.74292,-0.56619,0.35708,600.16,0.042194,0.49277,0.86914,46.321
> fitmap #17 inMap #15
Fit map emd_3722_2017_linkage1.map in map COPI_golph_linkage1_postprocess.mrc
using 723117 points
correlation = 0.9449, correlation about mean = 0.4447, overlap = 1.725e+04
steps = 64, shift = 0.139, angle = 1.54 degrees
Position of emd_3722_2017_linkage1.map (#17) relative to
COPI_golph_linkage1_postprocess.mrc (#15) coordinates:
Matrix rotation and translation
0.11577968 0.99298493 0.02400000 4.18525548
-0.99324192 0.11554509 0.01094590 377.50750041
0.00809604 -0.02510512 0.99965203 114.97681952
Axis -0.01814693 0.00800555 -0.99980328
Axis point 213.56543340 188.00511122 0.00000000
Rotation angle (degrees) 83.36820385
Shift along axis -112.00799683
> fitmap #17 inMap #15
Fit map emd_3722_2017_linkage1.map in map COPI_golph_linkage1_postprocess.mrc
using 723117 points
correlation = 0.9449, correlation about mean = 0.4447, overlap = 1.725e+04
steps = 24, shift = 0.0151, angle = 0.00227 degrees
Position of emd_3722_2017_linkage1.map (#17) relative to
COPI_golph_linkage1_postprocess.mrc (#15) coordinates:
Matrix rotation and translation
0.11574972 0.99298833 0.02400375 4.18939547
-0.99324562 0.11551574 0.01091971 377.51882888
0.00807034 -0.02510557 0.99965223 114.96666815
Axis -0.01813392 0.00802034 -0.99980340
Axis point 213.56917414 188.00831708 0.00000000
Rotation angle (degrees) 83.36990886
Shift along axis -111.99220521
> fitmap #17 inMap #15
Fit map emd_3722_2017_linkage1.map in map COPI_golph_linkage1_postprocess.mrc
using 723117 points
correlation = 0.9448, correlation about mean = 0.4448, overlap = 1.725e+04
steps = 28, shift = 0.0944, angle = 0.0261 degrees
Position of emd_3722_2017_linkage1.map (#17) relative to
COPI_golph_linkage1_postprocess.mrc (#15) coordinates:
Matrix rotation and translation
0.11612366 0.99294047 0.02417693 4.10484990
-0.99320060 0.11588337 0.01111788 377.40674556
0.00823769 -0.02530359 0.99964587 115.06782484
Axis -0.01833413 0.00802362 -0.99979972
Axis point 213.53212323 188.01353754 0.00000000
Rotation angle (degrees) 83.34870436
Shift along axis -112.09186818
> fitmap #17 inMap #15
Fit map emd_3722_2017_linkage1.map in map COPI_golph_linkage1_postprocess.mrc
using 723117 points
correlation = 0.9448, correlation about mean = 0.4448, overlap = 1.725e+04
steps = 40, shift = 0.0169, angle = 0.0175 degrees
Position of emd_3722_2017_linkage1.map (#17) relative to
COPI_golph_linkage1_postprocess.mrc (#15) coordinates:
Matrix rotation and translation
0.11589589 0.99297080 0.02402345 4.16654300
-0.99322813 0.11566026 0.01098070 377.47647231
0.00812495 -0.02513339 0.99965109 115.03925499
Axis -0.01817892 0.00800291 -0.99980272
Axis point 213.56129838 188.00272386 0.00000000
Rotation angle (degrees) 83.36155775
Shift along axis -112.07139468
> fitmap #17 inMap #15
Fit map emd_3722_2017_linkage1.map in map COPI_golph_linkage1_postprocess.mrc
using 723117 points
correlation = 0.9448, correlation about mean = 0.4448, overlap = 1.725e+04
steps = 44, shift = 0.0017, angle = 0.0108 degrees
Position of emd_3722_2017_linkage1.map (#17) relative to
COPI_golph_linkage1_postprocess.mrc (#15) coordinates:
Matrix rotation and translation
0.11604249 0.99295154 0.02411174 4.12742813
-0.99321047 0.11580416 0.01106106 377.43274324
0.00819086 -0.02523158 0.99964808 115.04508414
Axis -0.01826912 0.00801430 -0.99980099
Axis point 213.54398929 188.00902801 0.00000000
Rotation angle (degrees) 83.35326632
Shift along axis -112.07273251
> fitmap #17 inMap #15
Fit map emd_3722_2017_linkage1.map in map COPI_golph_linkage1_postprocess.mrc
using 723117 points
correlation = 0.9449, correlation about mean = 0.4447, overlap = 1.725e+04
steps = 28, shift = 0.0715, angle = 0.0128 degrees
Position of emd_3722_2017_linkage1.map (#17) relative to
COPI_golph_linkage1_postprocess.mrc (#15) coordinates:
Matrix rotation and translation
0.11613389 0.99294550 0.02391956 4.13714493
-0.99320018 0.11589886 0.01099299 377.42409910
0.00814319 -0.02503357 0.99965344 114.94432756
Axis -0.01813537 0.00794165 -0.99980400
Axis point 213.56768474 187.98538808 0.00000000
Rotation angle (degrees) 83.34774404
Shift along axis -111.99945594
> select subtract #17
Nothing selected
> ui mousemode right zoom
> hide #!15 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #3 models
> show #4 models
> show #6 models
> hide #3 models
> hide #4 models
> hide #6 models
> show #13 models
> hide #13 models
> show #!15 models
> show #13 models
> hide #13 models
> hide #!15 models
> hide #!17 models
> show #!15 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/Linkage_1_fitting_Golph_AF_RT.cxs"
[Repeated 1 time(s)]
——— End of log from Tue Dec 5 14:45:54 2023 ———
opened ChimeraX session
> hide #!15 target m
> show #!2 models
> volume #2 level 0.1535
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/COPI_golph_linkage2_postprocess.mrc"
Opened COPI_golph_linkage2_postprocess.mrc as #18, grid size 150,150,150,
pixel 3.4, shown at level 0.579, step 1, values float32
> color #18 #b2b2b2b5 models
> volume #18 level 0.4748
> select add #18
2 models selected
> show #8 models
> ui mousemode right "translate selected models"
> view matrix models #18,1,0,0,37.911,0,1,0,323.13,0,0,1,-76.889
> view matrix models #18,1,0,0,78.69,0,1,0,212.38,0,0,1,15.274
> view matrix models #18,1,0,0,41.63,0,1,0,189.41,0,0,1,-19.748
> view matrix models #18,1,0,0,166.87,0,1,0,48.28,0,0,1,-38.706
> view matrix models #18,1,0,0,212.77,0,1,0,89.771,0,0,1,-19.788
> view matrix models #18,1,0,0,370.65,0,1,0,-18.809,0,0,1,48.477
> view matrix models #18,1,0,0,-123.38,0,1,0,161.02,0,0,1,-93.371
> view matrix models #18,1,0,0,8.8176,0,1,0,138.79,0,0,1,-50.705
> view matrix models #18,1,0,0,-48.069,0,1,0,187.67,0,0,1,3.1902
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.92266,-0.045215,-0.38295,92.378,0.12648,0.97365,0.18977,105.95,0.36427,-0.22353,0.90407,-14.377
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.92266,-0.045215,-0.38295,114.12,0.12648,0.97365,0.18977,62.084,0.36427,-0.22353,0.90407,-3.5048
> show #3 models
> view matrix models
> #18,0.92266,-0.045215,-0.38295,157.67,0.12648,0.97365,0.18977,73.286,0.36427,-0.22353,0.90407,18.682
> view matrix models
> #18,0.92266,-0.045215,-0.38295,163.14,0.12648,0.97365,0.18977,98.07,0.36427,-0.22353,0.90407,26.33
> view matrix models
> #18,0.92266,-0.045215,-0.38295,170.88,0.12648,0.97365,0.18977,97.935,0.36427,-0.22353,0.90407,41.323
> view matrix models
> #18,0.92266,-0.045215,-0.38295,166.77,0.12648,0.97365,0.18977,87.449,0.36427,-0.22353,0.90407,32.195
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.91983,-0.20028,-0.33736,192.99,0.17356,0.97889,-0.10792,157.26,0.35185,0.040715,0.93517,-38.458
> view matrix models
> #18,0.97834,-0.12989,-0.16116,109.83,0.11624,0.989,-0.091499,165.84,0.17128,0.070784,0.98268,-9.7907
> view matrix models
> #18,0.91272,-0.39632,-0.099394,176.21,0.38748,0.91674,-0.097195,110.94,0.12964,0.050198,0.99029,4.5614
> view matrix models
> #18,0.96031,-0.12322,-0.25025,138.27,0.078274,0.98014,-0.18223,204.05,0.26774,0.15541,0.95088,-48.166
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> view matrix models
> #18,-0.26333,-0.74291,-0.61542,729.88,0.77204,-0.5448,0.32732,246.78,-0.57845,-0.38894,0.71702,384.29
> ui mousemode right "translate selected models"
> view matrix models
> #18,-0.26333,-0.74291,-0.61542,640.99,0.77204,-0.5448,0.32732,186.86,-0.57845,-0.38894,0.71702,316.02
> view matrix models
> #18,-0.26333,-0.74291,-0.61542,639.87,0.77204,-0.5448,0.32732,168.07,-0.57845,-0.38894,0.71702,316.46
> view matrix models
> #18,-0.26333,-0.74291,-0.61542,670.85,0.77204,-0.5448,0.32732,116.2,-0.57845,-0.38894,0.71702,308.88
> view matrix models
> #18,-0.26333,-0.74291,-0.61542,668.36,0.77204,-0.5448,0.32732,123.07,-0.57845,-0.38894,0.71702,309.05
> view matrix models
> #18,-0.26333,-0.74291,-0.61542,694.65,0.77204,-0.5448,0.32732,98.173,-0.57845,-0.38894,0.71702,322.41
> view matrix models
> #18,-0.26333,-0.74291,-0.61542,696.9,0.77204,-0.5448,0.32732,106.33,-0.57845,-0.38894,0.71702,322.54
> view matrix models
> #18,-0.26333,-0.74291,-0.61542,689.63,0.77204,-0.5448,0.32732,111.08,-0.57845,-0.38894,0.71702,323.37
> select subtract #18
Nothing selected
> ui tool show "Fit in Map"
> fitmap #18 inMap #2
Fit map COPI_golph_linkage2_postprocess.mrc in map emdb 3720 using 76728
points
correlation = 0.393, correlation about mean = 0.1787, overlap = 1304
steps = 416, shift = 13.5, angle = 30.6 degrees
Position of COPI_golph_linkage2_postprocess.mrc (#18) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
-0.29086353 0.88764467 0.35705090 -72.93361915
-0.93714915 -0.18913877 -0.29322005 460.35677211
-0.19274305 -0.41989697 0.88686901 -44.24127869
Axis -0.06632215 0.28784657 -0.95537727
Axis point 122.59971391 247.03643730 0.00000000
Rotation angle (degrees) 107.25150392
Shift along axis 179.61634476
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!18 models
> hide #!15 models
> show #!18 models
> show #!1 models
> hide #!1 models
> show #3 models
> show #4 models
> show #6 models
> show #7 models
> show #!9 models
> show #10 models
> hide #10 models
> show #11 models
> show #13 models
> show #14 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #4 models
> show #5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #14 models
> hide #13 models
> hide #11 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #3 models
> hide #!2 models
> hide #!1 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/References/emd_2987_2015_linkage2.map"
Opened emd_2987_2015_linkage2.map as #19, grid size 200,200,200, pixel 2.02,
shown at level 3.35, step 1, values float32
> volume #19 level 1.908
> select add #19
2 models selected
> view matrix models #19,1,0,0,281.34,0,1,0,349.41,0,0,1,125.42
> view matrix models #19,1,0,0,221.57,0,1,0,296.89,0,0,1,303
> ui mousemode right "rotate selected models"
> view matrix models
> #19,0.89469,0.0047926,-0.44667,207.18,0.15862,0.93137,0.32771,307.33,0.41758,-0.36405,0.83252,296.99
> view matrix models
> #19,0.96644,-0.22088,-0.13116,216.95,0.22139,0.97513,-0.010844,296.51,0.1303,-0.018558,0.9913,302.7
> view matrix models
> #19,0.60959,-0.39067,-0.68977,198.63,0.71217,0.65206,0.26007,304.7,0.34817,-0.64976,0.67571,291.43
> view matrix models
> #19,-0.58102,-0.73076,-0.35834,208.62,0.81146,-0.48613,-0.32437,283.86,0.062839,-0.47924,0.87543,298.14
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.58102,-0.73076,-0.35834,209.59,0.81146,-0.48613,-0.32437,286.9,0.062839,-0.47924,0.87543,328.25
> view matrix models
> #19,-0.58102,-0.73076,-0.35834,225.92,0.81146,-0.48613,-0.32437,276.76,0.062839,-0.47924,0.87543,330.19
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.51565,-0.72069,-0.46336,222.56,0.85324,-0.48117,-0.20114,280.74,-0.077999,-0.49907,0.86304,329.75
> view matrix models
> #19,-0.55739,-0.73804,-0.38027,225.2,0.83025,-0.49523,-0.25581,278.96,0.0004801,-0.45831,0.88879,330.65
> view matrix models
> #19,-0.65627,-0.64485,-0.39176,224.99,0.75157,-0.60456,-0.26389,278.49,-0.066669,-0.46762,0.88141,330.4
> fitmap #19 inMap #18
Fit map emd_2987_2015_linkage2.map in map COPI_golph_linkage2_postprocess.mrc
using 245288 points
correlation = 0.9621, correlation about mean = 0.4468, overlap = 4.315e+05
steps = 64, shift = 13.6, angle = 9.64 degrees
Position of emd_2987_2015_linkage2.map (#19) relative to
COPI_golph_linkage2_postprocess.mrc (#18) coordinates:
Matrix rotation and translation
0.99943198 -0.03369827 0.00038712 255.16295945
0.03369824 0.99943205 0.00008535 255.14695389
-0.00038977 -0.00007225 0.99999992 337.62488892
Axis -0.00233824 0.01152634 0.99993084
Axis point -7325.14771320 7719.05156474 0.00000000
Rotation angle (degrees) 1.93126701
Shift along axis 339.94581739
> select subtract #19
Nothing selected
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/References/emd_3723_2017_linkage2.map"
Opened emd_3723_2017_linkage2.map as #20, grid size 212,212,212, pixel 1.78,
shown at level 0.1, step 1, values float32
> select add #20
2 models selected
> volume #20 level 0.0556
> hide #!19 models
> view matrix models
> #20,0.97164,-0.02719,-0.2349,49.932,-0.049625,0.9478,-0.31498,72.049,0.23121,0.3177,0.91957,-88.787
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.97164,-0.02719,-0.2349,112.83,-0.049625,0.9478,-0.31498,201.68,0.23121,0.3177,0.91957,-14.58
> view matrix models
> #20,0.97164,-0.02719,-0.2349,66.5,-0.049625,0.9478,-0.31498,186.06,0.23121,0.3177,0.91957,18.141
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.8629,0.037701,-0.50397,119.87,-0.11576,0.98545,-0.12448,159.18,0.49195,0.16575,0.8547,9.1445
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.8629,0.037701,-0.50397,167.83,-0.11576,0.98545,-0.12448,147.77,0.49195,0.16575,0.8547,10.969
> fitmap #20 inMap #18
Fit map emd_3723_2017_linkage2.map in map COPI_golph_linkage2_postprocess.mrc
using 430908 points
correlation = 0.9553, correlation about mean = 0.437, overlap = 1.937e+04
steps = 128, shift = 13.7, angle = 16 degrees
Position of emd_3723_2017_linkage2.map (#20) relative to
COPI_golph_linkage2_postprocess.mrc (#18) coordinates:
Matrix rotation and translation
-0.52283140 0.85243566 0.00087740 192.72826004
-0.85243398 -0.52283212 0.00169730 514.37823243
0.00190557 0.00013948 0.99999818 127.27802922
Axis -0.00091375 -0.00060308 -0.99999940
Axis point 240.25113231 203.24167526 0.00000000
Rotation angle (degrees) 121.52245397
Shift along axis -127.76426867
> select subtract #20
Nothing selected
> show #13 models
> hide #13 models
> hide #!20 models
> show #!1 models
> volume #1 level 0.01004
> hide #!18 models
> show #!18 models
> show #13 models
> hide #13 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!18 models
> show #!18 models
> show #!2 models
> show #13 models
> show #8 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/Linkage_2_fitting_Golph_AF_RT.cxs"
> hide #!18 models
> hide #13 models
> hide #8 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/COPI_golph_linkage3_postprocess.mrc"
Opened COPI_golph_linkage3_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.731, step 1, values float32
> select add #21
2 models selected
> volume #21 level 0.6806
> color #21 #898bb8ff models
> color #21 #adb1b8ff models
> color #21 #adb1b8b6 models
> color #21 #adb1b8b8 models
> view matrix models #21,1,0,0,-69.887,0,1,0,-146.97,0,0,1,106.13
> view matrix models #21,1,0,0,69.289,0,1,0,-255.81,0,0,1,-21.636
> show #3 models
> view matrix models #21,1,0,0,-8.9068,0,1,0,-218.78,0,0,1,51.499
> view matrix models #21,1,0,0,-249.44,0,1,0,116.86,0,0,1,196.35
> view matrix models #21,1,0,0,-118.83,0,1,0,15.086,0,0,1,161.26
> view matrix models #21,1,0,0,-100.59,0,1,0,1.8365,0,0,1,14.26
> show #8 models
> view matrix models #21,1,0,0,-325.05,0,1,0,-185.92,0,0,1,143.76
> view matrix models #21,1,0,0,-157.21,0,1,0,-165.58,0,0,1,121.51
> view matrix models #21,1,0,0,306.48,0,1,0,-96.47,0,0,1,55.209
> show #6 models
> view matrix models #21,1,0,0,-106.18,0,1,0,-309.4,0,0,1,38.441
> view matrix models #21,1,0,0,62.295,0,1,0,-258.65,0,0,1,47.459
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.89043,-0.015893,-0.45484,225.84,0.21015,0.90083,0.37992,-396.93,0.4037,-0.43388,0.80547,111.02
> view matrix models
> #21,0.95587,-0.0064312,-0.29372,159.62,0.13825,0.892,0.43038,-389.32,0.25923,-0.45199,0.85352,141.6
> view matrix models
> #21,0.95548,-0.032907,-0.29323,166.79,0.12768,0.94202,0.31033,-365.9,0.26601,-0.33395,0.90428,93.187
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.95548,-0.032907,-0.29323,119.6,0.12768,0.94202,0.31033,-206.92,0.26601,-0.33395,0.90428,40.217
> view matrix models
> #21,0.95548,-0.032907,-0.29323,149.13,0.12768,0.94202,0.31033,-368.55,0.26601,-0.33395,0.90428,80.718
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.9092,0.00026127,-0.41635,187.73,0.1849,0.89572,0.40434,-398.27,0.37304,-0.44462,0.81434,107.29
> view matrix models
> #21,0.83643,0.54213,0.080568,-81.317,-0.51647,0.73041,0.44695,-174.53,0.18346,-0.41545,0.89092,129.17
> view matrix models
> #21,0.66015,0.7445,0.099557,-93.827,-0.71972,0.58903,0.3675,-58.129,0.21496,-0.31426,0.92468,83.446
> view matrix models
> #21,0.65675,0.64082,-0.39753,76.738,-0.65717,0.7449,0.11509,-45.764,0.36987,0.18566,0.91034,-90.693
> view matrix models
> #21,0.55552,0.79996,0.22686,-116.66,-0.65365,0.58877,-0.4755,163.79,-0.51395,0.11586,0.84996,186.01
> view matrix models
> #21,0.42233,0.88824,-0.18073,11.515,-0.77453,0.4572,0.43711,-27.136,0.47088,-0.044626,0.88107,-47.178
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.42233,0.88824,-0.18073,15.921,-0.77453,0.4572,0.43711,107.61,0.47088,-0.044626,0.88107,-95.497
> ui mousemode right "rotate selected models"
> view matrix models
> #21,-0.051729,0.72322,-0.68868,334.36,-0.99462,0.0247,0.10065,380.94,0.0898,0.69018,0.71804,-145.39
> view matrix models
> #21,0.71972,0.6719,0.17481,-107.28,-0.64086,0.73979,-0.20497,176.99,-0.26704,0.03549,0.96303,60.203
> view matrix models
> #21,0.67464,0.10107,0.73119,-97.944,-0.52359,0.76376,0.37753,-27.168,-0.5203,-0.63754,0.56818,424.64
> view matrix models
> #21,0.63817,0.076934,0.76604,-91.364,-0.55017,0.7416,0.38386,-15.703,-0.53856,-0.66642,0.51559,452.43
> view matrix models
> #21,0.8156,0.33852,0.46925,-126.41,-0.45267,0.87844,0.15308,-13.826,-0.36039,-0.33727,0.86969,213.61
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.96399,-0.2457,0.10178,96.753,0.21555,0.94601,0.24208,-239.39,-0.15577,-0.21143,0.9649,96.59
> view matrix models
> #21,0.88787,0.44868,0.10179,-71.52,-0.42413,0.88395,-0.19685,76.462,-0.1783,0.1316,0.97513,6.4523
> view matrix models
> #21,0.87685,0.46529,-0.12098,-9.6609,-0.48036,0.8582,-0.18097,94.255,0.019623,0.2168,0.97602,-70.851
> view matrix models
> #21,0.84503,0.45156,-0.2864,49.798,-0.44088,0.89144,0.10467,-6.8007,0.30257,0.037816,0.95238,-92.417
> view matrix models
> #21,0.8763,0.4523,-0.16591,6.8068,-0.44715,0.89176,0.06938,4.8586,0.17933,0.01339,0.9837,-61.141
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.8763,0.4523,-0.16591,7.7609,-0.44715,0.89176,0.06938,33.698,0.17933,0.01339,0.9837,-63.046
> view matrix models
> #21,0.8763,0.4523,-0.16591,11.927,-0.44715,0.89176,0.06938,0.32418,0.17933,0.01339,0.9837,-59.659
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.87736,0.47719,-0.050317,-28.021,-0.45683,0.86277,0.21663,-31.044,0.14679,-0.16708,0.97496,0.80283
> view matrix models
> #21,0.89949,0.22051,-0.37721,128.81,-0.43606,0.50769,-0.74304,332.97,0.027653,0.83284,0.55282,-118.82
> view matrix models
> #21,0.6141,0.77163,-0.16572,-3.682,-0.78752,0.61291,-0.06443,206.92,0.051854,0.17007,0.98407,-67.713
> show #!20 models
> hide #!20 models
> show #14 models
> hide #14 models
> show #14 models
> view matrix models
> #21,0.62161,0.77097,-0.1386,-13.258,-0.78327,0.61388,-0.098198,215.1,0.0093763,0.1696,0.98547,-56.424
> view matrix models
> #21,0.61443,0.78897,-0.00059291,-55.467,-0.7809,0.60803,-0.14316,228.84,-0.11259,0.088427,0.9897,-2.3412
> view matrix models
> #21,0.61932,0.77942,-0.094591,-27.456,-0.78481,0.61105,-0.10338,217.77,-0.022773,0.13826,0.99013,-40.471
> view matrix models
> #21,0.61178,0.7792,-0.13625,-13.493,-0.7897,0.6116,-0.04815,203.23,0.045815,0.13706,0.9895,-58.631
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.61178,0.7792,-0.13625,-3.561,-0.7897,0.6116,-0.04815,282.63,0.045815,0.13706,0.9895,-62.238
> view matrix models
> #21,0.61178,0.7792,-0.13625,1.5298,-0.7897,0.6116,-0.04815,286.54,0.045815,0.13706,0.9895,-68.99
> fitmap #21 inMap #2
Fit map COPI_golph_linkage3_postprocess.mrc in map emdb 3720 using 58728
points
correlation = 0.1315, correlation about mean = 0.07984, overlap = 363.5
steps = 352, shift = 41.4, angle = 14.7 degrees
Position of COPI_golph_linkage3_postprocess.mrc (#21) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.16511059 -0.95225260 0.25681409 278.85415999
0.97917838 0.18944830 0.07293179 -166.73320724
-0.11810248 0.23942499 0.96370508 -284.94197250
Axis 0.08432108 0.18987784 0.97818013
Axis point 219.08199993 126.15783603 0.00000000
Rotation angle (degrees) 80.84348286
Shift along axis -286.87023128
> select subtract #21
Nothing selected
> select add #21
2 models selected
> select subtract #21
Nothing selected
> select add #21
2 models selected
> view matrix models
> #21,0.74086,0.66295,-0.10782,2.8904,-0.6653,0.70229,-0.2533,307.02,-0.092205,0.25939,0.96136,-60.661
> view matrix models
> #21,0.74086,0.66295,-0.10782,41.238,-0.6653,0.70229,-0.2533,295.03,-0.092205,0.25939,0.96136,-61.116
> hide #14 models
> hide #3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.64157,0.66046,-0.3901,149.25,-0.76644,0.53146,-0.36072,399.61,-0.030916,0.53041,0.84717,-119.07
> view matrix models
> #21,0.62605,0.7716,-0.11263,44.28,-0.75233,0.55969,-0.34749,384.32,-0.20509,0.30228,0.93089,-33.401
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.62605,0.7716,-0.11263,159.7,-0.75233,0.55969,-0.34749,178.66,-0.20509,0.30228,0.93089,-67.969
> view matrix models
> #21,0.62605,0.7716,-0.11263,96.612,-0.75233,0.55969,-0.34749,145.01,-0.20509,0.30228,0.93089,-66.07
> ui mousemode right "rotate selected models"
> view matrix models
> #21,0.61094,0.58951,-0.52842,268.57,-0.72762,0.1551,-0.66822,339.65,-0.31196,0.79273,0.5237,-54.62
> view matrix models
> #21,0.67108,-0.25232,0.69712,132.66,0.74045,0.27512,-0.61322,-108.19,-0.037062,0.92771,0.37146,-122.86
> view matrix models
> #21,0.6657,-0.74269,0.072507,445.28,0.70491,0.59399,-0.38766,-249.48,0.24484,0.30917,0.91895,-186.99
> view matrix models
> #21,0.56881,-0.75008,-0.3374,590.28,0.70397,0.65614,-0.27188,-299.08,0.42531,-0.082869,0.90125,-124.37
> view matrix models
> #21,0.7031,-0.70799,-0.066332,465.16,0.54326,0.59501,-0.59231,-147.54,0.45881,0.38042,0.80298,-231.62
> view matrix models
> #21,0.69505,-0.58596,0.41661,296.74,0.66233,0.74727,-0.053969,-374.54,-0.2797,0.31345,0.90748,-42.142
> view matrix models
> #21,0.52953,0.81621,0.23108,12.954,-0.67392,0.57022,-0.46976,155.6,-0.51519,0.093022,0.85201,97.72
> view matrix models
> #21,0.87105,0.29814,0.39037,15.693,-0.16527,0.92628,-0.33866,-117.04,-0.46256,0.23047,0.85611,44.821
> view matrix models
> #21,0.96132,0.26759,0.065255,91.934,-0.26218,0.96162,-0.080898,-173.61,-0.084399,0.06066,0.99458,-51.273
> view matrix models
> #21,0.91601,0.39302,0.080397,65.82,-0.38782,0.91883,-0.073065,-130,-0.10259,0.035748,0.99408,-39.4
> view matrix models
> #21,0.91503,0.39345,0.088973,63.53,-0.38641,0.91825,-0.08662,-126.37,-0.11578,0.044879,0.99226,-37.777
> ui mousemode right "translate selected models"
> view matrix models
> #21,0.91503,0.39345,0.088973,-19.059,-0.38641,0.91825,-0.08662,121.8,-0.11578,0.044879,0.99226,-21.386
> view matrix models
> #21,0.91503,0.39345,0.088973,-47.686,-0.38641,0.91825,-0.08662,118.33,-0.11578,0.044879,0.99226,-1.0662
> view matrix models
> #21,0.91503,0.39345,0.088973,-64.92,-0.38641,0.91825,-0.08662,106.11,-0.11578,0.044879,0.99226,18.924
> fitmap #21 inMap #2
Fit map COPI_golph_linkage3_postprocess.mrc in map emdb 3720 using 58728
points
correlation = 0.3068, correlation about mean = 0.05618, overlap = 925.7
steps = 536, shift = 63.9, angle = 28.5 degrees
Position of COPI_golph_linkage3_postprocess.mrc (#21) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
-0.32253487 -0.83356760 0.44848222 337.87463973
0.94497750 -0.25619477 0.20342508 -53.16974935
-0.05466975 0.48941729 0.87033437 -358.85998503
Axis 0.15290911 0.26901615 0.95092014
Axis point 187.41204275 163.73321980 0.00000000
Rotation angle (degrees) 110.74427733
Shift along axis -303.88659719
> hide #!2 models
> show #!2 models
> hide #!2 models
> select subtract #21
Nothing selected
> volume #21 level 0.6057
> show #3 models
> show #4 models
> hide #4 models
> show #5 models
> show #7 models
> show #!9 models
> hide #!21 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!15 models
> show #!16 models
> show #!17 models
> show #13 models
> hide #!17 models
> hide #!16 models
> hide #13 models
> hide #!2 models
> show #!17 models
> volume #15 level 0.398
> hide #!17 models
> volume #15 level 0.2746
> show #!17 models
> hide #!15 models
> show #!15 models
> volume #15 level 0.3678
> show #3 models
> show #4 models
> hide #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #11 models
> show #13 models
> show #14 models
> hide #!17 models
> show #!2 models
> hide #!2 models
> hide #!15 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #!18 models
> show #!2 models
> hide #!2 models
> show #!20 models
> hide #!18 models
> show #!18 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!20 models
> show #!21 models
> show #!2 models
> hide #!21 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/COPI_golph_linkage4_postprocess.mrc"
Opened COPI_golph_linkage4_postprocess.mrc as #22, grid size 160,160,160,
pixel 3.4, shown at level 0.633, step 1, values float32
> volume #22 level 0.4998
> select add #22
2 models selected
> view matrix models #22,1,0,0,86.864,0,1,0,-163.53,0,0,1,-69.833
> color #22 #e0ecffff models
> color #22 #e9f5ffff models
> color #22 #b6c0c8ff models
> color #22 #b6c0c8a8 models
> ui mousemode right "rotate selected models"
> view matrix models
> #22,0.78147,0.50969,0.35989,-100.59,-0.15335,0.71601,-0.68104,160.15,-0.6048,0.47702,0.6377,73.713
> view matrix models
> #22,0.60302,0.64176,0.47383,-122.16,-0.25703,0.71861,-0.64617,177.24,-0.75519,0.26786,0.59828,183.56
> ui mousemode right "translate selected models"
> view matrix models
> #22,0.60302,0.64176,0.47383,-180.56,-0.25703,0.71861,-0.64617,159.86,-0.75519,0.26786,0.59828,231.55
> ui mousemode right "rotate selected models"
> view matrix models
> #22,0.28964,0.94666,0.14124,-78.437,-0.87363,0.32176,-0.36503,351.72,-0.391,-0.017664,0.92022,113.5
> ui mousemode right "translate selected models"
> view matrix models
> #22,0.28964,0.94666,0.14124,-122.45,-0.87363,0.32176,-0.36503,500.17,-0.391,-0.017664,0.92022,134.3
> view matrix models
> #22,0.28964,0.94666,0.14124,-182.04,-0.87363,0.32176,-0.36503,476.3,-0.391,-0.017664,0.92022,172.38
> view matrix models
> #22,0.28964,0.94666,0.14124,-66.429,-0.87363,0.32176,-0.36503,393.2,-0.391,-0.017664,0.92022,104.2
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.020676,0.93533,0.35317,-42.385,-0.88978,0.14387,-0.43312,466.54,-0.45592,-0.3232,0.82926,232.51
> view matrix models
> #22,0.22371,0.90492,0.36205,-103.37,-0.97381,0.22303,0.044274,324.54,-0.040683,-0.36247,0.93111,99.469
> view matrix models
> #22,-0.3087,0.70623,0.63713,13.335,-0.89783,0.0047913,-0.44032,508.82,-0.31402,-0.70796,0.6326,357.79
> view matrix models
> #22,0.026496,0.99882,-0.040736,45.701,-0.99955,0.02704,0.01285,394.43,0.013936,0.040377,0.99909,-45.666
> view matrix models
> #22,-0.052732,0.99411,0.094684,27.925,-0.99621,-0.0458,-0.073945,439.44,-0.069173,-0.098224,0.99276,16.677
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.052732,0.99411,0.094684,-41.077,-0.99621,-0.0458,-0.073945,493.16,-0.069173,-0.098224,0.99276,57.186
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.14698,0.89014,0.43133,-88.104,-0.98704,-0.16037,-0.005392,501.32,0.064374,-0.42653,0.90218,137.5
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.14698,0.89014,0.43133,-83.727,-0.98704,-0.16037,-0.005392,495.71,0.064374,-0.42653,0.90218,133.33
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.20349,0.87067,0.44781,-67.963,-0.91791,-0.010519,-0.39665,553.47,-0.34064,-0.49176,0.80133,291.78
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.20349,0.87067,0.44781,-69.471,-0.91791,-0.010519,-0.39665,595.62,-0.34064,-0.49176,0.80133,324.66
> view matrix models
> #22,-0.20349,0.87067,0.44781,-58.843,-0.91791,-0.010519,-0.39665,574.5,-0.34064,-0.49176,0.80133,304.63
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.20349,0.87067,0.44781,-115.69,-0.91791,-0.010519,-0.39665,427.17,-0.34064,-0.49176,0.80133,333.06
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.14719,0.55024,0.82193,-155.98,-0.98682,-0.025227,-0.15983,378.87,-0.067212,-0.83462,0.5467,428.46
> view matrix models
> #22,-0.53052,0.47552,0.70173,4.9543,-0.84215,-0.38997,-0.37242,502.71,0.096558,-0.78854,0.60735,353.05
> view matrix models
> #22,-0.6984,0.54898,0.4592,103.49,-0.70756,-0.43304,-0.55842,533.61,-0.10771,-0.71491,0.69087,363.57
> view matrix models
> #22,-0.67565,0.6076,0.41751,93.823,-0.71802,-0.41395,-0.55954,531.59,-0.16715,-0.67784,0.71596,362.14
> view matrix models
> #22,-0.80567,0.57276,-0.15112,309.47,0.22246,0.056121,-0.97333,271.31,-0.549,-0.8178,-0.17263,771.13
> view matrix models
> #22,-0.79633,0.079496,0.59961,216.04,-0.55232,-0.49969,-0.66727,542.15,0.24658,-0.86255,0.44182,382.03
> view matrix models
> #22,-0.67539,0.70693,0.21001,128.96,-0.59312,-0.68993,0.41497,280.24,0.43825,0.1557,0.88527,-80.968
> view matrix models
> #22,-0.71777,0.65524,-0.23553,288.36,-0.50949,-0.72481,-0.46376,530.76,-0.47459,-0.21287,0.85408,277.69
> view matrix models
> #22,-0.95603,0.2816,0.081864,359.89,-0.24094,-0.5951,-0.76668,513.14,-0.16718,-0.7527,0.63679,406.32
> view matrix models
> #22,-0.63322,-0.44634,-0.63231,684.79,0.66029,-0.73776,-0.14046,118.4,-0.4038,-0.50645,0.76188,366.12
> view matrix models
> #22,-0.90532,-0.34407,-0.249,615.99,0.18442,-0.84658,0.4993,85.715,-0.38259,0.4061,0.82988,91.111
> view matrix models
> #22,-0.96419,-0.26357,0.029355,526.52,0.24577,-0.84646,0.47234,77.053,-0.099647,0.46264,0.88093,-16.748
> view matrix models
> #22,-0.9526,-0.30268,-0.030562,552.02,0.25997,-0.8621,0.43496,88.669,-0.158,0.4064,0.89993,8.7874
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.9526,-0.30268,-0.030562,548.24,0.25997,-0.8621,0.43496,360.71,-0.158,0.4064,0.89993,-35.334
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.99238,-0.098069,-0.074577,516.51,0.065742,-0.93344,0.35266,457.81,-0.1042,0.34507,0.93278,-43.137
> view matrix models
> #22,-0.9771,-0.13873,-0.16136,549.49,0.090768,-0.95754,0.27364,481.28,-0.19247,0.25272,0.9482,1.4701
> view matrix models
> #22,-0.97138,-0.17322,-0.16255,557.69,0.1406,-0.97081,0.19431,495.13,-0.19147,0.16589,0.96738,19.115
> fitmap #22 inMap #2
Fit map COPI_golph_linkage4_postprocess.mrc in map emdb 3720 using 142370
points
correlation = 0.105, correlation about mean = 0.1014, overlap = 418.9
steps = 456, shift = 43.7, angle = 18 degrees
Position of COPI_golph_linkage4_postprocess.mrc (#22) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.18065176 0.97553304 -0.12530053 -137.14370480
-0.98279485 0.18402446 0.01578860 200.53879943
0.03846067 0.12029247 0.99199319 -248.35089122
Axis 0.05310318 -0.08321454 -0.99511577
Axis point 56.64088445 200.30404249 0.00000000
Rotation angle (degrees) 79.72722380
Shift along axis 223.16737748
> fitmap #22 inMap #2
Fit map COPI_golph_linkage4_postprocess.mrc in map emdb 3720 using 142370
points
correlation = 0.105, correlation about mean = 0.1014, overlap = 418.9
steps = 84, shift = 0.0353, angle = 0.0059 degrees
Position of COPI_golph_linkage4_postprocess.mrc (#22) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.18070188 0.97552181 -0.12531571 -137.12458394
-0.98278214 0.18408535 0.01586940 200.47306053
0.03854973 0.12029041 0.99198998 -248.35909451
Axis 0.05306161 -0.08326834 -0.99511349
Axis point 56.63115992 200.26664882 0.00000000
Rotation angle (degrees) 79.72408513
Shift along axis 223.17637501
> view matrix models
> #22,-0.93936,-0.33863,-0.054164,554.37,0.30927,-0.90475,0.29287,444.96,-0.14818,0.25836,0.95462,-2.8011
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.93936,-0.33863,-0.054164,564.72,0.30927,-0.90475,0.29287,411.18,-0.14818,0.25836,0.95462,-19.097
> view matrix models
> #22,-0.93936,-0.33863,-0.054164,564.29,0.30927,-0.90475,0.29287,411.41,-0.14818,0.25836,0.95462,-18.8
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.89677,-0.28818,-0.33579,623.47,0.18111,-0.93142,0.31568,446.76,-0.40373,0.22228,0.88746,80.848
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.89677,-0.28818,-0.33579,649.35,0.18111,-0.93142,0.31568,428.9,-0.40373,0.22228,0.88746,53.43
> view matrix models
> #22,-0.89677,-0.28818,-0.33579,645.65,0.18111,-0.93142,0.31568,429.61,-0.40373,0.22228,0.88746,54.541
> view matrix models
> #22,-0.89677,-0.28818,-0.33579,645.51,0.18111,-0.93142,0.31568,435.86,-0.40373,0.22228,0.88746,31.241
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.8453,-0.32892,-0.42105,668.18,0.20796,-0.92845,0.30779,430.11,-0.49216,0.17261,0.85322,79.168
> view matrix models
> #22,-0.8556,-0.21068,-0.47282,654.29,0.10806,-0.966,0.23488,489.46,-0.50623,0.14987,0.84927,90.385
> view matrix models
> #22,-0.81311,-0.2328,-0.53354,666.97,0.13587,-0.96713,0.21493,488.18,-0.56604,0.10227,0.81801,129.05
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.81311,-0.2328,-0.53354,684.47,0.13587,-0.96713,0.21493,485.98,-0.56604,0.10227,0.81801,126.21
> ui mousemode right "rotate selected models"
> view matrix models
> #22,-0.76856,-0.25226,-0.58794,693.97,0.15952,-0.96552,0.20574,481.85,-0.61957,0.064337,0.7823,161.86
> ui mousemode right "translate selected models"
> view matrix models
> #22,-0.76856,-0.25226,-0.58794,703.77,0.15952,-0.96552,0.20574,483.66,-0.61957,0.064337,0.7823,160.74
> fitmap #22 inMap #2
Fit map COPI_golph_linkage4_postprocess.mrc in map emdb 3720 using 142370
points
correlation = 0.3059, correlation about mean = 0.2109, overlap = 1480
steps = 204, shift = 13.8, angle = 5.22 degrees
Position of COPI_golph_linkage4_postprocess.mrc (#22) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.28958463 0.93486676 0.20534089 -256.62492522
-0.76616902 0.35499199 -0.53569181 321.19087280
-0.57369484 -0.00219771 0.81906617 -72.53866158
Axis 0.27421718 0.40042613 -0.87433624
Axis point 57.62625816 353.98226828 0.00000000
Rotation angle (degrees) 76.59567126
Shift along axis 121.66543499
> fitmap #22 inMap #2
Fit map COPI_golph_linkage4_postprocess.mrc in map emdb 3720 using 142370
points
correlation = 0.3059, correlation about mean = 0.2109, overlap = 1480
steps = 88, shift = 0.0174, angle = 0.00731 degrees
Position of COPI_golph_linkage4_postprocess.mrc (#22) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.28964240 0.93485647 0.20530625 -256.62582679
-0.76622235 0.35501920 -0.53559749 321.16894392
-0.57359444 -0.00217850 0.81913654 -72.57595607
Axis 0.27418379 0.40036434 -0.87437501
Axis point 57.61447724 353.97470394 0.00000000
Rotation angle (degrees) 76.59109653
Shift along axis 121.68055268
> fitmap #22 inMap #2
Fit map COPI_golph_linkage4_postprocess.mrc in map emdb 3720 using 142370
points
correlation = 0.3059, correlation about mean = 0.2109, overlap = 1480
steps = 100, shift = 0.00774, angle = 0.00167 degrees
Position of COPI_golph_linkage4_postprocess.mrc (#22) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.28966773 0.93485155 0.20529292 -256.62196414
-0.76621992 0.35503229 -0.53559230 321.16811315
-0.57358491 -0.00215572 0.81914327 -72.58416307
Axis 0.27419434 0.40035480 -0.87437606
Axis point 57.61876662 353.97615488 0.00000000
Rotation angle (degrees) 76.58976647
Shift along axis 121.68275949
> view matrix models
> #22,-0.78276,-0.20228,-0.58853,689.39,0.16549,-0.97931,0.11649,525.29,-0.59992,-0.0062104,0.80004,164.24
> fitmap #22 inMap #2
Fit map COPI_golph_linkage4_postprocess.mrc in map emdb 3720 using 142370
points
correlation = 0.3059, correlation about mean = 0.2109, overlap = 1480
steps = 184, shift = 0.712, angle = 0.00605 degrees
Position of COPI_golph_linkage4_postprocess.mrc (#22) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.28964597 0.93484993 0.20533098 -256.64138080
-0.76616354 0.35503650 -0.53567015 321.20226277
-0.57367120 -0.00216241 0.81908282 -72.54553467
Axis 0.27422830 0.40041489 -0.87433789
Axis point 57.63823332 354.01292382 0.00000000
Rotation angle (degrees) 76.59206352
Shift along axis 121.66514833
> fitmap #22 inMap #2
Fit map COPI_golph_linkage4_postprocess.mrc in map emdb 3720 using 142370
points
correlation = 0.3059, correlation about mean = 0.2109, overlap = 1480
steps = 148, shift = 0.0325, angle = 0.00987 degrees
Position of COPI_golph_linkage4_postprocess.mrc (#22) relative to emdb 3720
(#2) coordinates:
Matrix rotation and translation
0.28961107 0.93485553 0.20535473 -256.63781807
-0.76607236 0.35502191 -0.53581021 321.21240562
-0.57381057 -0.00214001 0.81898525 -72.51270302
Axis 0.27430686 0.40049152 -0.87427815
Axis point 57.64670127 354.01889608 0.00000000
Rotation angle (degrees) 76.59639446
Shift along axis 121.64160182
> select subtract #22
Nothing selected
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/Linkage_4_fitting_Golph_AF_RT.cxs"
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/References/emd_2989_2015_linkage4.map"
Opened emd_2989_2015_linkage4.map as #23, grid size 200,200,200, pixel 2.02,
shown at level 3.51, step 1, values float32
> select add #23
2 models selected
> hide #14 models
> hide #13 models
> hide #11 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #3 models
> hide #!2 models
> volume #23 level 1.736
> view matrix models #23,1,0,0,295.97,0,1,0,347.81,0,0,1,255.97
> view matrix models #23,1,0,0,252.37,0,1,0,338.98,0,0,1,288.4
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.34072,0.91035,-0.23488,246.73,-0.9102,-0.38198,-0.16012,331.16,-0.23548,0.15924,0.95875,287.41
> view matrix models
> #23,-0.90118,0.19951,-0.3848,241.1,-0.34473,-0.86806,0.35727,342.26,-0.26275,0.45462,0.85105,285.65
> view matrix models
> #23,-0.85105,0.18622,-0.49095,238.9,-0.45999,-0.7153,0.52607,345.96,-0.25321,0.67355,0.69442,282.76
> view matrix models
> #23,-0.94655,-0.003175,-0.32253,241.94,-0.056235,-0.98301,0.17471,338.66,-0.31761,0.18351,0.93029,286.7
> view matrix models
> #23,-0.80832,0.00038823,-0.58875,236.52,-0.12002,-0.97911,0.16414,338.33,-0.57638,0.20334,0.79148,283.31
> view matrix models
> #23,-0.93595,0.069976,-0.34511,241.63,-0.11716,-0.9861,0.11781,337.33,-0.33207,0.1507,0.93114,286.63
> view matrix models
> #23,-0.92252,-0.0074895,-0.38588,240.63,-0.12049,-0.94425,0.30639,341.43,-0.36666,0.32914,0.87019,285.62
> view matrix models
> #23,-0.83624,0.18925,-0.51467,238.43,-0.076264,-0.96958,-0.2326,329.96,-0.54303,-0.15526,0.82524,283.37
> view matrix models
> #23,-0.88583,0.03525,-0.46266,239.14,-0.093997,-0.99007,0.10454,337.08,-0.45438,0.13609,0.88035,285.29
> view matrix models
> #23,-0.79009,-0.25551,-0.5572,236.72,0.21743,-0.9667,0.13498,338.35,-0.57313,-0.014509,0.81933,283.47
> fitmap #23 inMap #22
Fit map emd_2989_2015_linkage4.map in map COPI_golph_linkage4_postprocess.mrc
using 407794 points
correlation = 0.9534, correlation about mean = 0.4429, overlap = 6.694e+05
steps = 84, shift = 30.2, angle = 4.21 degrees
Position of emd_2989_2015_linkage4.map (#23) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
0.99992754 -0.01202932 -0.00045014 272.13051854
0.01202914 0.99992757 -0.00039616 272.13870425
0.00045487 0.00039072 0.99999982 362.71293920
Axis 0.03266654 -0.03757050 0.99875991
Axis point -23619.40313077 21784.41257175 0.00000000
Rotation angle (degrees) 0.69009646
Shift along axis 360.92831745
> select subtract #23
Nothing selected
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/References/emd_3724_2017_linkage4.map"
Opened emd_3724_2017_linkage4.map as #24, grid size 212,212,212, pixel 1.78,
shown at level 0.0902, step 1, values float32
> hide #!23 models
> select add #24
2 models selected
> volume #24 level 0.05394
> view matrix models
> #24,0.78919,0.23102,-0.56904,99.742,-0.57051,0.61881,-0.53999,277.58,0.22738,0.7508,0.62016,-115.18
> view matrix models
> #24,0.78489,-0.47897,-0.39311,202.3,-0.091465,0.53791,-0.83803,256.77,0.61285,0.69372,0.37839,-133.08
> view matrix models
> #24,0.83222,-0.29524,-0.46929,172.63,-0.21993,0.60119,-0.76824,256.36,0.50895,0.74256,0.4354,-133.08
> view matrix models
> #24,0.95159,-0.26646,-0.15322,87.201,0.21686,0.93528,-0.27968,22.214,0.21783,0.23291,0.94779,-75.429
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.95159,-0.26646,-0.15322,153.28,0.21686,0.93528,-0.27968,174.12,0.21783,0.23291,0.94779,46.043
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.71759,-0.051309,-0.69458,255.34,0.34165,0.89498,0.28686,55.113,0.60691,-0.44315,0.65975,152.49
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.71759,-0.051309,-0.69458,221.99,0.34165,0.89498,0.28686,49.003,0.60691,-0.44315,0.65975,138.27
> fitmap #24 inMap #22
Fit map emd_3724_2017_linkage4.map in map COPI_golph_linkage4_postprocess.mrc
using 315646 points
correlation = 0.9467, correlation about mean = 0.3516, overlap = 1.568e+04
steps = 104, shift = 11.9, angle = 14.3 degrees
Position of emd_3724_2017_linkage4.map (#24) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
-0.85806817 0.51353579 0.00010753 337.14467445
-0.51353580 -0.85806817 -0.00005229 530.96482694
0.00006542 -0.00010009 1.00000000 166.67646029
Axis -0.00004654 0.00004100 -1.00000000
Axis point 241.94384893 218.89661548 0.00000000
Rotation angle (degrees) 149.10036440
Shift along axis -166.67037970
> select subtract #24
Nothing selected
> select add #24
2 models selected
> select subtract #24
Nothing selected
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!2 models
> hide #!22 models
> volume #24 level 0.03927
> show #!22 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!2 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!21 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> hide #!21 models
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #!2 models
> show #!2 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/References/emd_3720_2017_leaf.map"
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.226, step 1, values float32
> volume #25 level 0.1454
> color #2 #929292ff models
> color #2 #73fdffff models
> color #2 #fffc79ff models
> color #2 #999999ff models
> color #2 #fffc79ff models
> color #2 #ffffb0ff models
> color #2 #f2ffbaff models
> color #2 #fcffcfff models
> color #2 #f2ffaeff models
> color #2 #ffd8f4ff models
> color #2 #fffccaff models
> color #2 #f7ffcdff models
> color #2 #fffabeff models
> color #25 #e9ebb8ff models
> color #25 #deeb9eff models
> color #25 #ebf9a7ff models
> color #25 #f3f9a6ff models
> color #25 #f3f9aaff models
> show #!24 models
> select add #25
2 models selected
> view matrix models #25,1,0,0,-41.912,0,1,0,34.291,0,0,1,2.5166
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.96426,-0.23087,-0.12999,5.6177,0.18956,0.94394,-0.27028,52.776,0.1851,0.23598,0.95397,-40.863
> view matrix models
> #25,0.91729,-0.16267,-0.36348,31.464,0.012177,0.92379,-0.3827,89.007,0.39803,0.34662,0.84937,-65.244
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.91729,-0.16267,-0.36348,126.12,0.012177,0.92379,-0.3827,161.5,0.39803,0.34662,0.84937,124.78
> hide #!24 models
> view matrix models
> #25,0.91729,-0.16267,-0.36348,7.3962,0.012177,0.92379,-0.3827,284.85,0.39803,0.34662,0.84937,98.36
> view matrix models
> #25,0.91729,-0.16267,-0.36348,27.37,0.012177,0.92379,-0.3827,196.31,0.39803,0.34662,0.84937,88.723
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.65529,0.18882,-0.7314,60.216,-0.017341,0.97176,0.23534,118.01,0.75518,-0.14153,0.64006,132.33
> view matrix models
> #25,0.95499,-0.28566,0.079919,-16.677,0.064815,0.46387,0.88353,89.693,-0.28946,-0.83858,0.46151,355.29
> view matrix models
> #25,0.33031,-0.036013,-0.94319,149.72,0.85537,-0.41104,0.31525,174.59,-0.39904,-0.9109,-0.10497,445.86
> view matrix models
> #25,-0.77549,-0.4415,0.45133,151.62,0.46194,-0.88406,-0.071088,322.85,0.43039,0.15336,0.88952,103.19
> view matrix models
> #25,-0.84286,-0.41501,0.34258,169.42,0.25572,-0.86901,-0.42358,387.63,0.4735,-0.26942,0.83858,154.99
> view matrix models
> #25,0.12351,-0.9746,-0.18682,192.09,0.73033,0.21673,-0.6478,232.12,0.67183,-0.056431,0.73855,119.49
> view matrix models
> #25,0.010832,-0.96658,-0.25615,212.37,0.80335,0.16094,-0.57335,221.39,0.59541,-0.19957,0.77824,140.31
> view matrix models
> #25,-0.48903,-0.59127,-0.64129,271.34,0.39209,0.50772,-0.76712,250.25,0.77917,-0.62659,-0.016461,268.1
> view matrix models
> #25,0.021881,-0.9866,-0.16166,201.9,0.85769,0.10161,-0.50403,213.82,0.51371,-0.12763,0.84842,132.34
> view matrix models
> #25,0.1303,-0.99144,0.0079275,169.41,0.81674,0.11186,0.56605,85.788,-0.5621,-0.067281,0.82433,249.53
> view matrix models
> #25,0.0062707,0.97016,-0.24238,-19.761,0.46687,0.2115,0.85866,77.46,0.8843,-0.11854,-0.45161,249.09
> view matrix models
> #25,0.41662,0.7801,0.46676,-130.51,-0.52765,-0.2106,0.82294,244.44,0.74028,-0.58914,0.32388,226.22
> view matrix models
> #25,0.4615,0.5753,0.67531,-136.77,-0.676,0.721,-0.15225,269.86,-0.57449,-0.38625,0.72165,301.57
> view matrix models
> #25,0.43916,0.89229,-0.10472,-76.243,-0.89059,0.44771,0.079981,298.15,0.11825,0.058135,0.99128,137.27
> view matrix models
> #25,0.20078,0.35184,0.91427,-110.04,-0.97403,0.17138,0.14795,332.17,-0.10463,-0.92024,0.37712,354.53
> view matrix models
> #25,-0.84154,0.1305,0.5242,81.912,-0.53283,-0.040844,-0.84523,429.66,-0.088896,-0.99061,0.10391,394.7
> show #!24 models
> view matrix models
> #25,-0.90431,0.37116,0.21085,98.786,-0.42686,-0.78377,-0.4511,457.89,-0.002175,-0.49794,0.86721,232.42
> hide #!24 models
> view matrix models
> #25,-0.95634,-0.1526,-0.24927,223.63,-0.11247,-0.59506,0.79577,246.76,-0.26976,0.78906,0.55191,147.87
> view matrix models
> #25,-0.89731,-0.0033763,-0.44139,222.76,0.076106,-0.98618,-0.14717,387.92,-0.43479,-0.16565,0.88516,239.42
> view matrix models
> #25,-0.87865,-0.056022,-0.47416,230.96,0.04276,-0.99833,0.038717,370.31,-0.47554,0.013744,0.87959,223.31
> view matrix models
> #25,-0.91901,-0.029536,-0.39314,222.41,0.024052,-0.99953,0.018868,375,-0.39351,0.0078841,0.91929,209.87
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.91901,-0.029536,-0.39314,470.33,0.024052,-0.99953,0.018868,458.63,-0.39351,0.0078841,0.91929,197.95
> view matrix models
> #25,-0.91901,-0.029536,-0.39314,464.34,0.024052,-0.99953,0.018868,465.68,-0.39351,0.0078841,0.91929,268.78
> view matrix models
> #25,-0.91901,-0.029536,-0.39314,527.77,0.024052,-0.99953,0.018868,479.54,-0.39351,0.0078841,0.91929,251.92
> view matrix models
> #25,-0.91901,-0.029536,-0.39314,593.7,0.024052,-0.99953,0.018868,474.77,-0.39351,0.0078841,0.91929,75.514
> view matrix models
> #25,-0.91901,-0.029536,-0.39314,598.58,0.024052,-0.99953,0.018868,483.44,-0.39351,0.0078841,0.91929,137.26
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.76838,-0.51111,-0.38516,638.02,-0.034123,-0.56825,0.82215,339.92,-0.63908,0.64487,0.41919,150.44
> view matrix models
> #25,-0.99982,0.017582,-0.0068337,554.63,-0.013343,-0.40312,0.91505,306.47,0.013334,0.91498,0.40328,46.544
> view matrix models
> #25,-0.47493,-0.79027,0.38719,543.33,0.53905,-0.60902,-0.58183,452.52,0.69561,-0.067615,0.71523,48.391
> view matrix models
> #25,-0.19314,-0.95942,0.20546,554.01,0.76506,-0.27837,-0.58068,387.44,0.61431,0.045032,0.78778,35.225
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.19314,-0.95942,0.20546,220.47,0.76506,-0.27837,-0.58068,240.93,0.61431,0.045032,0.78778,244.62
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.30827,-0.90601,-0.29002,287.95,0.66898,0.010287,-0.74321,237.32,0.67634,-0.42312,0.60293,316.15
> view matrix models
> #25,-0.4948,-0.4633,-0.73521,310.89,0.59277,0.43871,-0.67539,186.5,0.63545,-0.76999,0.057559,429.11
> view matrix models
> #25,0.65402,-0.7261,0.21223,96.193,0.1317,-0.16698,-0.97712,347.83,0.74493,0.66701,-0.013583,254.13
> view matrix models
> #25,0.4121,-0.52999,0.74113,35.154,0.69997,0.70488,0.11486,45.605,-0.58328,0.47144,0.66146,344.46
> view matrix models
> #25,0.90161,-0.29113,-0.31992,81.737,0.36619,0.90739,0.20626,47.904,0.23025,-0.30312,0.92472,312.66
> view matrix models
> #25,0.88191,-0.075398,-0.46534,76.094,-0.061894,0.96006,-0.27286,148.79,0.46733,0.26944,0.84202,227.79
> view matrix models
> #25,0.76612,-0.34609,0.54156,-2.224,0.40585,0.91389,0.0098876,66.772,-0.49835,0.21222,0.8406,343.78
> view matrix models
> #25,0.54482,0.50226,0.67149,-94.367,-0.33773,0.86439,-0.37251,203.57,-0.76753,-0.023832,0.64057,426.88
> view matrix models
> #25,0.64577,0.53526,0.5445,-94.099,-0.46545,0.84127,-0.27498,208.76,-0.60526,-0.075863,0.79241,396.12
> show #!24 models
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.67418,0.66192,-0.32764,-5.2941,-0.71997,0.68792,-0.09167,233.27,0.16471,0.29769,0.94035,246.5
> view matrix models
> #25,0.5916,0.74324,-0.31243,-7.538,-0.64796,0.6689,0.36431,171.4,0.47975,-0.013081,0.87731,255.74
> view matrix models
> #25,0.7763,0.62354,-0.092497,-41.124,-0.6114,0.78051,0.13034,182.7,0.15347,-0.044628,0.98715,282.84
> view matrix models
> #25,0.51427,0.8541,0.07768,-59.943,-0.66054,0.33669,0.67106,174.76,0.547,-0.39642,0.73732,311.05
> view matrix models
> #25,0.76581,0.64046,0.057799,-60.417,-0.62728,0.76379,-0.15211,221.18,-0.14157,0.080233,0.98667,301.31
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.76581,0.64046,0.057799,-226.92,-0.62728,0.76379,-0.15211,234.51,-0.14157,0.080233,0.98667,258.34
> view matrix models
> #25,0.76581,0.64046,0.057799,-170.52,-0.62728,0.76379,-0.15211,170.2,-0.14157,0.080233,0.98667,62.307
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.058443,0.83177,-0.55204,-38.594,-0.88813,0.29583,0.35171,193.56,0.45585,0.46973,0.75601,-23.243
> view matrix models
> #25,0.14464,0.67021,-0.72794,-7.4537,-0.73788,0.56321,0.37192,142.24,0.65925,0.48334,0.576,-25.715
> view matrix models
> #25,0.14867,0.52468,-0.83822,22.99,-0.85703,0.49125,0.15548,190.85,0.49335,0.69526,0.5227,-25.715
> view matrix models
> #25,0.20723,0.47079,-0.85756,25.183,-0.80501,0.58016,0.12397,178.25,0.55589,0.66466,0.49921,-26.24
> view matrix models
> #25,0.20617,0.46946,-0.85855,25.582,-0.80524,0.57989,0.12372,178.34,0.55595,0.66583,0.49758,-26.186
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.20617,0.46946,-0.85855,45.406,-0.80524,0.57989,0.12372,368.39,0.55595,0.66583,0.49758,47.974
> view matrix models
> #25,0.20617,0.46946,-0.85855,107.16,-0.80524,0.57989,0.12372,347.44,0.55595,0.66583,0.49758,7.5907
> view matrix models
> #25,0.20617,0.46946,-0.85855,105.66,-0.80524,0.57989,0.12372,402.82,0.55595,0.66583,0.49758,12.549
> view matrix models
> #25,0.20617,0.46946,-0.85855,103.33,-0.80524,0.57989,0.12372,417.75,0.55595,0.66583,0.49758,5.057
> view matrix models
> #25,0.20617,0.46946,-0.85855,117.56,-0.80524,0.57989,0.12372,396.23,0.55595,0.66583,0.49758,-6.4383
> view matrix models
> #25,0.20617,0.46946,-0.85855,118.34,-0.80524,0.57989,0.12372,406.81,0.55595,0.66583,0.49758,-5.2511
> view matrix models
> #25,0.20617,0.46946,-0.85855,141.83,-0.80524,0.57989,0.12372,379.88,0.55595,0.66583,0.49758,14.412
> hide #!24 models
> show #!22 models
> view matrix models
> #25,0.20617,0.46946,-0.85855,106.87,-0.80524,0.57989,0.12372,394.09,0.55595,0.66583,0.49758,-16.511
> fitmap #25 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 65799 points
correlation = 0.8265, correlation about mean = 0.04987, overlap = 5750
steps = 204, shift = 81.5, angle = 36.7 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
-0.88574578 -0.10173812 0.45288384 439.94615531
0.24571279 -0.93053807 0.27152188 352.11709037
0.39380153 0.35177871 0.84921852 134.03743636
Axis 0.22203459 0.16345421 0.96124053
Axis point 190.00483138 182.52401271 0.00000000
Rotation angle (degrees) 169.58768934
Shift along axis 284.08050099
> view matrix models
> #25,0.41163,0.060752,-0.90932,179.23,-0.34128,0.93545,-0.091991,326.68,0.84504,0.3482,0.40579,-31.482
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.46191,-0.20129,-0.86379,199.21,-0.2006,0.92496,-0.32281,340.4,0.86395,0.32238,0.38687,-28.213
> view matrix models
> #25,0.57997,0.041302,-0.81359,150.79,-0.50212,0.80457,-0.31709,388.09,0.64149,0.59242,0.48736,-47.649
> hide #!22 models
> show #!22 models
> hide #!25 models
> show #!25 models
> view matrix models
> #25,0.62791,-0.011837,-0.7782,147.37,-0.51511,0.74323,-0.42694,410.36,0.58343,0.66893,0.46058,-46.93
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.62791,-0.011837,-0.7782,149.03,-0.51511,0.74323,-0.42694,375.5,0.58343,0.66893,0.46058,-40.828
> view matrix models
> #25,0.62791,-0.011837,-0.7782,153.93,-0.51511,0.74323,-0.42694,370.82,0.58343,0.66893,0.46058,-36.477
> view matrix models
> #25,0.62791,-0.011837,-0.7782,166,-0.51511,0.74323,-0.42694,385.93,0.58343,0.66893,0.46058,16.622
> fitmap #25 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 65799 points
correlation = 0.8267, correlation about mean = 0.05035, overlap = 5750
steps = 144, shift = 41.1, angle = 26.6 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
-0.88557913 -0.10013770 0.45356593 439.65237921
0.24461362 -0.93064817 0.27213628 352.23089454
0.39485921 0.35194662 0.84865764 133.94323367
Axis 0.22249542 0.16366274 0.96109848
Axis point 189.94292506 182.41568594 0.00000000
Rotation angle (degrees) 169.66793830
Shift along axis 284.20035559
> view matrix models
> #25,0.4111,0.059423,-0.90965,177.79,-0.34005,0.93584,-0.092545,262.62,0.84579,0.34737,0.40493,5.601
> view matrix models
> #25,0.4111,0.059423,-0.90965,178.44,-0.34005,0.93584,-0.092545,284.58,0.84579,0.34737,0.40493,9.3357
> view matrix models
> #25,0.4111,0.059423,-0.90965,175.29,-0.34005,0.93584,-0.092545,289.9,0.84579,0.34737,0.40493,4.0216
> view matrix models
> #25,0.4111,0.059423,-0.90965,20.079,-0.34005,0.93584,-0.092545,43.072,0.84579,0.34737,0.40493,-77.647
> hide #!22 models
> show #!22 models
> view matrix models
> #25,0.4111,0.059423,-0.90965,316.66,-0.34005,0.93584,-0.092545,-42.739,0.84579,0.34737,0.40493,215.63
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.68725,-0.081414,-0.72185,279.22,-0.55997,0.57362,-0.59783,87.337,0.46273,0.81507,0.34863,210.01
> view matrix models
> #25,0.65499,-0.071784,-0.75222,285.44,-0.60503,0.54655,-0.57898,93.337,0.45269,0.83435,0.31455,213.03
> view matrix models
> #25,-0.25359,-0.95698,0.14101,383.84,0.54222,-0.019905,0.84,-142.89,-0.80106,0.28947,0.52394,393.8
> view matrix models
> #25,0.10223,-0.9479,0.30171,322.86,0.79835,0.25912,0.5436,-168.67,-0.59346,0.1853,0.78325,350.94
> view matrix models
> #25,0.54789,-0.78857,0.27923,256.32,0.80996,0.58354,0.058703,-149.11,-0.20923,0.194,0.95843,285.02
> view matrix models
> #25,0.65616,-0.56688,-0.4981,313.14,0.74969,0.41436,0.51601,-178.3,-0.086123,-0.71201,0.69687,411.29
> view matrix models
> #25,0.29889,-0.25568,-0.9194,368.09,0.91319,0.35632,0.19778,-150.75,0.27703,-0.8987,0.33998,436.39
> view matrix models
> #25,0.17207,-0.32966,-0.92829,392.32,0.97418,0.19675,0.11071,-127.91,0.14614,-0.92337,0.355,452.26
> view matrix models
> #25,0.31825,-0.24155,-0.91672,363.89,0.89993,0.38101,0.21203,-153.95,0.29806,-0.89246,0.33863,433.44
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.31825,-0.24155,-0.91672,230.47,0.89993,0.38101,0.21203,185.62,0.29806,-0.89246,0.33863,222.8
> view matrix models
> #25,0.31825,-0.24155,-0.91672,230.82,0.89993,0.38101,0.21203,189.52,0.29806,-0.89246,0.33863,231.16
> fitmap #25 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 65799 points
correlation = 0.9378, correlation about mean = 0.08362, overlap = 8320
steps = 68, shift = 3.58, angle = 3.59 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
-0.30044297 0.76040022 0.57578255 266.90286957
-0.93094345 -0.36514623 -0.00353977 420.26956071
0.20755318 -0.53708449 0.81759522 283.85937535
Axis -0.29456010 0.20329257 -0.93375933
Axis point 249.68421694 176.04374912 0.00000000
Rotation angle (degrees) 115.08719265
Shift along axis -258.23759378
> select subtract #25
Nothing selected
> select add #25
2 models selected
> select subtract #25
Nothing selected
> select add #25
2 models selected
> select subtract #25
Nothing selected
> select add #25
2 models selected
> select subtract #25
Nothing selected
> hide #!25 models
> show #!25 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/References/emd_3720_2017_leaf.map"
Opened emd_3720_2017_leaf.map as #26, grid size 128,128,128, pixel 1.78, shown
at level 0.226, step 1, values float32
> volume #26 level 0.1148
> select add #26
2 models selected
> view matrix models #26,1,0,0,96.524,0,1,0,-184.96,0,0,1,89.501
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.13949,-0.21888,0.96573,137.67,-0.988,0.096085,-0.12093,49.163,-0.066322,-0.97101,-0.22966,358.18
> view matrix models
> #26,0.094026,-0.16046,0.98255,102.27,-0.83889,-0.54424,-0.0086031,95.53,0.53612,-0.82344,-0.18578,267.17
> view matrix models
> #26,0.5468,0.51282,-0.66183,164.68,-0.33482,0.85845,0.38854,-176.01,0.7674,0.0091376,0.6411,43.903
> view matrix models
> #26,0.24967,0.4646,-0.84959,226.24,-0.32688,0.86631,0.37769,-176.57,0.91149,0.18342,0.36816,38.987
> view matrix models
> #26,0.40334,0.60908,-0.68289,171.9,-0.36513,0.79143,0.49023,-176.57,0.83904,0.051609,0.54161,42.463
> view matrix models
> #26,0.95778,-0.020064,-0.28681,137.56,-0.047641,0.9727,-0.22714,-149.49,0.28353,0.23122,0.93067,37.962
> view matrix models
> #26,0.1681,-0.2563,-0.95187,333.68,-0.078132,0.95911,-0.27204,-139.11,0.98267,0.1201,0.1412,65.286
> view matrix models
> #26,0.1449,-0.40682,-0.90194,348.4,0.35155,0.87325,-0.3374,-169.78,0.92489,-0.26819,0.26955,103.07
> view matrix models
> #26,-0.056096,-0.592,-0.80398,381.72,0.91057,0.29996,-0.28441,-170.82,0.40954,-0.74804,0.52223,188.92
> view matrix models
> #26,-0.39145,-0.53188,-0.75091,406.23,0.79975,-0.60028,0.008276,-85.265,-0.45516,-0.5973,0.66035,252.49
> view matrix models
> #26,-0.25922,-0.59649,-0.75961,400.01,0.9591,-0.25156,-0.12977,-128.68,-0.11368,-0.76218,0.63731,236.25
> view matrix models
> #26,0.44596,-0.32102,-0.8355,296.23,0.84165,-0.1672,0.51349,-201.39,-0.30454,-0.9322,0.19562,330.31
> view matrix models
> #26,0.33725,-0.27315,-0.90092,310.53,0.73746,-0.51819,0.43317,-138.18,-0.58516,-0.81048,0.026681,367.48
> view matrix models
> #26,-0.2791,-0.21998,-0.93472,377.95,0.87927,-0.44982,-0.15668,-92.772,-0.38599,-0.86561,0.31897,317.01
> view matrix models
> #26,-0.28495,-0.21552,-0.934,377.99,0.8701,-0.46696,-0.1577,-89.566,-0.40215,-0.85761,0.32059,317.7
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.28495,-0.21552,-0.934,380.88,0.8701,-0.46696,-0.1577,251.66,-0.40215,-0.85761,0.32059,386.05
> view matrix models
> #26,-0.28495,-0.21552,-0.934,480.26,0.8701,-0.46696,-0.1577,-37.198,-0.40215,-0.85761,0.32059,507.75
> hide #!22 models
> show #!24 models
> color #24 #e2cefcff models
> color #24 #e7d8fcff models
> color #24 #e7d8fcc7 models
> color #26 #eaeab5ff models
> view matrix models
> #26,-0.28495,-0.21552,-0.934,388,0.8701,-0.46696,-0.1577,-4.1271,-0.40215,-0.85761,0.32059,407.06
> view matrix models
> #26,-0.28495,-0.21552,-0.934,462.9,0.8701,-0.46696,-0.1577,-9.4884,-0.40215,-0.85761,0.32059,495.83
> view matrix models
> #26,-0.28495,-0.21552,-0.934,320.61,0.8701,-0.46696,-0.1577,155.28,-0.40215,-0.85761,0.32059,477.73
> view matrix models
> #26,-0.28495,-0.21552,-0.934,322.5,0.8701,-0.46696,-0.1577,214.78,-0.40215,-0.85761,0.32059,441.07
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.57986,-0.30806,-0.75423,345.72,0.3439,-0.93179,0.11618,297.56,-0.73858,-0.19201,0.64625,361.19
> view matrix models
> #26,-0.75763,-0.18356,-0.62634,335.87,0.32369,-0.93898,-0.11636,328.15,-0.56676,-0.2909,0.77082,338.85
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.75763,-0.18356,-0.62634,349.47,0.32369,-0.93898,-0.11636,391.07,-0.56676,-0.2909,0.77082,345.79
> view matrix models
> #26,-0.75763,-0.18356,-0.62634,358.5,0.32369,-0.93898,-0.11636,366.64,-0.56676,-0.2909,0.77082,306.11
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.62073,-0.6716,-0.40454,375.13,0.23861,-0.65332,0.7185,243.59,-0.74684,0.34947,0.56578,274.18
> view matrix models
> #26,-0.52014,-0.37907,-0.76535,371.38,0.27944,-0.92232,0.26691,324.42,-0.80707,-0.075042,0.58567,329.37
> hide #!25 models
> hide #!2 models
> view matrix models
> #26,-0.47579,0.24569,-0.84455,301.06,0.24709,-0.88419,-0.39642,401.83,-0.84414,-0.39729,0.35998,398.71
> view matrix models
> #26,-0.52333,0.18217,-0.83243,312.6,0.24078,-0.90546,-0.34952,399.55,-0.81741,-0.38334,0.42999,385.76
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.52333,0.18217,-0.83243,322.46,0.24078,-0.90546,-0.34952,382.47,-0.81741,-0.38334,0.42999,399.23
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.7351,0.33096,-0.59168,300.24,0.26758,-0.66025,-0.70176,391.72,-0.62292,-0.67419,0.3968,415.88
> view matrix models
> #26,-0.35108,0.6519,-0.67214,227.92,0.22599,-0.63762,-0.73646,397.82,-0.90867,-0.41045,0.076532,454.52
> view matrix models
> #26,-0.87619,0.10208,-0.47103,329.31,0.3082,-0.63271,-0.71042,384.85,-0.37054,-0.76763,0.52291,383.59
> view matrix models
> #26,-0.63742,-0.76569,0.086096,340.2,0.69136,-0.61769,-0.37481,300.06,0.34017,-0.17939,0.9231,185.61
> view matrix models
> #26,0.36742,-0.92496,-0.097251,267.12,0.48645,0.10199,0.86774,90.596,-0.7927,-0.36613,0.48742,387.6
> view matrix models
> #26,-0.035903,-0.94768,-0.31719,341.46,0.85844,-0.19175,0.47573,129.86,-0.51166,-0.25521,0.82041,303.22
> view matrix models
> #26,0.49042,-0.85306,-0.17826,254.17,0.41024,0.045507,0.91084,100.88,-0.76889,-0.51982,0.37228,416.86
> view matrix models
> #26,0.69954,-0.66305,-0.26647,218.21,0.67611,0.4934,0.5472,60.197,-0.23135,-0.56295,0.79345,311.44
> view matrix models
> #26,0.56193,-0.50217,-0.65731,260.7,0.81701,0.46121,0.3461,71.832,0.12935,-0.73151,0.66945,305.39
> view matrix models
> #26,0.53207,-0.83781,0.12241,212.14,0.84506,0.53446,-0.015123,102.55,-0.052755,0.11149,0.99236,187.16
> view matrix models
> #26,0.93919,-0.3008,-0.16563,135.89,0.33731,0.71785,0.60902,64.435,-0.0643,-0.62786,0.77567,302.39
> view matrix models
> #26,0.43866,-0.58484,-0.68231,287.48,0.58417,0.76252,-0.27803,135.86,0.68288,-0.27662,0.67613,187.59
> view matrix models
> #26,0.91234,-0.39758,-0.097779,142.49,0.31358,0.83209,-0.45748,179.37,0.26325,0.38672,0.88383,131.32
> view matrix models
> #26,0.63945,0.02757,-0.76833,201.74,0.15525,0.97414,0.16416,106.94,0.75299,-0.22425,0.61864,180.18
> view matrix models
> #26,0.99662,0.019371,-0.079834,81.009,-0.03519,0.97879,-0.20181,171.14,0.074231,0.20394,0.97617,163.65
> view matrix models
> #26,0.86423,-0.01501,-0.50287,150.04,-0.041301,0.99406,-0.10065,158.07,0.50139,0.10776,0.85848,140.68
> view matrix models
> #26,0.84915,-0.015085,-0.52794,154.72,-0.04001,0.99488,-0.09278,156.89,0.52664,0.099907,0.8442,140.45
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.84915,-0.015085,-0.52794,138.01,-0.04001,0.99488,-0.09278,176.54,0.52664,0.099907,0.8442,119.16
> view matrix models
> #26,0.84915,-0.015085,-0.52794,143.94,-0.04001,0.99488,-0.09278,167.3,0.52664,0.099907,0.8442,127.09
> fitmap #26 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 93502 points
correlation = 0.7498, correlation about mean = 0.04308, overlap = 5998
steps = 120, shift = 44.7, angle = 10.8 degrees
Position of emd_3720_2017_leaf.map (#26) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
-0.99752873 0.05994955 0.03663985 346.15620260
-0.05632233 -0.99406404 0.09308312 452.37718258
0.04200265 0.09078945 0.99498394 220.70010831
Axis -0.01970204 -0.04606500 -0.99874413
Axis point 177.33157534 216.12223197 0.00000000
Rotation angle (degrees) 176.66298139
Shift along axis -248.08167899
> view matrix models
> #26,0.76733,0.10072,-0.6333,168.13,-0.10499,0.99399,0.030875,167.58,0.6326,0.0428,0.77329,98.713
> view matrix models
> #26,0.76733,0.10072,-0.6333,157.02,-0.10499,0.99399,0.030875,159.86,0.6326,0.0428,0.77329,112.62
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.76486,0.29299,-0.57371,127.29,-0.12989,0.94244,0.30812,136.11,0.63096,-0.16115,0.75889,138.88
> view matrix models
> #26,0.98138,-0.11947,0.15038,66.585,0.1547,0.95574,-0.25027,168.22,-0.11382,0.26887,0.95643,148.49
> view matrix models
> #26,0.73144,-0.67654,-0.085371,189.27,0.47774,0.59774,-0.6438,220.88,0.48659,0.43011,0.76042,84.395
> view matrix models
> #26,0.75471,-0.35463,-0.55195,203.25,0.26169,0.93421,-0.24241,157.75,0.6016,0.038507,0.79787,113.74
> hide #!24 models
> show #!24 models
> view matrix models
> #26,0.75259,-0.35974,-0.55153,204.05,0.26218,0.93203,-0.25017,158.88,0.60404,0.043677,0.79575,113.1
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!2 models
> show #!26 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!24 models
> show #!24 models
> show #!2 models
> view matrix models
> #26,0.41557,-0.18056,-0.89146,260.92,-0.0038894,0.97974,-0.20025,177.4,0.90955,0.086688,0.40645,119.33
> view matrix models
> #26,0.99774,0.058716,-0.032707,65.055,-0.060258,0.56591,-0.82226,306.65,-0.029771,0.82237,0.56817,118.67
> view matrix models
> #26,0.67073,0.19286,-0.71619,166.73,-0.2059,0.97607,0.07001,168.81,0.71255,0.1005,0.69439,105.99
> view matrix models
> #26,-0.43931,-0.65376,-0.61612,381.73,-0.73161,-0.13763,0.66769,290.83,-0.5213,0.74408,-0.41784,300.06
> view matrix models
> #26,-0.54478,0.76628,-0.34062,191.48,-0.51896,-0.62714,-0.58085,472.63,-0.65871,-0.13966,0.73932,284.61
> view matrix models
> #26,-0.46118,0.71836,-0.52084,209.02,-0.51955,-0.69446,-0.49778,470.94,-0.71929,0.041039,0.6935,275.29
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.46118,0.71836,-0.52084,142.24,-0.51955,-0.69446,-0.49778,338.77,-0.71929,0.041039,0.6935,155.72
> show #!25 models
> view matrix models
> #26,-0.46118,0.71836,-0.52084,237.16,-0.51955,-0.69446,-0.49778,363.17,-0.71929,0.041039,0.6935,222.26
> view matrix models
> #26,-0.46118,0.71836,-0.52084,83.898,-0.51955,-0.69446,-0.49778,398.51,-0.71929,0.041039,0.6935,108.18
> view matrix models
> #26,-0.46118,0.71836,-0.52084,154.78,-0.51955,-0.69446,-0.49778,295.45,-0.71929,0.041039,0.6935,113.59
> view matrix models
> #26,-0.46118,0.71836,-0.52084,126.47,-0.51955,-0.69446,-0.49778,307.49,-0.71929,0.041039,0.6935,105.68
> view matrix models
> #26,-0.46118,0.71836,-0.52084,124.21,-0.51955,-0.69446,-0.49778,308.74,-0.71929,0.041039,0.6935,105.23
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.38554,0.80657,-0.4481,96.523,-0.60555,-0.58761,-0.53668,310.3,-0.69618,0.064439,0.71497,97.281
> view matrix models
> #26,-0.37906,0.92056,0.094306,18.142,-0.58365,-0.15875,-0.79634,287.23,-0.7181,-0.3569,0.59745,163.98
> view matrix models
> #26,-0.55593,0.66189,-0.50283,139.56,-0.68414,-0.70793,-0.17548,290.93,-0.47212,0.24645,0.84638,34.657
> view matrix models
> #26,-0.7847,-0.055307,-0.61741,264.67,-0.5058,-0.51866,0.68931,146.05,-0.35835,0.85319,0.37902,4.4531
> view matrix models
> #26,0.19358,0.91096,0.36426,-77.402,-0.98106,0.17702,0.078668,188.81,0.0071824,-0.37259,0.92797,44.731
> view matrix models
> #26,0.401,0.64535,0.65017,-102.9,-0.58738,0.72577,-0.35811,130.24,-0.70298,-0.23829,0.6701,139.52
> view matrix models
> #26,0.32629,0.93814,-0.11586,-38.999,-0.88387,0.25935,-0.38925,223.21,-0.33513,0.22941,0.91382,13.224
> view matrix models
> #26,-0.10398,0.8308,-0.54677,73.401,-0.99041,-0.036189,0.13335,208.89,0.091004,0.55539,0.82659,-63.668
> view matrix models
> #26,0.43436,0.25503,-0.86388,118.69,-0.713,0.68342,-0.15674,125.75,0.55042,0.68403,0.47869,-89.976
> view matrix models
> #26,0.87334,0.083429,-0.47992,44.172,-0.42329,0.61753,-0.66294,160.58,0.24105,0.78211,0.57462,-77.999
> view matrix models
> #26,0.90567,0.32089,-0.27712,-11.798,-0.40491,0.84845,-0.34084,92.884,0.12576,0.4209,0.89835,-60.003
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.90567,0.32089,-0.27712,92.66,-0.40491,0.84845,-0.34084,238.75,0.12576,0.4209,0.89835,85.291
> view matrix models
> #26,0.90567,0.32089,-0.27712,74.635,-0.40491,0.84845,-0.34084,239.88,0.12576,0.4209,0.89835,93.592
> view matrix models
> #26,0.90567,0.32089,-0.27712,84.593,-0.40491,0.84845,-0.34084,207.82,0.12576,0.4209,0.89835,85.417
> view matrix models
> #26,0.90567,0.32089,-0.27712,59.959,-0.40491,0.84845,-0.34084,218.88,0.12576,0.4209,0.89835,113.58
> view matrix models
> #26,0.90567,0.32089,-0.27712,55.258,-0.40491,0.84845,-0.34084,196.72,0.12576,0.4209,0.89835,113.74
> view matrix models
> #26,0.90567,0.32089,-0.27712,50.73,-0.40491,0.84845,-0.34084,201.11,0.12576,0.4209,0.89835,123.93
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.29654,0.53167,-0.79334,155.44,-0.70136,0.68506,0.19695,190.71,0.64819,0.49802,0.57604,93.624
> view matrix models
> #26,0.15048,0.56432,-0.81173,170.24,-0.69067,0.64748,0.3221,179.22,0.70734,0.51216,0.48719,95.726
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.15048,0.56432,-0.81173,176.11,-0.69067,0.64748,0.3221,266.02,0.70734,0.51216,0.48719,78.265
> view matrix models
> #26,0.15048,0.56432,-0.81173,15.001,-0.69067,0.64748,0.3221,32.363,0.70734,0.51216,0.48719,-105.62
> view matrix models
> #26,0.15048,0.56432,-0.81173,68.34,-0.69067,0.64748,0.3221,34.256,0.70734,0.51216,0.48719,-43.798
> view matrix models
> #26,0.15048,0.56432,-0.81173,222.36,-0.69067,0.64748,0.3221,245.86,0.70734,0.51216,0.48719,53.586
> fitmap #26 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 93502 points
correlation = 0.877, correlation about mean = 0.1072, overlap = 7580
steps = 144, shift = 67.3, angle = 23.8 degrees
Position of emd_3720_2017_leaf.map (#26) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
-0.88225376 -0.44406300 0.15632130 356.95023437
0.45852205 -0.88579944 0.07153241 358.90152443
0.10670443 0.13478650 0.98511256 161.26481449
Axis 0.06980469 0.05475520 0.99605681
Axis point 131.01986728 216.21673342 0.00000000
Rotation angle (degrees) 153.05859172
Shift along axis 205.19744356
> view matrix models
> #26,0.53487,0.44736,-0.71679,195.09,-0.58257,0.80971,0.070631,247.8,0.61198,0.3798,0.69371,41.474
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.33353,0.59398,-0.73209,202.17,-0.64664,0.70922,0.28083,242.24,0.68602,0.37973,0.62063,41.728
> hide #!26 models
> show #!26 models
> hide #!25 models
> show #!25 models
> view matrix models
> #26,0.56048,0.7964,-0.22716,92.688,-0.62523,0.58679,0.51455,226.86,0.54308,-0.14637,0.82682,96.428
> view matrix models
> #26,0.58459,0.77181,-0.25011,95.606,-0.62987,0.62605,0.45971,229.17,0.51139,-0.1112,0.85212,92.828
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.58459,0.77181,-0.25011,-111.93,-0.62987,0.62605,0.45971,22.697,0.51139,-0.1112,0.85212,-45.366
> view matrix models
> #26,0.58459,0.77181,-0.25011,-97.192,-0.62987,0.62605,0.45971,54.683,0.51139,-0.1112,0.85212,-33.781
> view matrix models
> #26,0.58459,0.77181,-0.25011,-102.44,-0.62987,0.62605,0.45971,99.852,0.51139,-0.1112,0.85212,-39.495
> view matrix models
> #26,0.58459,0.77181,-0.25011,-107.59,-0.62987,0.62605,0.45971,111.38,0.51139,-0.1112,0.85212,-44.174
> view matrix models
> #26,0.58459,0.77181,-0.25011,-109.08,-0.62987,0.62605,0.45971,115.45,0.51139,-0.1112,0.85212,-41.523
> view matrix models
> #26,0.58459,0.77181,-0.25011,-89.696,-0.62987,0.62605,0.45971,95.493,0.51139,-0.1112,0.85212,-49.625
> view matrix models
> #26,0.58459,0.77181,-0.25011,-82.584,-0.62987,0.62605,0.45971,61.158,0.51139,-0.1112,0.85212,-74.18
> view matrix models
> #26,0.58459,0.77181,-0.25011,-95.828,-0.62987,0.62605,0.45971,107.52,0.51139,-0.1112,0.85212,-42.496
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.25756,0.86769,-0.42519,-49.595,0.57601,0.21543,0.78854,-18.743,0.7758,-0.44801,-0.44432,120.85
> view matrix models
> #26,0.75076,-0.42093,-0.5091,58.444,0.26374,0.8976,-0.35322,69.88,0.60564,0.13091,0.78489,-74.158
> view matrix models
> #26,0.40853,0.33683,-0.84832,46.691,0.046773,0.92047,0.388,4.211,0.91155,-0.19819,0.36028,-19.343
> view matrix models
> #26,0.01264,0.0016047,-0.99992,149.45,-0.4635,0.88608,-0.0044373,112.41,0.886,0.46352,0.011944,-54.394
> view matrix models
> #26,0.34103,0.24805,-0.90674,71.834,-0.017243,0.96605,0.25779,21.383,0.93989,-0.07228,0.33373,-34.461
> view matrix models
> #26,-0.011437,-0.33687,-0.94148,185.72,-0.82667,0.53291,-0.18063,216.52,0.56257,0.77623,-0.28457,-20.141
> view matrix models
> #26,0.9393,0.3009,-0.16485,-89.781,-0.2782,0.38675,-0.87922,254.36,-0.2008,0.87171,0.44699,-31.49
> view matrix models
> #26,0.67367,0.71528,0.18586,-150.62,-0.72541,0.68806,-0.018625,167.39,-0.14121,-0.12228,0.9824,17.325
> view matrix models
> #26,-0.21604,0.9618,0.16814,-77.266,-0.65223,-0.014014,-0.75789,330.26,-0.72658,-0.2734,0.63035,143.21
> view matrix models
> #26,-0.50268,0.85836,0.10262,-24.725,-0.81347,-0.4295,-0.39217,354.98,-0.29254,-0.28061,0.91415,61.432
> view matrix models
> #26,-0.68495,0.72817,-0.024797,26.505,-0.72314,-0.68359,-0.09887,340.5,-0.088945,-0.049789,0.99479,1.2852
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.68495,0.72817,-0.024797,226.05,-0.72314,-0.68359,-0.09887,458.07,-0.088945,-0.049789,0.99479,194.14
> view matrix models
> #26,-0.68495,0.72817,-0.024797,214.85,-0.72314,-0.68359,-0.09887,456.73,-0.088945,-0.049789,0.99479,191.67
> view matrix models
> #26,-0.68495,0.72817,-0.024797,219.41,-0.72314,-0.68359,-0.09887,443.07,-0.088945,-0.049789,0.99479,190.09
> fitmap #26 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 93502 points
correlation = 0.8691, correlation about mean = -0.03408, overlap = 7035
steps = 168, shift = 71.3, angle = 28.9 degrees
Position of emd_3720_2017_leaf.map (#26) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
0.67126351 -0.61872807 -0.40814319 246.12148248
0.72190094 0.42083648 0.54932293 164.03711823
-0.16811997 -0.66337939 0.72915255 303.22204906
Axis -0.66500184 -0.13162000 0.73515218
Axis point 82.38815567 394.48105210 0.00000000
Rotation angle (degrees) 65.75581751
Shift along axis 37.65254755
> view matrix models
> #26,-0.57238,0.78964,-0.221,59.226,-0.61549,-0.59182,-0.5205,262.25,-0.5418,-0.1619,0.82477,60.766
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.88426,0.42008,-0.20402,136.68,-0.18135,-0.71147,-0.67891,246.1,-0.43035,-0.56333,0.70531,110.22
> view matrix models
> #26,-0.91128,0.35438,-0.20971,148.26,-0.114,-0.70649,-0.69848,240.19,-0.39568,-0.61261,0.68421,114.67
> view matrix models
> #26,-0.80102,-0.435,-0.41127,253.89,0.54473,-0.24474,-0.80211,122.69,0.24826,-0.86653,0.433,101.77
> view matrix models
> #26,-0.95892,0.1552,-0.23745,180.73,0.07831,-0.6597,-0.74744,218.61,-0.27265,-0.73533,0.62044,122.93
> view matrix models
> #26,-0.81813,-0.23357,-0.52546,245.24,0.38933,-0.89748,-0.20725,148.05,-0.42318,-0.37413,0.82519,72.646
> view matrix models
> #26,-0.24551,-0.55843,-0.79239,250.74,0.85357,-0.51198,0.096347,13.597,-0.45949,-0.65271,0.60236,136.35
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.24551,-0.55843,-0.79239,249.96,0.85357,-0.51198,0.096347,11.663,-0.45949,-0.65271,0.60236,136.34
> view matrix models
> #26,-0.24551,-0.55843,-0.79239,592.64,0.85357,-0.51198,0.096347,599.4,-0.45949,-0.65271,0.60236,153.8
> view matrix models
> #26,-0.24551,-0.55843,-0.79239,532.97,0.85357,-0.51198,0.096347,618.49,-0.45949,-0.65271,0.60236,132.21
> view matrix models
> #26,-0.24551,-0.55843,-0.79239,420.87,0.85357,-0.51198,0.096347,614.97,-0.45949,-0.65271,0.60236,209.09
> view matrix models
> #26,-0.24551,-0.55843,-0.79239,397.78,0.85357,-0.51198,0.096347,574.65,-0.45949,-0.65271,0.60236,224.44
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.60445,-0.44131,-0.66323,409.18,0.79565,-0.29287,-0.53026,629,0.039771,-0.84822,0.52815,200.04
> view matrix models
> #26,-0.25929,-0.77775,-0.57261,399.6,0.95494,-0.2951,-0.031597,552.37,-0.1444,-0.555,0.81922,151.5
> view matrix models
> #26,-0.18014,-0.78848,-0.58809,393.75,0.94986,-0.29479,0.10429,536.87,-0.25559,-0.53981,0.80205,164.3
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.18014,-0.78848,-0.58809,398.98,0.94986,-0.29479,0.10429,336.22,-0.25559,-0.53981,0.80205,227.86
> hide #!2 models
> hide #!25 models
> view matrix models
> #26,-0.18014,-0.78848,-0.58809,387.14,0.94986,-0.29479,0.10429,330.24,-0.25559,-0.53981,0.80205,227.27
> view matrix models
> #26,-0.18014,-0.78848,-0.58809,381.59,0.94986,-0.29479,0.10429,316.26,-0.25559,-0.53981,0.80205,259.11
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.069801,-0.42594,-0.90206,347.04,0.93145,-0.29589,0.21179,305.79,-0.35712,-0.855,0.37608,358.54
> view matrix models
> #26,0.11925,-0.75307,-0.64705,350.43,0.7515,-0.35744,0.55451,293.05,-0.64886,-0.55238,0.52331,338.03
> view matrix models
> #26,0.033708,-0.97476,-0.22071,336.27,0.96158,-0.02857,0.27303,263.21,-0.27245,-0.22143,0.93634,207.12
> view matrix models
> #26,-0.10186,-0.38367,-0.91784,363.29,0.87074,-0.48057,0.10425,347.42,-0.48108,-0.78858,0.38303,363.82
> view matrix models
> #26,-0.05811,-0.50264,-0.86254,366.02,0.77085,-0.57161,0.28117,348.72,-0.63436,-0.64855,0.42067,360
> view matrix models
> #26,0.045534,0.040464,-0.99814,305.4,0.73674,-0.67615,0.0061988,397.53,-0.67464,-0.73565,-0.060599,431.77
> view matrix models
> #26,0.0073716,-0.41136,-0.91144,353.47,0.60513,-0.7238,0.33156,379.72,-0.7961,-0.55398,0.24359,387.91
> view matrix models
> #26,0.021642,-0.086929,-0.99598,323.07,0.76262,-0.64275,0.072671,382.76,-0.64648,-0.76113,0.052383,418.29
> show #!2 models
> show #14 models
> hide #14 models
> show #14 models
> hide #!24 models
> view matrix models
> #26,-0.21784,-0.75425,-0.61939,385.46,0.8863,-0.41862,0.19806,327.18,-0.40868,-0.50582,0.75969,277.38
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.21784,-0.75425,-0.61939,316.76,0.8863,-0.41862,0.19806,384.77,-0.40868,-0.50582,0.75969,217.83
> view matrix models
> #26,-0.21784,-0.75425,-0.61939,326.64,0.8863,-0.41862,0.19806,395.43,-0.40868,-0.50582,0.75969,209.78
> view matrix models
> #26,-0.21784,-0.75425,-0.61939,309.39,0.8863,-0.41862,0.19806,411.56,-0.40868,-0.50582,0.75969,196.15
> view matrix models
> #26,-0.21784,-0.75425,-0.61939,315.14,0.8863,-0.41862,0.19806,414.61,-0.40868,-0.50582,0.75969,189.93
> hide #14 models
> hide #!2 models
> show #!24 models
> view matrix models
> #26,-0.21784,-0.75425,-0.61939,420.73,0.8863,-0.41862,0.19806,552.8,-0.40868,-0.50582,0.75969,126.98
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.51625,-0.43407,-0.73828,430.29,0.81685,0.0095092,-0.57678,600.98,0.25738,-0.90083,0.34966,147.18
> view matrix models
> #26,-0.68081,-0.26296,-0.68363,422.02,0.70913,-0.0029331,-0.70507,629.8,0.1834,-0.9648,0.18847,182.23
> view matrix models
> #26,-0.34302,0.054922,-0.93772,375.79,0.93822,0.068485,-0.3392,552.15,0.04559,-0.99614,-0.075021,232.68
> view matrix models
> #26,-0.044818,0.28108,-0.95864,317.48,0.99878,0.032376,-0.037202,513.95,0.02058,-0.95914,-0.28219,255.54
> view matrix models
> #26,0.97922,-0.0934,-0.18,154.39,0.048241,0.96943,-0.24058,533.61,0.19697,0.2269,0.95379,-52.037
> view matrix models
> #26,0.7558,-0.32714,-0.56723,253.32,0.39406,0.91907,-0.005006,472.67,0.52297,-0.21974,0.82354,-20.201
> view matrix models
> #26,0.49746,0.46252,-0.73389,207.89,-0.11953,0.87448,0.4701,480.05,0.85921,-0.14614,0.49031,-27.722
> view matrix models
> #26,0.53292,0.77579,-0.33785,119.69,-0.8442,0.51463,-0.14993,678.27,0.057552,0.36511,0.92918,-49.863
> view matrix models
> #26,0.39221,0.91279,-0.11396,92.824,-0.90758,0.40417,0.11377,667.52,0.1499,0.058805,0.98695,-30.539
> show #14 models
> hide #14 models
> show #14 models
> show #!2 models
> hide #!24 models
> show #!24 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #14 models
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.39221,0.91279,-0.11396,-11.208,-0.90758,0.40417,0.11377,640.17,0.1499,0.058805,0.98695,-91.938
> view matrix models
> #26,0.39221,0.91279,-0.11396,-27.887,-0.90758,0.40417,0.11377,602.33,0.1499,0.058805,0.98695,-95.765
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.49159,0.86948,-0.048413,-41.7,-0.86875,0.48582,-0.096179,612.96,-0.060106,0.08934,0.99419,-76.494
> view matrix models
> #26,0.63015,0.72034,-0.28988,-11.061,-0.77523,0.56251,-0.2874,615.78,-0.043966,0.40583,0.91289,-106.54
> view matrix models
> #26,0.18166,0.81837,-0.54522,58.138,-0.93619,-0.02574,-0.35055,711.75,-0.30092,0.57411,0.76147,-79.684
> view matrix models
> #26,-0.065015,0.73106,-0.67921,112.31,-0.88132,-0.36131,-0.30453,740.19,-0.46803,0.5788,0.66778,-50.267
> view matrix models
> #26,0.76476,-0.62586,-0.15307,118.4,0.61006,0.62695,0.48452,360.14,-0.20728,-0.46393,0.86128,21.961
> view matrix models
> #26,0.53158,-0.80095,-0.2755,180.17,0.7559,0.30184,0.58096,371.1,-0.38216,-0.51707,0.76589,59.368
> view matrix models
> #26,0.22358,-0.68272,-0.69564,250.5,0.91149,0.39925,-0.098881,422.09,0.34524,-0.61196,0.71156,-5.2251
> view matrix models
> #26,-0.10881,-0.70329,-0.70252,291.4,0.707,0.44205,-0.55204,493.62,0.6988,-0.55675,0.44913,-20.868
> view matrix models
> #26,0.16701,0.038305,-0.98521,204.94,0.17251,0.9827,0.067452,416.4,0.97075,-0.18123,0.15751,-62.097
> view matrix models
> #26,0.71839,0.024035,-0.69522,109.99,0.069176,0.99198,0.10578,422.47,0.69219,-0.12408,0.71097,-102.72
> view matrix models
> #26,0.51369,-0.58015,-0.6321,197.9,0.73544,0.67717,-0.023849,399.96,0.44187,-0.45262,0.77452,-42.636
> view matrix models
> #26,0.6187,-0.68507,-0.38457,169.33,0.69559,0.70522,-0.1372,414.5,0.3652,-0.18262,0.91284,-82.543
> view matrix models
> #26,0.80188,-0.18928,-0.56671,110.86,0.10444,0.9783,-0.17897,453.72,0.58828,0.084321,0.80425,-126.87
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.80188,-0.18928,-0.56671,236.45,0.10444,0.9783,-0.17897,319.92,0.58828,0.084321,0.80425,-22.749
> view matrix models
> #26,0.80188,-0.18928,-0.56671,242.7,0.10444,0.9783,-0.17897,300.28,0.58828,0.084321,0.80425,29.395
> view matrix models
> #26,0.80188,-0.18928,-0.56671,191.08,0.10444,0.9783,-0.17897,321.71,0.58828,0.084321,0.80425,90.841
> view matrix models
> #26,0.80188,-0.18928,-0.56671,182.54,0.10444,0.9783,-0.17897,326.98,0.58828,0.084321,0.80425,80.916
> view matrix models
> #26,0.80188,-0.18928,-0.56671,182.69,0.10444,0.9783,-0.17897,327.89,0.58828,0.084321,0.80425,80.843
> fitmap #26 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 93502 points
correlation = 0.8191, correlation about mean = 0.04296, overlap = 7085
steps = 180, shift = 57.1, angle = 36.5 degrees
Position of emd_3720_2017_leaf.map (#26) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
-0.93252958 0.26581440 -0.24439980 437.12443068
-0.18450015 -0.93256337 -0.31029862 395.49279816
-0.31040014 -0.24427084 0.91868574 266.69578048
Axis 0.14357295 0.14351329 -0.97917861
Axis point 262.85810028 190.06906788 -0.00000000
Rotation angle (degrees) 166.70616314
Shift along axis -141.62508659
> view matrix models
> #26,0.94986,0.12444,-0.28683,108.02,-0.0097878,0.92877,0.37052,253.1,0.31251,-0.34913,0.88343,168.61
> view matrix models
> #26,0.94986,0.12444,-0.28683,99.574,-0.0097878,0.92877,0.37052,228.44,0.31251,-0.34913,0.88343,163.46
> fitmap #26 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 93502 points
correlation = 0.8192, correlation about mean = 0.04309, overlap = 7085
steps = 180, shift = 53.5, angle = 0.044 degrees
Position of emd_3720_2017_leaf.map (#26) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
-0.93270694 0.26582143 -0.24371438 437.05105992
-0.18476560 -0.93258596 -0.31007271 395.52547842
-0.30970858 -0.24417694 0.91894407 266.51240542
Axis 0.14320899 0.14342291 -0.97924515
Axis point 262.77060575 190.05227553 0.00000000
Rotation angle (degrees) 166.69889182
Shift along axis -141.66392298
> view matrix models
> #26,0.94965,0.12438,-0.28757,108.3,-0.0094766,0.92881,0.37044,287.59,0.31317,-0.34906,0.88322,198.4
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.98636,-0.009641,-0.16433,105.6,0.013796,0.99961,0.024164,317.38,0.16403,-0.026101,0.98611,164.55
> view matrix models
> #26,0.90223,0.27722,-0.33034,100.45,0.0083559,0.75463,0.6561,272.67,0.43116,-0.59471,0.67854,238.56
> view matrix models
> #26,0.97795,0.18433,-0.098135,75.567,-0.19537,0.97357,-0.11826,360.98,0.073742,0.13483,0.98812,155.31
> view matrix models
> #26,0.98831,-0.084837,-0.12669,109.93,0.13292,0.88649,0.44324,267.94,0.074706,-0.4549,0.8874,237.55
> view matrix models
> #26,0.45356,0.16623,-0.87559,228.87,0.63581,0.6281,0.4486,241.25,0.62452,-0.76017,0.17919,295.38
> view matrix models
> #26,0.48239,0.19903,-0.85305,219.02,0.62258,0.60715,0.49372,239.92,0.6162,-0.76925,0.16897,298.62
> view matrix models
> #26,0.39996,0.17569,-0.89954,236.63,0.65873,0.62731,0.41541,242.67,0.63727,-0.7587,0.13517,298.96
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.39996,0.17569,-0.89954,220.75,0.65873,0.62731,0.41541,229.35,0.63727,-0.7587,0.13517,271.21
> view matrix models
> #26,0.39996,0.17569,-0.89954,223.18,0.65873,0.62731,0.41541,415.04,0.63727,-0.7587,0.13517,169.51
> view matrix models
> #26,0.39996,0.17569,-0.89954,222.24,0.65873,0.62731,0.41541,222.72,0.63727,-0.7587,0.13517,282.19
> show #!25 models
> hide #!24 models
> view matrix models
> #26,0.39996,0.17569,-0.89954,250.7,0.65873,0.62731,0.41541,297.87,0.63727,-0.7587,0.13517,290.12
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.72297,0.092659,-0.68464,198.69,0.36577,0.78936,0.49308,302.5,0.58611,-0.6069,0.53679,230.36
> view matrix models
> #26,0.94252,-0.0065676,-0.33407,144.31,0.14611,0.90725,0.39439,324.93,0.3005,-0.42053,0.85607,202.74
> view matrix models
> #26,0.75485,0.21363,-0.62013,173.01,0.41313,0.57948,0.70251,297.49,0.50943,-0.78649,0.34916,282.65
> view matrix models
> #26,0.7639,0.072934,-0.6412,191.29,-0.0057774,0.99433,0.10622,365.74,0.64531,-0.077434,0.75998,134.05
> view matrix models
> #26,0.84667,0.53025,-0.044432,56.829,-0.42374,0.72239,0.54644,393.58,0.32185,-0.44383,0.83632,205.44
> view matrix models
> #26,0.78791,0.55369,-0.26947,87.245,-0.29707,0.7251,0.62128,370.08,0.53939,-0.40946,0.7358,188.57
> show #!24 models
> view matrix models
> #26,0.69494,0.52906,-0.48699,126.39,-0.14795,0.76796,0.62318,347.85,0.70368,-0.36102,0.61196,178.8
> view matrix models
> #26,0.57492,0.81224,0.098684,37.007,-0.81802,0.56796,0.090909,510.43,0.017791,-0.13299,0.99096,184.46
> view matrix models
> #26,0.66417,0.74742,0.015822,44.43,-0.7138,0.62772,0.31058,465.57,0.2222,-0.21757,0.95042,176.21
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.66417,0.74742,0.015822,60.06,-0.7138,0.62772,0.31058,450.95,0.2222,-0.21757,0.95042,177.54
> view matrix models
> #26,0.66417,0.74742,0.015822,62.679,-0.7138,0.62772,0.31058,438.29,0.2222,-0.21757,0.95042,184.42
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.62092,0.68679,-0.37785,121.29,-0.56834,0.72642,0.3864,401.08,0.53985,-0.025178,0.84138,138.34
> view matrix models
> #26,0.50831,0.32462,-0.79765,226.87,-0.54067,0.84123,-0.0021948,430.1,0.6703,0.43238,0.60312,97.032
> view matrix models
> #26,0.4757,0.28143,-0.83337,239.93,-0.52107,0.85346,-0.0092249,427.25,0.70865,0.43863,0.55264,97.902
> view matrix models
> #26,0.23458,0.15317,-0.95995,297.49,-0.34217,0.93732,0.065949,388.1,0.90989,0.31299,0.27229,123.23
> view matrix models
> #26,0.67714,0.59448,-0.43368,132.54,-0.70882,0.36868,-0.60137,576.33,-0.19761,0.71461,0.67103,153.54
> view matrix models
> #26,0.30651,0.95186,-0.0026574,80.92,-0.47629,0.15095,-0.86624,607.28,-0.82414,0.26678,0.49963,298.21
> view matrix models
> #26,-0.90777,0.31468,0.27735,261.46,-0.3425,-0.93779,-0.056967,626.69,0.24217,-0.14671,0.95908,172.67
> view matrix models
> #26,-0.95054,0.092395,-0.29655,360.61,-0.24645,-0.80546,0.53897,529.66,-0.18907,0.5854,0.78839,154.16
> view matrix models
> #26,-0.64685,0.23093,-0.72681,360.46,-0.24434,-0.96557,-0.089336,622.72,-0.72242,0.1198,0.681,282.85
> view matrix models
> #26,-0.45956,0.76938,-0.44369,241.51,-0.40389,-0.62596,-0.66711,668.41,-0.79099,-0.12738,0.59842,329.89
> view matrix models
> #26,-0.98818,-0.1014,0.11501,339.44,0.007034,-0.77928,-0.62664,635.43,0.15316,-0.61842,0.77078,261.33
> view matrix models
> #26,-0.80115,-0.57571,-0.16347,407.81,0.35468,-0.67675,0.64514,433.7,-0.48204,0.45887,0.74637,207.41
> view matrix models
> #26,0.028152,-0.34522,-0.9381,377.83,0.081628,-0.93454,0.34636,530.68,-0.99627,-0.086326,0.0018701,418.64
> view matrix models
> #26,-0.59574,-0.59267,-0.54207,431.28,0.62167,-0.76759,0.15602,472.07,-0.50855,-0.24404,0.82573,285.02
> view matrix models
> #26,-0.55578,-0.14471,-0.81864,405.88,0.63036,-0.71536,-0.3015,518.85,-0.54199,-0.68361,0.4888,381.1
> view matrix models
> #26,-0.27457,-0.89244,-0.35801,409.01,0.89272,-0.37493,0.24996,383.38,-0.3573,-0.25097,0.89964,260
> view matrix models
> #26,-0.25988,-0.85719,-0.44462,413.36,0.87504,-0.40377,0.26698,386.82,-0.40838,-0.31968,0.855,279.27
> view matrix models
> #26,-0.27306,-0.90879,-0.31552,405.77,0.89632,-0.35945,0.25962,379.98,-0.34935,-0.21191,0.91272,252.89
> view matrix models
> #26,-0.2585,-0.94035,-0.22116,396.76,0.90227,-0.31682,0.29247,370.34,-0.34509,-0.12394,0.93035,239.82
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.2585,-0.94035,-0.22116,378.78,0.90227,-0.31682,0.29247,361.51,-0.34509,-0.12394,0.93035,233.92
> view matrix models
> #26,-0.2585,-0.94035,-0.22116,395.2,0.90227,-0.31682,0.29247,535.16,-0.34509,-0.12394,0.93035,46.461
> view matrix models
> #26,-0.2585,-0.94035,-0.22116,429.09,0.90227,-0.31682,0.29247,603.62,-0.34509,-0.12394,0.93035,61.304
> view matrix models
> #26,-0.2585,-0.94035,-0.22116,377.36,0.90227,-0.31682,0.29247,554.14,-0.34509,-0.12394,0.93035,21.232
> view matrix models
> #26,-0.2585,-0.94035,-0.22116,358.41,0.90227,-0.31682,0.29247,559.46,-0.34509,-0.12394,0.93035,-0.86888
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.2358,-0.91371,-0.33095,365.62,0.8913,-0.33905,0.30104,562.34,-0.38727,-0.22399,0.89434,20.11
> view matrix models
> #26,-0.21257,-0.40815,-0.88782,368.32,0.91596,-0.3997,-0.035558,606.53,-0.34035,-0.82076,0.45881,137.51
> view matrix models
> #26,-0.73074,0.45324,-0.51048,279.51,-0.51806,-0.85516,-0.017677,821.18,-0.44456,0.25154,0.85971,-26.133
> view matrix models
> #26,-0.36839,0.55336,-0.74705,254.46,-0.58202,-0.76388,-0.27881,848.34,-0.72494,0.33208,0.60347,26.231
> view matrix models
> #26,-0.59807,0.34857,-0.72168,301.93,-0.58645,-0.80408,0.097626,809.2,-0.54626,0.48161,0.68531,-21.524
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.59807,0.34857,-0.72168,391.36,-0.58645,-0.80408,0.097626,575.05,-0.54626,0.48161,0.68531,148.98
> view matrix models
> #26,-0.59807,0.34857,-0.72168,361.82,-0.58645,-0.80408,0.097626,532.94,-0.54626,0.48161,0.68531,200.94
> view matrix models
> #26,-0.59807,0.34857,-0.72168,356.4,-0.58645,-0.80408,0.097626,558.7,-0.54626,0.48161,0.68531,176.41
> view matrix models
> #26,-0.59807,0.34857,-0.72168,368.66,-0.58645,-0.80408,0.097626,557.25,-0.54626,0.48161,0.68531,214.27
> view matrix models
> #26,-0.59807,0.34857,-0.72168,320.04,-0.58645,-0.80408,0.097626,573.85,-0.54626,0.48161,0.68531,204.67
> view matrix models
> #26,-0.59807,0.34857,-0.72168,318.61,-0.58645,-0.80408,0.097626,590.51,-0.54626,0.48161,0.68531,205.24
> view matrix models
> #26,-0.59807,0.34857,-0.72168,312.51,-0.58645,-0.80408,0.097626,585.13,-0.54626,0.48161,0.68531,203.51
> view matrix models
> #26,-0.59807,0.34857,-0.72168,312.1,-0.58645,-0.80408,0.097626,578.25,-0.54626,0.48161,0.68531,215.8
> hide #!2 models
> hide #!25 models
> view matrix models
> #26,-0.59807,0.34857,-0.72168,312.84,-0.58645,-0.80408,0.097626,591.21,-0.54626,0.48161,0.68531,214.33
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.62408,0.41993,-0.65893,299.85,-0.5729,-0.81937,0.020419,600.62,-0.53133,0.39024,0.75193,215.69
> view matrix models
> #26,-0.63461,0.48084,-0.60504,287.4,-0.76945,-0.3199,0.55282,500.34,0.072262,0.81637,0.573,117.57
> view matrix models
> #26,-0.63776,0.48805,-0.59588,285.82,-0.76503,-0.31164,0.56356,497.59,0.089345,0.81528,0.57213,115.87
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.63776,0.48805,-0.59588,227.16,-0.76503,-0.31164,0.56356,692.79,0.089345,0.81528,0.57213,2.3047
> hide #!24 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.65811,0.75193,0.038762,123.02,-0.69008,-0.62297,0.36838,744.55,0.30114,0.21568,0.92887,7.8591
> view matrix models
> #26,0.64657,0.73269,-0.21242,7.2717,-0.13939,0.38723,0.91138,497.41,0.75002,-0.55966,0.3525,117.72
> view matrix models
> #26,0.87638,0.30024,-0.37658,52.303,-0.25871,0.95299,0.15774,532.28,0.40624,-0.040819,0.91286,28.499
> view matrix models
> #26,0.96603,-0.20024,-0.16339,76.788,0.24354,0.9169,0.31619,461.03,0.086499,-0.34524,0.93452,98.51
> view matrix models
> #26,0.62093,-0.18719,-0.76119,184.86,0.56613,0.77874,0.27031,446.44,0.54216,-0.59877,0.58951,117.95
> view matrix models
> #26,0.62142,0.048735,-0.78196,159.07,0.36972,0.8617,0.34752,449.64,0.69075,-0.50507,0.51746,98.434
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.62142,0.048735,-0.78196,178.93,0.36972,0.8617,0.34752,255.45,0.69075,-0.50507,0.51746,215.24
> view matrix models
> #26,0.62142,0.048735,-0.78196,178.44,0.36972,0.8617,0.34752,250.07,0.69075,-0.50507,0.51746,184.98
> view matrix models
> #26,0.62142,0.048735,-0.78196,186.12,0.36972,0.8617,0.34752,252.09,0.69075,-0.50507,0.51746,191.86
> view matrix models
> #26,0.62142,0.048735,-0.78196,178.97,0.36972,0.8617,0.34752,238.6,0.69075,-0.50507,0.51746,178.28
> view matrix models
> #26,0.62142,0.048735,-0.78196,181.67,0.36972,0.8617,0.34752,243.68,0.69075,-0.50507,0.51746,183.36
> view matrix models
> #26,0.62142,0.048735,-0.78196,188,0.36972,0.8617,0.34752,242.78,0.69075,-0.50507,0.51746,190.9
> view matrix models
> #26,0.62142,0.048735,-0.78196,181.45,0.36972,0.8617,0.34752,464.58,0.69075,-0.50507,0.51746,12.856
> view matrix models
> #26,0.62142,0.048735,-0.78196,166.35,0.36972,0.8617,0.34752,436.96,0.69075,-0.50507,0.51746,19.663
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.54567,0.45958,-0.70074,116.25,-0.17903,0.88083,0.43828,486.09,0.81865,-0.11371,0.56292,-46.942
> view matrix models
> #26,0.7665,0.32532,-0.55375,89.944,-0.045829,0.88772,0.45809,467.85,0.6406,-0.32575,0.69535,-17.084
> view matrix models
> #26,-0.87301,-0.22576,-0.43231,327.05,-0.48636,0.33712,0.80611,542.42,-0.036249,0.91399,-0.4041,41.196
> show #!2 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.93178,-0.35392,0.080729,288.46,0.020776,0.17003,0.98522,483.83,-0.36242,0.91969,-0.15108,47.57
> view matrix models
> #26,-0.8114,-0.20862,-0.546,331.45,-0.58143,0.38366,0.71746,558.09,0.059797,0.8996,-0.4326,35.407
> view matrix models
> #26,-0.9453,-0.28424,-0.16007,310.08,-0.23189,0.2404,0.94257,509.06,-0.22943,0.92812,-0.29316,48.281
> view matrix models
> #26,-0.83291,-0.21342,-0.5106,330.28,-0.55266,0.36871,0.74741,553.08,0.02875,0.90471,-0.42505,37.419
> view matrix models
> #26,-0.78517,-0.204,-0.58471,332.5,-0.61194,0.40054,0.68198,563.71,0.09507,0.89328,-0.43933,32.963
> view matrix models
> #26,-0.68822,0.44367,-0.57403,242.88,-0.67297,-0.68599,0.27664,748.29,-0.27105,0.5767,0.77069,-30.601
> view matrix models
> #26,-0.80555,0.23125,-0.54554,278.18,-0.45282,-0.83407,0.31509,736.52,-0.38215,0.50085,0.7766,-9.6594
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.80555,0.23125,-0.54554,406.6,-0.45282,-0.83407,0.31509,506.62,-0.38215,0.50085,0.7766,109.41
> view matrix models
> #26,-0.80555,0.23125,-0.54554,340.76,-0.45282,-0.83407,0.31509,529.94,-0.38215,0.50085,0.7766,184.06
> view matrix models
> #26,-0.80555,0.23125,-0.54554,370.8,-0.45282,-0.83407,0.31509,551.4,-0.38215,0.50085,0.7766,188.66
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.86554,0.34384,-0.36416,342.73,-0.3952,-0.91554,0.074845,582.97,-0.30766,0.20869,0.92833,197.22
> view matrix models
> #26,-0.57435,-0.048218,-0.81719,410.09,-0.54075,-0.72712,0.42296,535.84,-0.61459,0.68482,0.39155,238.45
> view matrix models
> #26,-0.58147,0.72857,0.36205,178.88,-0.67902,-0.67973,0.27732,563.02,0.44814,-0.084588,0.88995,151.24
> view matrix models
> #26,-0.45583,0.77778,-0.43275,252.6,-0.84755,-0.52777,-0.055811,603.27,-0.2718,0.34134,0.89978,180.69
> view matrix models
> #26,-0.56126,0.73968,0.3713,174.17,-0.82748,-0.49272,-0.26928,622,-0.016233,-0.45837,0.88861,248.62
> view matrix models
> #26,-0.39826,0.79346,-0.46023,247.45,-0.9024,-0.42891,0.041432,586.18,-0.16452,0.43181,0.88683,159.26
> view matrix models
> #26,-0.3309,0.18376,-0.9256,367.61,-0.94159,0.0006637,0.33675,504.43,0.062497,0.98297,0.17281,151.99
> view matrix models
> #26,0.013316,0.99308,-0.11664,136.45,-0.84079,0.074259,0.53625,460.68,0.5412,0.090931,0.83596,126.1
> view matrix models
> #26,0.10532,0.98267,0.15251,95.505,-0.72568,-0.028914,0.68742,442.13,0.67992,-0.18307,0.71006,158
> view matrix models
> #26,0.15571,0.98292,0.098089,96.195,-0.91903,0.10775,0.37918,484.08,0.36214,-0.14919,0.92011,165.13
> view matrix models
> #26,0.018866,0.74254,-0.66953,231.02,-0.93228,0.25502,0.25655,482.46,0.36124,0.61935,0.69707,99.734
> view matrix models
> #26,0.33265,0.91006,0.24723,67.264,-0.82541,0.15418,0.54307,448.59,0.45611,-0.38472,0.80247,196.52
> view matrix models
> #26,0.31892,0.9244,0.20922,71.593,-0.82434,0.16161,0.54253,447.64,0.46771,-0.34549,0.81356,189.21
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.31892,0.9244,0.20922,90.128,-0.82434,0.16161,0.54253,444.09,0.46771,-0.34549,0.81356,194.9
> view matrix models
> #26,0.31892,0.9244,0.20922,73.346,-0.82434,0.16161,0.54253,453.64,0.46771,-0.34549,0.81356,188.67
> view matrix models
> #26,0.31892,0.9244,0.20922,46.838,-0.82434,0.16161,0.54253,446.35,0.46771,-0.34549,0.81356,203.89
> view matrix models
> #26,0.31892,0.9244,0.20922,84.565,-0.82434,0.16161,0.54253,459.95,0.46771,-0.34549,0.81356,199.98
> view matrix models
> #26,0.31892,0.9244,0.20922,66.802,-0.82434,0.16161,0.54253,459.73,0.46771,-0.34549,0.81356,198.58
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.097853,0.95756,-0.27113,166.72,-0.93201,0.0073568,0.36236,511.62,0.34897,0.28815,0.89173,127.08
> view matrix models
> #26,-0.11013,0.98108,-0.15921,152.09,-0.92073,-0.040374,0.38811,513.01,0.37434,0.18933,0.90775,134.13
> hide #!25 models
> hide #!2 models
> view matrix models
> #26,-0.13278,0.99067,0.030754,131.09,-0.73407,-0.11915,0.66854,468.19,0.66597,0.066196,0.74304,135.27
> view matrix models
> #26,-0.17767,0.76886,-0.61423,238.81,-0.97125,-0.036499,0.23526,536.31,0.15846,0.63837,0.75324,123.15
> view matrix models
> #26,-0.098417,0.66235,-0.74271,257.73,-0.99477,-0.086007,0.055117,566.15,-0.027371,0.74425,0.66735,141.68
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.098417,0.66235,-0.74271,292.75,-0.99477,-0.086007,0.055117,574.99,-0.027371,0.74425,0.66735,158.53
> view matrix models
> #26,-0.098417,0.66235,-0.74271,279.24,-0.99477,-0.086007,0.055117,567.68,-0.027371,0.74425,0.66735,152.74
> fitmap #26 inMap #22
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage4_postprocess.mrc
using 93502 points
correlation = 0.8595, correlation about mean = 0.125, overlap = 7142
steps = 212, shift = 65.3, angle = 45.1 degrees
Position of emd_3720_2017_leaf.map (#26) relative to
COPI_golph_linkage4_postprocess.mrc (#22) coordinates:
Matrix rotation and translation
0.58096256 -0.81277432 -0.04336329 248.78856339
0.77815419 0.57025937 -0.26321146 48.14211366
0.23865984 0.11917268 0.96376310 148.92251809
Axis 0.23030141 -0.16985622 0.95818063
Axis point 27.47095454 237.58404923 0.00000000
Rotation angle (degrees) 56.11743390
Shift along axis 191.81379244
> view matrix models
> #26,-0.75258,0.45055,-0.48023,356.33,-0.63811,-0.67905,0.36292,555.02,-0.16258,0.57957,0.79854,172.51
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/All_Linkages_fitting_Golph_AF_RT.cxs"
——— End of log from Tue Dec 5 16:56:09 2023 ———
opened ChimeraX session
> hide #!26 models
> show #!22 models
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> show #!24 models
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> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> rename #3 CopA_F8WHL2.pdb
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> rename #4 CopB_Q9JIF7.pdb
> rename #5 CopB_Q9JIF7.pdb
> show #!1 models
> hide #!1 models
> show #!1 models
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> show #!1 models
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> show #!26 models
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> hide #!25 models
> show #!25 models
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> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
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> hide #!26 models
> hide #!25 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/postprocess_20231221.mrc"
Opened postprocess_20231221.mrc as #27, grid size 156,156,156, pixel 2.55,
shown at level 0.00309, step 1, values float32
> hide #!27 models
> show #!27 models
> volume #27 level 0.003558
> select add #27
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #27,1,0,0,118.22,0,1,0,38.774,0,0,1,134.02
> view matrix models #27,1,0,0,113.07,0,1,0,116.67,0,0,1,119.27
> select subtract #27
Nothing selected
> ui tool show "Fit in Map"
> fitmap #27 inMap #1
Fit map postprocess_20231221.mrc in map postprocess.mrc using 21338 points
correlation = 0.8877, correlation about mean = 0.5599, overlap = 1.959
steps = 52, shift = 8.5, angle = 0.087 degrees
Position of postprocess_20231221.mrc (#27) relative to postprocess.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999899 -0.00050038 -0.00133045 112.66315082
0.00049967 0.99999973 -0.00053675 112.06763162
0.00133072 0.00053609 0.99999897 111.78054676
Axis 0.35307466 -0.87579648 0.32911823
Axis point -89267.57947714 0.00000000 90475.31997439
Rotation angle (degrees) 0.08704872
Shift along axis -21.58091769
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess.mrc using 59756 points
correlation = 0.8696, correlation about mean = 0.2876, overlap = 132.2
steps = 60, shift = 0.0416, angle = 0.0228 degrees
Position of emdb 3720 (#2) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
-0.53664251 0.84318753 -0.03239775 278.61248582
-0.84367719 -0.53684303 0.00289191 482.08699507
-0.01495408 0.02888517 0.99947087 223.63820801
Axis 0.01540656 -0.01033910 -0.99982786
Axis point 272.71090587 162.46815483 0.00000000
Rotation angle (degrees) 122.48014641
Shift along axis -224.29159627
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess.mrc using 59756 points
correlation = 0.8696, correlation about mean = 0.2876, overlap = 132.2
steps = 40, shift = 0.0164, angle = 0.0168 degrees
Position of emdb 3720 (#2) relative to postprocess.mrc (#1) coordinates:
Matrix rotation and translation
-0.53641656 0.84333481 -0.03230586 278.56998005
-0.84382076 -0.53661774 0.00281701 482.07814301
-0.01496021 0.02877145 0.99947406 223.65821367
Axis 0.01538092 -0.01027924 -0.99982887
Axis point 272.73010610 162.45893437 0.00000000
Rotation angle (degrees) 122.46471538
Shift along axis -224.29067599
> hide #!2 models
> show #3 models
> hide #3 atoms
> show #4 models
> hide #3-4 atoms
> show #5 models
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> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #4 models
> show #5 models
> hide #!1 models
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> show #5 models
> show #6 models
> hide #6 models
> show #6 models
> show #7 models
> show #12 models
> hide #7 models
> hide #6 models
> hide #12 models
> show #6 models
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> show #6 models
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> show #4 models
> show #7 models
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> hide #8 models
> show #8 models
> show #!9 models
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> show #11 models
> hide #3-8,10-11#!9 atoms
> show #12 models
> show #13 models
> hide #3-8,10-13#!9 atoms
> show #14 models
> hide atoms
> show #!15 models
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> show #!2 models
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> show #!2 models
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> show #3 models
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> show #4 models
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> hide #4 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> show #!27 models
> close #1
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/postprocess_20231221.mrc"
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00309, step 1, values float32
> color #1 silver models
> select add #1
2 models selected
> volume #1 level 0.004024
> view matrix models #1,1,0,0,78.299,0,1,0,79.616,0,0,1,143.65
> view matrix models #1,1,0,0,117.94,0,1,0,120,0,0,1,119.56
> fitmap #1 inMap #27
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 15259
points
correlation = 0.6104, correlation about mean = 0.1891, overlap = 0.3765
steps = 196, shift = 13, angle = 5.06 degrees
Position of postprocess_20231221.mrc (#1) relative to postprocess_20231221.mrc
(#27) coordinates:
Matrix rotation and translation
0.99600058 -0.00210606 0.08932196 -8.32184849
0.00171311 0.99998852 0.00447574 -2.40606876
-0.08933036 -0.00430482 0.99599275 19.94289709
Axis -0.04907846 0.99856678 0.02134700
Axis point 218.96581399 0.00000000 103.83296215
Rotation angle (degrees) 5.13221794
Shift along axis -1.56847579
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui mousemode right "translate selected models"
> select add #1
2 models selected
> view matrix models
> #1,0.99612,-0.0026007,0.087995,94.016,0.0022587,0.99999,0.0039858,110.22,-0.088004,-0.0037715,0.99611,133.13
> fitmap #1 inMap #27
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 15259
points
correlation = 1, correlation about mean = 0.9999, overlap = 1.098
steps = 72, shift = 0.746, angle = 5.14 degrees
Position of postprocess_20231221.mrc (#1) relative to postprocess_20231221.mrc
(#27) coordinates:
Matrix rotation and translation
0.99999999 0.00007881 -0.00009844 -0.00444357
-0.00007883 0.99999998 -0.00017015 0.03235540
0.00009842 0.00017015 0.99999998 -0.03743463
Axis 0.80342059 -0.46476274 -0.37217060
Axis point 0.00000000 230.25071217 177.36655494
Rotation angle (degrees) 0.01213425
Shift along axis -0.00467558
> fitmap #1 inMap #27
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 15259
points
correlation = 1, correlation about mean = 0.9999, overlap = 1.097
steps = 44, shift = 0.0686, angle = 0.00641 degrees
Position of postprocess_20231221.mrc (#1) relative to postprocess_20231221.mrc
(#27) coordinates:
Matrix rotation and translation
0.99999999 0.00005046 -0.00009993 0.02040220
-0.00005047 1.00000000 -0.00006202 0.05116219
0.00009993 0.00006202 0.99999999 -0.05958419
Axis 0.48458800 -0.78082282 -0.39432244
Axis point 622.17817535 0.00000000 235.95812245
Rotation angle (degrees) 0.00733296
Shift along axis -0.00656656
> fitmap #1 inMap #27
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 15259
points
correlation = 1, correlation about mean = 0.9999, overlap = 1.098
steps = 28, shift = 0.069, angle = 0.00187 degrees
Position of postprocess_20231221.mrc (#1) relative to postprocess_20231221.mrc
(#27) coordinates:
Matrix rotation and translation
1.00000000 0.00002294 -0.00009459 -0.00628371
-0.00002294 1.00000000 -0.00007871 -0.00459590
0.00009459 0.00007871 0.99999999 -0.03170221
Axis 0.62880180 -0.75566048 -0.18326354
Axis point 324.80810106 0.00000000 -101.88546019
Rotation angle (degrees) 0.00717226
Shift along axis 0.00533159
> fitmap #1 inMap #27
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 15259
points
correlation = 0.9999, correlation about mean = 0.9998, overlap = 1.095
steps = 28, shift = 0.0687, angle = 0.0208 degrees
Position of postprocess_20231221.mrc (#1) relative to postprocess_20231221.mrc
(#27) coordinates:
Matrix rotation and translation
0.99999994 -0.00033897 -0.00011199 0.10258927
0.00033896 0.99999994 -0.00008446 -0.02689940
0.00011202 0.00008442 0.99999999 -0.06841419
Axis 0.23018010 -0.30531490 0.92401295
Axis point 107.68870552 323.94093990 0.00000000
Rotation angle (degrees) 0.02101864
Shift along axis -0.03138880
> fitmap #1 inMap #27
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 15259
points
correlation = 1, correlation about mean = 0.9998, overlap = 1.097
steps = 28, shift = 0.073, angle = 0.0235 degrees
Position of postprocess_20231221.mrc (#1) relative to postprocess_20231221.mrc
(#27) coordinates:
Matrix rotation and translation
0.99999999 0.00007038 -0.00009217 -0.02132593
-0.00007038 1.00000000 -0.00006245 -0.00222104
0.00009217 0.00006245 0.99999999 -0.03014411
Axis 0.47413336 -0.69976129 -0.53435166
Axis point 283.26765369 0.00000000 -270.23361389
Rotation angle (degrees) 0.00754671
Shift along axis 0.00755042
> fitmap #1 inMap #27
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 15259
points
correlation = 1, correlation about mean = 0.9998, overlap = 1.097
steps = 44, shift = 0.0615, angle = 0.00861 degrees
Position of postprocess_20231221.mrc (#1) relative to postprocess_20231221.mrc
(#27) coordinates:
Matrix rotation and translation
0.99999999 -0.00000533 -0.00010912 0.01841063
0.00000534 1.00000000 0.00006615 -0.01182827
0.00010912 -0.00006615 0.99999999 -0.05324245
Axis -0.51796938 -0.85437798 0.04178502
Axis point 487.31525535 0.00000000 160.83942816
Rotation angle (degrees) 0.00731758
Shift along axis -0.00165507
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7167, correlation about mean = 0.2038, overlap = 49.31
steps = 48, shift = 0.122, angle = 0.144 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53823184 0.84226442 -0.02995221 166.48800349
-0.84266804 -0.53843091 0.00165497 370.29528312
-0.01473327 0.02613053 0.99954996 111.78150021
Axis 0.01452401 -0.00903105 -0.99985374
Axis point 185.18798690 138.59937710 0.00000000
Rotation angle (degrees) 122.58541990
Shift along axis -112.69123289
> show #!2 models
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7166, correlation about mean = 0.2038, overlap = 49.31
steps = 64, shift = 0.0413, angle = 0.00764 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53816911 0.84230315 -0.02999017 166.44451641
-0.84270928 -0.53836604 0.00175716 370.29964567
-0.01466563 0.02621865 0.99954865 111.76370628
Axis 0.01451497 -0.00909329 -0.99985330
Axis point 185.17390242 138.60620608 0.00000000
Rotation angle (degrees) 122.58112651
Shift along axis -112.69861478
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7166, correlation about mean = 0.2039, overlap = 49.31
steps = 48, shift = 0.00275, angle = 0.00297 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53816849 0.84230535 -0.02993964 166.43685310
-0.84270998 -0.53836497 0.00174583 370.30180649
-0.01464793 0.02616999 0.99955019 111.76946153
Axis 0.01449280 -0.00907379 -0.99985380
Axis point 185.17023970 138.61104222 0.00000000
Rotation angle (degrees) 122.58101693
Shift along axis -112.70102697
> hide #!2 models
> show #3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/20240123_Golph3_fitting.cxs"
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #!9 models
> hide #!9 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/20240124_Golph3_fitting.cxs"
——— End of log from Wed Jan 24 14:57:19 2024 ———
opened ChimeraX session
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!1 models
> show #!1 models
> hide #3 models
> hide #4 models
> show #!2 models
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7165, correlation about mean = 0.2037, overlap = 49.31
steps = 40, shift = 0.00989, angle = 0.0208 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53791695 0.84245856 -0.03014864 166.42009772
-0.84286797 -0.53811777 0.00169321 370.30672430
-0.01479705 0.02632213 0.99954400 111.77203531
Axis 0.01461157 -0.00910762 -0.99985177
Axis point 185.20412256 138.59647932 0.00000000
Rotation angle (degrees) 122.56427261
Shift along axis -112.69641943
> volume #1 level 0.01671
> volume #27 level 0.001721
> hide #!15 models
> volume #27 level 0.004894
> hide #!2 models
> show #!2 models
> volume #1 level 0.01454
> volume #27 level 0.004059
> show #3 models
> volume #27 level 0.004059
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #5 models
> hide #!2 models
> hide #4 models
> show #4 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> close #5
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!27 models
> volume #27 level 0.003892
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> volume #27 level 0.003558
> show #6 models
> show #7 models
> fitmap #3 inMap #1
Fit molecule CopA_F8WHL2.pdb (#3) to map postprocess_20231221.mrc (#1) using
9810 atoms
average map value = 0.001845, steps = 68
shifted from previous position = 2.81
rotated from previous position = 2.93 degrees
atoms outside contour = 9809, contour level = 0.014544
Position of CopA_F8WHL2.pdb (#3) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.90015953 0.40379294 0.16329137 162.19633365
-0.20930428 0.72979075 -0.65084342 244.64037543
-0.38197451 0.55168533 0.74144369 239.08869520
Axis 0.82604072 0.37455388 -0.42114857
Axis point 0.00000000 -323.35348746 438.23786746
Rotation angle (degrees) 46.70955347
Shift along axis 124.91991652
> select add #3
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.90081,0.40263,0.16255,273.54,-0.20867,0.72973,-0.65111,361.1,-0.38078,0.55261,0.74137,353.84
> view matrix models
> #3,0.90081,0.40263,0.16255,270.87,-0.20867,0.72973,-0.65111,363.77,-0.38078,0.55261,0.74137,353.1
> view matrix models
> #3,0.90081,0.40263,0.16255,268.91,-0.20867,0.72973,-0.65111,361.96,-0.38078,0.55261,0.74137,352.8
> fitmap #3 inMap #1
Fit molecule CopA_F8WHL2.pdb (#3) to map postprocess_20231221.mrc (#1) using
9810 atoms
average map value = 0.001845, steps = 92
shifted from previous position = 7.82
rotated from previous position = 0.0457 degrees
atoms outside contour = 9809, contour level = 0.014544
Position of CopA_F8WHL2.pdb (#3) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.89988106 0.40450120 0.16307313 162.23059759
-0.20991408 0.72944940 -0.65102968 244.65358931
-0.38229588 0.55161793 0.74132820 239.10376091
Axis 0.82572966 0.37444665 -0.42185334
Axis point 0.00000000 -323.24381504 438.40289313
Rotation angle (degrees) 46.73848720
Shift along axis 124.70161062
> show #!2 models
> hide #!2 models
> view matrix models
> #3,0.90054,0.40334,0.16233,272.03,-0.20928,0.72939,-0.6513,359.41,-0.3811,0.55254,0.74126,352.35
> fitmap #3 inMap #1
Fit molecule CopA_F8WHL2.pdb (#3) to map postprocess_20231221.mrc (#1) using
9810 atoms
average map value = 0.001846, steps = 52
shifted from previous position = 3.78
rotated from previous position = 0.132 degrees
atoms outside contour = 9809, contour level = 0.014544
Position of CopA_F8WHL2.pdb (#3) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.90082714 0.40253743 0.16270854 162.19530232
-0.20889682 0.73035632 -0.65033972 244.66834799
-0.38062130 0.55185437 0.74201359 239.15350985
Axis 0.82677669 0.37366050 -0.42049749
Axis point -0.00000000 -323.55120767 438.57037778
Rotation angle (degrees) 46.63854764
Shift along axis 124.95874311
> select subtract #3
Nothing selected
> show #8 models
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003728, steps = 156
shifted from previous position = 3.77
rotated from previous position = 19 degrees
atoms outside contour = 1446, contour level = 0.014544
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23871334 0.93126401 0.27525132 -92.96159773
-0.88635655 0.09315163 0.45353595 105.90758790
0.39672159 -0.35223589 0.84766849 472.49244217
Axis -0.40451903 -0.06098133 -0.91249418
Axis point -102.33853573 189.91429951 0.00000000
Rotation angle (degrees) 84.84981260
Shift along axis -400.00025351
> select add #8
1462 atoms, 1481 bonds, 179 residues, 1 model selected
> view matrix models
> #8,-0.04305,0.99254,0.11405,-54.036,-0.90935,-0.086208,0.407,269.6,0.4138,-0.086188,0.90628,503.09
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003728, steps = 156
shifted from previous position = 2.35
rotated from previous position = 19 degrees
atoms outside contour = 1446, contour level = 0.014544
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23975825 0.93129673 0.27423055 -92.95768275
-0.88585521 0.09429203 0.45427918 105.66614145
0.39721096 -0.35184574 0.84760134 472.42121763
Axis -0.40473531 -0.06174541 -0.91234688
Axis point -102.65876100 189.81188561 0.00000000
Rotation angle (degrees) 84.78888270
Shift along axis -399.91316667
> color #1 #c0c0c09a models
> color #1 #c0c0c0a6 models
> hide #!27 models
> volume #27 level 0.006063
> hide #!27 models
> volume #1 level 0.004859
> volume #1 level 0.00369
> select subtract #8
Nothing selected
> show #!9 models
> hide #!9 models
> show #!9 models
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 64
shifted from previous position = 0.586
rotated from previous position = 0.992 degrees
atoms outside contour = 4569, contour level = 0.0036898
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48946039 -0.51119098 -0.70647881 223.52094052
0.54881092 -0.44901255 0.70512006 282.30283630
-0.67766887 -0.73285162 0.06077334 258.73062006
Axis -0.80483252 -0.01612492 0.59328290
Axis point 0.00000000 245.01292905 103.84475236
Rotation angle (degrees) 116.70451631
Shift along axis -30.94857928
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 48
shifted from previous position = 0.00538
rotated from previous position = 0.0139 degrees
atoms outside contour = 4570, contour level = 0.0036898
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48927229 -0.51133667 -0.70650367 223.52773984
0.54886344 -0.44901336 0.70507867 282.30389544
-0.67776216 -0.73274949 0.06096421 258.73180389
Axis -0.80475175 -0.01608661 0.59339350
Axis point 0.00000000 245.01905582 103.85933152
Rotation angle (degrees) 116.70445294
Shift along axis -30.89588036
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 48
shifted from previous position = 0.0168
rotated from previous position = 0.0102 degrees
atoms outside contour = 4571, contour level = 0.0036898
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48915096 -0.51134415 -0.70658227 223.52965885
0.54885208 -0.44914905 0.70500108 282.29080176
-0.67785893 -0.73266110 0.06095061 258.73832985
Axis -0.80472018 -0.01607766 0.59343656
Axis point 0.00000000 244.99753955 103.89134370
Rotation angle (degrees) 116.71313164
Shift along axis -30.87261952
> show #10 models
> fitmap #10 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#10) to map postprocess_20231221.mrc (#1) using
1463 atoms
average map value = 0.003943, steps = 48
shifted from previous position = 0.417
rotated from previous position = 1.46 degrees
atoms outside contour = 792, contour level = 0.0036898
Position of CopZ2_Q9CTG7.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.81864305 0.29541521 -0.49249716 229.58444037
0.42688194 0.88667169 -0.17772211 242.05157821
0.38418147 -0.35572911 -0.85197502 217.24514022
Axis -0.19687193 -0.96958778 0.14539939
Axis point 59.00002771 0.00000000 149.03806421
Rotation angle (degrees) 153.12225239
Shift along axis -248.30167204
> fitmap #10 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#10) to map postprocess_20231221.mrc (#1) using
1463 atoms
average map value = 0.003943, steps = 28
shifted from previous position = 0.0492
rotated from previous position = 0.0271 degrees
atoms outside contour = 792, contour level = 0.0036898
Position of CopZ2_Q9CTG7.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.81849776 0.29524030 -0.49284341 229.56017056
0.42694330 0.88660030 -0.17793076 242.03285382
0.38442278 -0.35605212 -0.85173121 217.28362866
Axis -0.19686199 -0.96956572 0.14555984
Axis point 58.95712397 0.00000000 149.09318624
Rotation angle (degrees) 153.10212696
Shift along axis -248.23066084
> hide #10 models
> show #11 models
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 44
shifted from previous position = 0.312
rotated from previous position = 1.46 degrees
atoms outside contour = 727, contour level = 0.0036898
Position of CopZ1_P61924.pdb (#11) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16479913 -0.93983802 -0.29924197 230.49736056
-0.38664204 0.21755152 -0.89620270 241.46224490
0.90738591 0.26339295 -0.32752859 218.19778081
Axis 0.65790199 -0.68458595 0.31385831
Axis point 143.42213466 -0.00000000 249.43293093
Rotation angle (degrees) 118.20248350
Shift along axis 54.82620005
> fitmap #11 inMap #1
Fit molecule CopZ1_P61924.pdb (#11) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 40
shifted from previous position = 0.00516
rotated from previous position = 0.0582 degrees
atoms outside contour = 729, contour level = 0.0036898
Position of CopZ1_P61924.pdb (#11) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16557357 -0.93960238 -0.29955428 230.49711147
-0.38616785 0.21772091 -0.89636600 241.45978242
0.90744685 0.26409275 -0.32679540 218.19963395
Axis 0.65805631 -0.68444890 0.31383372
Axis point 143.36639957 0.00000000 249.52617996
Rotation angle (degrees) 118.14798262
Shift along axis 54.89159910
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> close #12
> show #13 models
> fitmap #7 inMap #1
Fit molecule hArf1_P84078 (#7) to map postprocess_20231221.mrc (#1) using 1457
atoms
average map value = 0.003766, steps = 56
shifted from previous position = 0.864
rotated from previous position = 4.14 degrees
atoms outside contour = 770, contour level = 0.0036898
Position of hArf1_P84078 (#7) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.84483130 -0.49393057 0.20565176 243.02165057
-0.47593422 0.51817889 -0.71061750 195.90564270
0.24443130 -0.69822863 -0.67285221 220.58765330
Axis 0.27833451 -0.87124025 0.40431464
Axis point 151.35909954 0.00000000 157.32737010
Rotation angle (degrees) 178.72475613
Shift along axis -13.85275083
> fitmap #6 inMap #1
Fit molecule hArf1_P84078 (#6) to map postprocess_20231221.mrc (#1) using 1457
atoms
average map value = 0.002587, steps = 44
shifted from previous position = 2.4
rotated from previous position = 3.14 degrees
atoms outside contour = 1383, contour level = 0.0036898
Position of hArf1_P84078 (#6) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.15746228 0.02392526 0.98723513 126.72965474
-0.68671732 -0.71576648 0.12687654 200.57796574
0.70966537 -0.69792974 -0.09627633 178.39429805
Axis -0.73410771 0.24704722 -0.63249785
Axis point 0.00000000 138.26513657 -15.48328042
Rotation angle (degrees) 145.82138083
Shift along axis -156.31499806
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 64
shifted from previous position = 0.356
rotated from previous position = 1.5 degrees
atoms outside contour = 1694, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66106910 -0.23543049 0.71243254 198.02566618
-0.68861463 -0.56745520 0.45144710 233.21553124
0.29798913 -0.78902920 -0.53724798 191.32656018
Axis -0.89618921 0.29941701 -0.32740548
Axis point 0.00000000 180.09147202 -4.24254670
Rotation angle (degrees) 136.20470288
Shift along axis -170.28113246
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 48
shifted from previous position = 0.0608
rotated from previous position = 0.0836 degrees
atoms outside contour = 1695, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66033234 -0.23665806 0.71270903 198.05899585
-0.68948127 -0.56717145 0.45047989 233.25398840
0.29761852 -0.78886596 -0.53769295 191.34695105
Axis -0.89597915 0.30008770 -0.32736637
Axis point 0.00000000 180.19607325 -4.21984410
Rotation angle (degrees) 136.24188641
Shift along axis -170.10063410
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 48
shifted from previous position = 0.0614
rotated from previous position = 0.0877 degrees
atoms outside contour = 1694, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66111688 -0.23537988 0.71240493 198.02527108
-0.68855172 -0.56750955 0.45147474 233.21545821
0.29802854 -0.78900521 -0.53726136 191.32659705
Axis -0.89620533 0.29937310 -0.32740152
Axis point 0.00000000 180.08399595 -4.23802996
Rotation angle (degrees) 136.20552929
Shift along axis -170.29348570
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 48
shifted from previous position = 0.0592
rotated from previous position = 0.0908 degrees
atoms outside contour = 1696, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66032840 -0.23672237 0.71269132 198.05842868
-0.68951672 -0.56712470 0.45048447 233.25039753
0.29754511 -0.78888028 -0.53771258 191.34783844
Axis -0.89597713 0.30012272 -0.32733979
Axis point 0.00000000 180.20108391 -4.21779697
Rotation angle (degrees) 136.24092631
Shift along axis -170.08783960
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 44
shifted from previous position = 0.075
rotated from previous position = 0.112 degrees
atoms outside contour = 1694, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66127138 -0.23504648 0.71237161 198.01452577
-0.68840739 -0.56742096 0.45180606 233.20554172
0.29801916 -0.78916830 -0.53702698 191.32490872
Axis -0.89624017 0.29924817 -0.32742035
Axis point 0.00000000 180.07264602 -4.26204900
Rotation angle (degrees) 136.18576759
Shift along axis -170.32590854
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 36
shifted from previous position = 0.0635
rotated from previous position = 0.105 degrees
atoms outside contour = 1695, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66042804 -0.23664749 0.71262386 198.05230461
-0.68940567 -0.56720478 0.45055361 233.24248648
0.29758128 -0.78884517 -0.53774407 191.34290893
Axis -0.89600980 0.30005049 -0.32731658
Axis point 0.00000000 180.18416582 -4.20856795
Rotation angle (degrees) 136.24142035
Shift along axis -170.10198828
> fitmap #13 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#13) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 44
shifted from previous position = 0.00651
rotated from previous position = 0.0146 degrees
atoms outside contour = 1696, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#13) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66047830 -0.23642569 0.71265089 198.04833551
-0.68934139 -0.56715067 0.45072005 233.23896951
0.29761863 -0.78895057 -0.53756873 191.34102815
Axis -0.89601715 0.29997970 -0.32736134
Axis point 0.00000000 180.17843945 -4.22962225
Rotation angle (degrees) 136.22983542
Shift along axis -170.12540314
> show #14 models
> fitmap #14 inMap #1
Fit molecule CopBprime_O55029.pdb (#14) to map postprocess_20231221.mrc (#1)
using 7214 atoms
average map value = 0.00312, steps = 44
shifted from previous position = 0.476
rotated from previous position = 0.838 degrees
atoms outside contour = 4439, contour level = 0.0036898
Position of CopBprime_O55029.pdb (#14) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.16270681 -0.17514830 -0.97100441 188.48036639
-0.01393129 -0.98361241 0.17975692 177.43794261
-0.98657610 0.04277502 0.15760039 238.55464879
Axis -0.64575721 0.07340777 0.76000588
Axis point 189.56540435 85.43326979 0.00000000
Rotation angle (degrees) 173.91158591
Shift along axis 72.61570301
> fitmap #14 inMap #1
Fit molecule CopBprime_O55029.pdb (#14) to map postprocess_20231221.mrc (#1)
using 7214 atoms
average map value = 0.00312, steps = 48
shifted from previous position = 0.0351
rotated from previous position = 0.00705 degrees
atoms outside contour = 4437, contour level = 0.0036898
Position of CopBprime_O55029.pdb (#14) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.16280622 -0.17508181 -0.97099974 188.50106463
-0.01396996 -0.98362224 0.17970011 177.41019990
-0.98655916 0.04282112 0.15769393 238.55155391
Axis -0.64572039 0.07340086 0.76003783
Axis point 189.56979851 85.41555075 0.00000000
Rotation angle (degrees) 173.91582886
Shift along axis 72.61128521
> show #10 models
> hide #10 models
> rename #6 #5
No name or id option specified for renaming
> rename #6 id #5
> rename #7 id #6
> rename #14 id #7
> rename #10 id #12
> rename #11 id #10
> rename #13 id #11
> show #12 models
> hide #12 models
> show #12 models
> show #!2 models
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7167, correlation about mean = 0.2038, overlap = 49.31
steps = 60, shift = 0.05, angle = 0.016 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53806318 0.84237008 -0.03001127 166.46851211
-0.84277337 -0.53826641 0.00152601 370.30102779
-0.01486859 0.02611378 0.99954840 111.80242990
Axis 0.01458877 -0.00898467 -0.99985321
Axis point 185.20870656 138.59733883 0.00000000
Rotation angle (degrees) 122.57414654
Shift along axis -112.68447858
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7166, correlation about mean = 0.2037, overlap = 49.32
steps = 48, shift = 0.0158, angle = 0.0192 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53783250 0.84252302 -0.02985225 166.40464852
-0.84292358 -0.53803088 0.00161764 370.29565125
-0.01469853 0.02603319 0.99955302 111.79406715
Axis 0.01448399 -0.00898962 -0.99985469
Axis point 185.20258353 138.59990210 0.00000000
Rotation angle (degrees) 122.55814219
Shift along axis -112.69643449
> hide #!2 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> rename #15 id #13
> rename #16 id #14
> rename #17 id #15
> rename #18 id #16
> rename #19 id #17
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> rename #20 id #18
> rename #21 id #19
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Reference structures/emd_2988_2015_linkage3.map"
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 3.38, step 1, values float32
> color #20 #fffb00ff models
> color #20 #fffeb6ff models
> hide #!20 models
> color #24 #b9ffffff models
> color #23 #fffeb6ff models
> rename #22 id #21
> rename #23 id #22
> rename #24 id #23
> rename #27 id #24
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> select add #25
2 models selected
> view matrix models
> #25,0.30125,-0.20502,-0.93124,395.8,0.88616,0.4208,0.19403,158.36,0.35209,-0.88368,0.30844,247.86
> view matrix models
> #25,0.30125,-0.20502,-0.93124,409.18,0.88616,0.4208,0.19403,140.07,0.35209,-0.88368,0.30844,349.72
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.67645,-0.68438,0.27211,276.2,0.719,0.6937,-0.042662,155.46,-0.15957,0.22451,0.96132,195.14
> view matrix models
> #25,0.90086,-0.29707,-0.31655,276.98,0.27566,0.95477,-0.11151,182.83,0.33536,0.013191,0.942,166.85
> view matrix models
> #25,0.051634,0.99551,-0.079348,189.57,-0.99444,0.043954,-0.095665,432.86,-0.091748,0.083846,0.99225,200.46
> view matrix models
> #25,0.16593,0.98421,-0.061601,175.83,-0.9838,0.16092,-0.078982,415.66,-0.067822,0.073708,0.99497,198.63
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.16593,0.98421,-0.061601,175.86,-0.9838,0.16092,-0.078982,412.23,-0.067822,0.073708,0.99497,198.86
> fitmap #25 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 65799
points
correlation = 0.701, correlation about mean = 0.05315, overlap = 29.32
steps = 192, shift = 9.35, angle = 11.1 degrees
Position of emd_3720_2017_leaf.map (#25) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
0.11163403 0.96487176 -0.23782420 100.11400997
-0.99372584 0.11003505 -0.02003119 302.54909941
0.00684146 0.23856822 0.97110165 55.58840087
Axis 0.12990453 -0.12290507 -0.98387965
Axis point 217.66156287 86.02522080 0.00000000
Rotation angle (degrees) 84.46893874
Shift along axis -78.87185003
> hide #!24 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #!9 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #!2 models
> hide #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.63698,0.76915,-0.051509,297.36,-0.7325,-0.62474,-0.27045,503.5,-0.2402,-0.13454,0.96135,241.27
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.63698,0.76915,-0.051509,313.09,-0.7325,-0.62474,-0.27045,513.45,-0.2402,-0.13454,0.96135,244.01
> fitmap #25 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 65799
points
correlation = 0.7202, correlation about mean = 0.04691, overlap = 31.12
steps = 68, shift = 2.64, angle = 2.35 degrees
Position of emd_3720_2017_leaf.map (#25) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.62028881 0.78213998 -0.05915118 199.52960692
-0.75199071 -0.61443165 -0.23871268 400.80293035
-0.22305108 -0.10358966 0.96928706 124.65272239
Axis 0.08724556 0.10582608 -0.99054987
Axis point 202.82248950 157.96163882 0.00000000
Rotation angle (degrees) 129.25084103
Shift along axis -63.65126554
> fitmap #25 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 65799
points
correlation = 0.7202, correlation about mean = 0.04691, overlap = 31.12
steps = 60, shift = 0.00106, angle = 0.00153 degrees
Position of emd_3720_2017_leaf.map (#25) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.62027380 0.78215072 -0.05916661 199.52866252
-0.75200210 -0.61442174 -0.23870231 400.80080185
-0.22305443 -0.10356737 0.96928868 124.65051550
Axis 0.08725203 0.10581679 -0.99055030
Axis point 202.82380680 157.95891904 0.00000000
Rotation angle (degrees) 129.24985933
Shift along axis -63.65186843
> view matrix models
> #25,-0.61957,0.78261,-0.060441,305.75,-0.75221,-0.61398,-0.23919,515.13,-0.2243,-0.10273,0.96909,279.3
> fitmap #25 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 65799
points
correlation = 0.7136, correlation about mean = 0.2086, overlap = 51.77
steps = 116, shift = 15, angle = 15.4 degrees
Position of emd_3720_2017_leaf.map (#25) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.53778248 0.84255214 -0.02993196 166.42872750
-0.84295720 -0.53797769 0.00178284 370.26748854
-0.01460059 0.02619014 0.99955036 111.74859963
Axis 0.01447855 -0.00909466 -0.99985382
Axis point 185.21029499 138.57045048 0.00000000
Rotation angle (degrees) 122.55472415
Shift along axis -112.69007224
> select subtract #25
Nothing selected
> hide #!25 models
> show #!26 models
> select add #26
2 models selected
> view matrix models
> #26,-0.75258,0.45055,-0.48023,398.01,-0.63811,-0.67905,0.36292,440.39,-0.16258,0.57957,0.79854,206.22
> view matrix models
> #26,-0.75258,0.45055,-0.48023,400.22,-0.63811,-0.67905,0.36292,430.28,-0.16258,0.57957,0.79854,190.52
> fitmap #26 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 93502
points
correlation = 0.6814, correlation about mean = 0.03275, overlap = 39.46
steps = 124, shift = 28.5, angle = 15.4 degrees
Position of emd_3720_2017_leaf.map (#26) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.80048790 0.52354068 -0.29176061 280.40193069
-0.58964709 -0.77515357 0.22683301 354.89939910
-0.10740297 0.35361289 0.92920530 65.62061675
Axis 0.11165601 -0.16236519 -0.98039302
Axis point 197.96082438 125.87878286 0.00000000
Rotation angle (degrees) 145.40824645
Shift along axis -90.64874260
> color #26 #942192ff models
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.3094,0.90104,-0.30396,293.42,-0.95088,-0.28979,0.10884,463.8,0.0099835,0.32271,0.94645,166.13
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.3094,0.90104,-0.30396,284.24,-0.95088,-0.28979,0.10884,440.35,0.0099835,0.32271,0.94645,163.75
> view matrix models
> #26,-0.3094,0.90104,-0.30396,272,-0.95088,-0.28979,0.10884,447.96,0.0099835,0.32271,0.94645,177.38
> fitmap #26 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 93502
points
correlation = 0.6077, correlation about mean = 0.05609, overlap = 37.22
steps = 120, shift = 6.67, angle = 4.48 degrees
Position of emd_3720_2017_leaf.map (#26) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.36623360 0.88241853 -0.29531417 171.46423215
-0.92983541 -0.35924163 0.07969649 341.21826856
-0.03576348 0.30378111 0.95207036 68.32737423
Axis 0.12149399 -0.14072295 -0.98256616
Axis point 200.93863242 103.81171509 0.00000000
Rotation angle (degrees) 112.74947034
Shift along axis -94.32153342
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.5533,-0.49401,-0.67068,388.41,0.45321,0.85409,-0.25521,191.27,0.69889,-0.16275,0.69646,183.19
> view matrix models
> #26,0.047803,-0.54747,-0.83546,471.47,0.78383,0.53901,-0.30836,197.77,0.61914,-0.64012,0.45489,277.77
> view matrix models
> #26,-0.59372,0.26561,-0.75957,437.99,0.11032,-0.90817,-0.40381,458.19,-0.79708,-0.32354,0.50989,393.77
> view matrix models
> #26,-0.86755,0.4472,0.21766,331.93,-0.045965,-0.50786,0.86021,278.84,0.49523,0.73627,0.46115,126.6
> view matrix models
> #26,-0.50461,0.3957,-0.76733,413.27,-0.62236,-0.78271,0.0056417,477.81,-0.59836,0.4804,0.64123,259.72
> view matrix models
> #26,-0.018439,0.87805,-0.47821,266.48,-0.99131,-0.07836,-0.10565,448.55,-0.13024,0.47211,0.87187,180.49
> fitmap #26 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 93502
points
correlation = 0.643, correlation about mean = 0.05332, overlap = 36.5
steps = 128, shift = 10, angle = 3.19 degrees
Position of emd_3720_2017_leaf.map (#26) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.04984739 0.89805451 -0.43705068 146.96444675
-0.99215656 -0.09475011 -0.08153366 331.54326175
-0.11463228 0.42955846 0.89573374 60.08760303
Axis 0.25754769 -0.16247191 -0.95250830
Axis point 229.66777164 83.83264256 0.00000000
Rotation angle (degrees) 97.14794883
Shift along axis -73.25005349
> view matrix models
> #26,-0.072354,0.97321,0.21824,175.47,-0.95136,-0.13304,0.27786,401.14,0.29945,-0.18752,0.9355,194.35
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.072354,0.97321,0.21824,181.5,-0.95136,-0.13304,0.27786,422.24,0.29945,-0.18752,0.9355,225.11
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.55847,0.82251,0.10764,267.59,-0.82054,-0.5668,0.073894,483.33,0.12179,-0.047053,0.99144,221.84
> fitmap #26 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 93502
points
correlation = 0.704, correlation about mean = 0.2338, overlap = 60.62
steps = 116, shift = 10.2, angle = 9.2 degrees
Position of emd_3720_2017_leaf.map (#26) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.53804057 0.84238896 -0.02988589 166.48440525
-0.84278216 -0.53825370 0.00107146 370.35180431
-0.01518361 0.02576378 0.99955273 111.83435343
Axis 0.01465058 -0.00872323 -0.99985462
Axis point 185.24518036 138.63002335 0.00000000
Rotation angle (degrees) 122.57279905
Shift along axis -112.60966719
> select subtract #26
Nothing selected
> hide #!26 models
> color #26 #f6f9afff models
> show #!25 models
> color #25 #f9f9b4ff models
> show #!26 models
> hide #!25 models
> show #!25 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> hide #!25 models
> show #!1 models
> show #!24 models
> fitmap #24 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 6862
points
correlation = 1, correlation about mean = 0.9998, overlap = 0.8994
steps = 44, shift = 0.0835, angle = 0.0216 degrees
Position of postprocess_20231221.mrc (#24) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99999998 0.00009904 -0.00019217 0.02086519
-0.00009901 0.99999999 0.00013925 0.00946728
0.00019218 -0.00013923 0.99999997 -0.04895539
Axis -0.54148696 -0.74733003 -0.38508401
Axis point 253.79232735 0.00000000 109.89549266
Rotation angle (degrees) 0.01473352
Shift along axis 0.00047852
> hide #!24 models
> show #!25 models
> hide #!25 models
> rename #26 id #40
> show #3 models
> combine #3 modelId #26
> select add #26
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> select subtract #26
Nothing selected
> select add #26
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> select subtract #26
Nothing selected
> hide #26 models
> combine #4 modelId #27
> hide #27 models
> combine #5 modelId #26
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/cmd.py", line 80, in combine_cmd
session.models.add([combination])
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 699, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 766, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
ValueError: Tried to add model copy of hArf1_P84078 #26 with the same id as
another model copy of CopA_F8WHL2.pdb #26
ValueError: Tried to add model copy of hArf1_P84078 #26 with the same id as
another model copy of CopA_F8WHL2.pdb #26
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 766, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
See log for complete Python traceback.
> combine #5 modelId #28
> combine #6 modelId #29
> combine #7 modelId #30
> combine #8 modelId #31
> combine #9 modelId #32
> combine #10 modelId #33
> combine #11 modelId #34
> combine #12 modelId #35
> show #27 models
> show #26 models
> show #!25 models
> show #!24 models
> hide #3 models
> select add #24
2 models selected
> select add #25
4 models selected
> select add #26
9810 atoms, 10032 bonds, 1233 residues, 5 models selected
> select add #27
17311 atoms, 17651 bonds, 2186 residues, 6 models selected
> select add #28
18768 atoms, 19134 bonds, 2367 residues, 7 models selected
> select add #29
20225 atoms, 20617 bonds, 2548 residues, 8 models selected
> select add #30
27439 atoms, 27990 bonds, 3453 residues, 9 models selected
> select add #31
28901 atoms, 29471 bonds, 3632 residues, 10 models selected
> select add #32
35574 atoms, 36257 bonds, 1 pseudobond, 4485 residues, 12 models selected
> select add #33
36994 atoms, 37698 bonds, 1 pseudobond, 4662 residues, 13 models selected
> select add #34
39361 atoms, 40096 bonds, 1 pseudobond, 4960 residues, 14 models selected
> select add #35
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 15 models selected
> show #!13 models
> view matrix models
> #25,-0.34889,0.93716,-0.003888,242.9,-0.93695,-0.34889,-0.019709,475.09,-0.019827,-0.0032334,0.9998,227.68,#24,0.97737,-0.20999,0.025535,155.17,0.21041,0.9775,-0.015062,79.841,-0.021798,0.020094,0.99956,112.1,#26,0.9145,0.2542,0.31475,268.43,-0.0087926,0.79028,-0.61269,349.5,-0.40449,0.55754,0.72494,352.58,#27,-0.028359,-0.84788,0.52942,286,-0.059539,0.53013,0.84583,313.33,-0.99782,-0.0075343,-0.065516,349,#28,0.31644,0.15578,0.93574,241.47,-0.64886,-0.68403,0.3333,299.86,0.69199,-0.71263,-0.11537,291.74,#29,-0.71941,-0.60958,0.33295,357.19,-0.64676,0.41312,-0.64112,319.13,0.25327,-0.67657,-0.69145,331.26,#30,-0.18159,0.036625,-0.98269,308.25,-0.032973,-0.99897,-0.031139,289.3,-0.98282,0.026748,0.18261,350.04,#31,0.43065,0.88133,0.19441,54.266,-0.82145,0.29354,0.48893,156.38,0.37384,-0.37026,0.85039,588.54,#32,0.34531,-0.42427,-0.83711,320.98,0.64973,-0.53557,0.53946,398.89,-0.67721,-0.73018,0.090725,371.57,#33,0.26632,-0.95725,-0.11288,335.32,-0.35637,0.011022,-0.93428,361.06,0.89559,0.28904,-0.3382,330.07,#34,0.798,-0.13224,0.58798,304.64,-0.53929,-0.59219,0.59873,346.6,0.26901,-0.79488,-0.54388,303.77,#35,-0.87975,0.093127,-0.46623,334.26,0.2392,0.93418,-0.26476,361.44,0.41089,-0.34444,-0.84411,329.19
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.34889,0.93716,-0.003888,259.26,-0.93695,-0.34889,-0.019709,272.45,-0.019827,-0.0032334,0.9998,250.74,#24,0.97737,-0.20999,0.025535,171.52,0.21041,0.9775,-0.015062,-122.8,-0.021798,0.020094,0.99956,135.16,#26,0.9145,0.2542,0.31475,284.79,-0.0087926,0.79028,-0.61269,146.86,-0.40449,0.55754,0.72494,375.64,#27,-0.028359,-0.84788,0.52942,302.35,-0.059539,0.53013,0.84583,110.69,-0.99782,-0.0075343,-0.065516,372.05,#28,0.31644,0.15578,0.93574,257.82,-0.64886,-0.68403,0.3333,97.217,0.69199,-0.71263,-0.11537,314.79,#29,-0.71941,-0.60958,0.33295,373.55,-0.64676,0.41312,-0.64112,116.49,0.25327,-0.67657,-0.69145,354.31,#30,-0.18159,0.036625,-0.98269,324.61,-0.032973,-0.99897,-0.031139,86.663,-0.98282,0.026748,0.18261,373.09,#31,0.43065,0.88133,0.19441,70.621,-0.82145,0.29354,0.48893,-46.259,0.37384,-0.37026,0.85039,611.6,#32,0.34531,-0.42427,-0.83711,337.33,0.64973,-0.53557,0.53946,196.25,-0.67721,-0.73018,0.090725,394.62,#33,0.26632,-0.95725,-0.11288,351.67,-0.35637,0.011022,-0.93428,158.42,0.89559,0.28904,-0.3382,353.12,#34,0.798,-0.13224,0.58798,321,-0.53929,-0.59219,0.59873,143.96,0.26901,-0.79488,-0.54388,326.82,#35,-0.87975,0.093127,-0.46623,350.61,0.2392,0.93418,-0.26476,158.8,0.41089,-0.34444,-0.84411,352.24
> view matrix models
> #25,-0.34889,0.93716,-0.003888,248.71,-0.93695,-0.34889,-0.019709,636.82,-0.019827,-0.0032334,0.9998,207.75,#24,0.97737,-0.20999,0.025535,160.98,0.21041,0.9775,-0.015062,241.57,-0.021798,0.020094,0.99956,92.166,#26,0.9145,0.2542,0.31475,274.24,-0.0087926,0.79028,-0.61269,511.23,-0.40449,0.55754,0.72494,332.65,#27,-0.028359,-0.84788,0.52942,291.81,-0.059539,0.53013,0.84583,475.06,-0.99782,-0.0075343,-0.065516,329.06,#28,0.31644,0.15578,0.93574,247.28,-0.64886,-0.68403,0.3333,461.59,0.69199,-0.71263,-0.11537,271.8,#29,-0.71941,-0.60958,0.33295,363,-0.64676,0.41312,-0.64112,480.86,0.25327,-0.67657,-0.69145,311.32,#30,-0.18159,0.036625,-0.98269,314.06,-0.032973,-0.99897,-0.031139,451.03,-0.98282,0.026748,0.18261,330.11,#31,0.43065,0.88133,0.19441,60.076,-0.82145,0.29354,0.48893,318.11,0.37384,-0.37026,0.85039,568.61,#32,0.34531,-0.42427,-0.83711,326.79,0.64973,-0.53557,0.53946,560.62,-0.67721,-0.73018,0.090725,351.64,#33,0.26632,-0.95725,-0.11288,341.13,-0.35637,0.011022,-0.93428,522.79,0.89559,0.28904,-0.3382,310.14,#34,0.798,-0.13224,0.58798,310.45,-0.53929,-0.59219,0.59873,508.33,0.26901,-0.79488,-0.54388,283.84,#35,-0.87975,0.093127,-0.46623,340.07,0.2392,0.93418,-0.26476,523.16,0.41089,-0.34444,-0.84411,309.25
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.18237,0.97993,0.080544,169.64,-0.98154,0.18625,-0.043568,594.7,-0.057694,-0.071112,0.9958,219.25,#24,0.72524,-0.6807,0.10328,289.46,0.686,0.72719,-0.02437,214.03,-0.058512,0.088521,0.99435,85.025,#26,0.75605,-0.14818,0.63752,265.26,0.47541,0.7938,-0.3793,497.36,-0.44986,0.58986,0.67059,335.05,#27,-0.06719,-0.99766,0.012461,298.61,-0.040957,0.015236,0.99904,475.59,-0.9969,0.066615,-0.041885,328.44,#28,0.65513,0.43237,0.61956,263.27,-0.40857,-0.48705,0.77192,442.45,0.63551,-0.75884,-0.14243,272.8,#29,-0.26333,-0.78321,0.56324,355.15,-0.93163,0.054896,-0.35923,517.81,0.25043,-0.61933,-0.74412,307.52,#30,-0.21067,0.54708,-0.81013,330.06,-0.097844,-0.83637,-0.53936,466.52,-0.97265,-0.034359,0.22973,326.94,#31,0.81803,0.57472,-0.022662,199.01,-0.4893,0.71607,0.49783,215.56,0.30234,-0.39615,0.86698,569.64,#32,-0.089093,-0.14088,-0.98601,286.16,0.75118,-0.65958,0.026363,566.32,-0.65406,-0.73832,0.16459,354.25,#33,0.47688,-0.80224,0.35916,314.81,-0.18928,-0.49276,-0.84933,542.4,0.85834,0.33705,-0.38684,309.92,#34,0.97903,0.13299,0.15431,294.1,-0.055335,-0.55539,0.82975,514.82,0.19604,-0.82089,-0.53639,284.39,#35,-0.84439,-0.42632,-0.32442,313.64,-0.26047,0.85589,-0.44678,542.2,0.46814,-0.29275,-0.83375,309.11
> view matrix models
> #25,0.21528,0.97374,-0.074004,187.61,-0.96375,0.19962,-0.17704,606.21,-0.15762,0.10943,0.98142,212.92,#24,0.70693,-0.70538,-0.051845,336.95,0.69167,0.70478,-0.1577,247.8,0.14778,0.07562,0.98613,50.064,#26,0.80378,-0.25918,0.53551,266.65,0.53597,0.70614,-0.46272,494.68,-0.25821,0.65894,0.70649,328.42,#27,0.089621,-0.99594,-0.0078889,301.19,0.093512,0.00052849,0.99562,474.19,-0.99158,-0.089966,0.09318,324.33,#28,0.55913,0.55788,0.61331,275.82,-0.48688,-0.37781,0.78753,448.66,0.67106,-0.73894,0.060377,259.93,#29,-0.27405,-0.67866,0.68141,359.14,-0.95836,0.13355,-0.25242,519.16,0.080305,-0.72221,-0.687,318.35,#30,-0.05431,0.56793,-0.82128,332.72,0.033072,-0.82102,-0.56994,465.58,-0.99798,-0.058115,0.025807,326.61,#31,0.77391,0.60995,-0.17038,172.31,-0.52102,0.76617,0.3762,183.44,0.36,-0.20238,0.91074,510.27,#32,-0.0064415,-0.006784,-0.99996,282.45,0.83203,-0.55473,-0.0015962,560.54,-0.5547,-0.832,0.0092177,359.63,#33,0.34263,-0.8314,0.43747,318.27,-0.30066,-0.5382,-0.78736,542.98,0.89006,0.13825,-0.43437,317.59,#34,0.93781,0.2737,0.21353,302.52,-0.075794,-0.43883,0.89537,518.97,0.33876,-0.85587,-0.3908,285.69,#35,-0.8996,-0.39839,-0.17889,317.26,-0.32596,0.88516,-0.33204,542.88,0.29063,-0.24039,-0.92615,316.59
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.21528,0.97374,-0.074004,186.53,-0.96375,0.19962,-0.17704,728.02,-0.15762,0.10943,0.98142,198.35,#24,0.70693,-0.70538,-0.051845,335.87,0.69167,0.70478,-0.1577,369.61,0.14778,0.07562,0.98613,35.494,#26,0.80378,-0.25918,0.53551,265.57,0.53597,0.70614,-0.46272,616.5,-0.25821,0.65894,0.70649,313.85,#27,0.089621,-0.99594,-0.0078889,300.1,0.093512,0.00052849,0.99562,596,-0.99158,-0.089966,0.09318,309.76,#28,0.55913,0.55788,0.61331,274.74,-0.48688,-0.37781,0.78753,570.47,0.67106,-0.73894,0.060377,245.36,#29,-0.27405,-0.67866,0.68141,358.06,-0.95836,0.13355,-0.25242,640.97,0.080305,-0.72221,-0.687,303.78,#30,-0.05431,0.56793,-0.82128,331.64,0.033072,-0.82102,-0.56994,587.39,-0.99798,-0.058115,0.025807,312.04,#31,0.77391,0.60995,-0.17038,171.23,-0.52102,0.76617,0.3762,305.26,0.36,-0.20238,0.91074,495.7,#32,-0.0064415,-0.006784,-0.99996,281.37,0.83203,-0.55473,-0.0015962,682.35,-0.5547,-0.832,0.0092177,345.06,#33,0.34263,-0.8314,0.43747,317.19,-0.30066,-0.5382,-0.78736,664.79,0.89006,0.13825,-0.43437,303.02,#34,0.93781,0.2737,0.21353,301.44,-0.075794,-0.43883,0.89537,640.78,0.33876,-0.85587,-0.3908,271.12,#35,-0.8996,-0.39839,-0.17889,316.17,-0.32596,0.88516,-0.33204,664.69,0.29063,-0.24039,-0.92615,302.02
> view matrix models
> #25,0.21528,0.97374,-0.074004,221.97,-0.96375,0.19962,-0.17704,638.99,-0.15762,0.10943,0.98142,223.97,#24,0.70693,-0.70538,-0.051845,371.32,0.69167,0.70478,-0.1577,280.59,0.14778,0.07562,0.98613,61.119,#26,0.80378,-0.25918,0.53551,301.01,0.53597,0.70614,-0.46272,527.47,-0.25821,0.65894,0.70649,339.47,#27,0.089621,-0.99594,-0.0078889,335.55,0.093512,0.00052849,0.99562,506.98,-0.99158,-0.089966,0.09318,335.39,#28,0.55913,0.55788,0.61331,310.18,-0.48688,-0.37781,0.78753,481.44,0.67106,-0.73894,0.060377,270.98,#29,-0.27405,-0.67866,0.68141,393.5,-0.95836,0.13355,-0.25242,551.95,0.080305,-0.72221,-0.687,329.4,#30,-0.05431,0.56793,-0.82128,367.08,0.033072,-0.82102,-0.56994,498.37,-0.99798,-0.058115,0.025807,337.67,#31,0.77391,0.60995,-0.17038,206.67,-0.52102,0.76617,0.3762,216.23,0.36,-0.20238,0.91074,521.32,#32,-0.0064415,-0.006784,-0.99996,316.81,0.83203,-0.55473,-0.0015962,593.32,-0.5547,-0.832,0.0092177,370.69,#33,0.34263,-0.8314,0.43747,352.63,-0.30066,-0.5382,-0.78736,575.76,0.89006,0.13825,-0.43437,328.65,#34,0.93781,0.2737,0.21353,336.88,-0.075794,-0.43883,0.89537,551.76,0.33876,-0.85587,-0.3908,296.75,#35,-0.8996,-0.39839,-0.17889,351.62,-0.32596,0.88516,-0.33204,575.66,0.29063,-0.24039,-0.92615,327.65
> view matrix models
> #25,0.21528,0.97374,-0.074004,190.23,-0.96375,0.19962,-0.17704,638.64,-0.15762,0.10943,0.98142,205.91,#24,0.70693,-0.70538,-0.051845,339.58,0.69167,0.70478,-0.1577,280.23,0.14778,0.07562,0.98613,43.056,#26,0.80378,-0.25918,0.53551,269.27,0.53597,0.70614,-0.46272,527.12,-0.25821,0.65894,0.70649,321.41,#27,0.089621,-0.99594,-0.0078889,303.81,0.093512,0.00052849,0.99562,506.62,-0.99158,-0.089966,0.09318,317.32,#28,0.55913,0.55788,0.61331,278.44,-0.48688,-0.37781,0.78753,481.09,0.67106,-0.73894,0.060377,252.92,#29,-0.27405,-0.67866,0.68141,361.76,-0.95836,0.13355,-0.25242,551.59,0.080305,-0.72221,-0.687,311.34,#30,-0.05431,0.56793,-0.82128,335.34,0.033072,-0.82102,-0.56994,498.01,-0.99798,-0.058115,0.025807,319.61,#31,0.77391,0.60995,-0.17038,174.93,-0.52102,0.76617,0.3762,215.88,0.36,-0.20238,0.91074,503.26,#32,-0.0064415,-0.006784,-0.99996,285.07,0.83203,-0.55473,-0.0015962,592.97,-0.5547,-0.832,0.0092177,352.63,#33,0.34263,-0.8314,0.43747,320.9,-0.30066,-0.5382,-0.78736,575.41,0.89006,0.13825,-0.43437,310.59,#34,0.93781,0.2737,0.21353,305.14,-0.075794,-0.43883,0.89537,551.4,0.33876,-0.85587,-0.3908,278.69,#35,-0.8996,-0.39839,-0.17889,319.88,-0.32596,0.88516,-0.33204,575.31,0.29063,-0.24039,-0.92615,309.59
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.50923,0.84815,0.14602,141.9,-0.85927,0.51059,0.03087,569.07,-0.048376,-0.14119,0.9888,217.99,#24,0.4365,-0.88527,0.16053,379.09,0.89134,0.44977,0.056666,247.89,-0.12237,0.11835,0.9854,84.349,#26,0.51686,-0.38221,0.76601,271.72,0.68743,0.71858,-0.10529,516.05,-0.5102,0.581,0.63415,329.17,#27,-0.10416,-0.93516,-0.33857,310.14,-0.10551,-0.32811,0.93873,506.9,-0.98895,0.1335,-0.064494,320.81,#28,0.79073,0.53192,0.30302,285.51,-0.12816,-0.34017,0.93159,461.16,0.5986,-0.77547,-0.20081,268.42,#29,0.091956,-0.78651,0.61069,347.17,-0.95321,-0.2469,-0.17445,565.11,0.28798,-0.56608,-0.77241,295.19,#30,-0.21726,0.80127,-0.55747,342.64,-0.20742,-0.59596,-0.77576,509.22,-0.95382,-0.052911,0.29567,317.38,#31,0.95271,0.26637,-0.14626,320.93,-0.1621,0.85256,0.49685,239.34,0.25704,-0.44965,0.85542,573.82,#32,-0.38139,0.056717,-0.92267,268.33,0.64435,-0.69938,-0.30934,588.75,-0.66284,-0.7125,0.23019,345.41,#33,0.55998,-0.56032,0.61029,301,0.025451,-0.72464,-0.68866,574.3,0.82811,0.40117,-0.39152,299.77,#34,0.94633,0.2721,-0.17443,289.8,0.29564,-0.51058,0.80741,540.15,0.13064,-0.81564,-0.56362,276.31,#35,-0.67336,-0.71329,-0.19445,299.93,-0.51577,0.64165,-0.56768,573.67,0.52969,-0.28196,-0.79995,299.05
> view matrix models
> #25,0.42548,0.84231,-0.33087,215.81,-0.77652,0.52757,0.3445,513.87,0.46474,0.11035,0.87855,153.55,#24,0.4908,-0.81231,-0.31508,470.14,0.85183,0.3714,0.36939,193.32,-0.18304,-0.44969,0.87423,252.75,#26,0.73166,-0.56955,0.37455,275.65,0.5491,0.81802,0.17126,510.7,-0.40393,0.080366,0.91125,322.17,#27,0.36385,-0.90563,-0.21784,312.97,-0.41097,-0.36596,0.83498,503.43,-0.8359,-0.21428,-0.50533,335.73,#28,0.41171,0.81299,0.41176,313.2,0.14132,-0.50332,0.85247,441.67,0.90029,-0.29278,-0.32212,295.37,#29,-0.10494,-0.44353,0.8901,360.78,-0.80605,-0.48629,-0.33735,554.58,0.58247,-0.75286,-0.30647,313.05,#30,0.24209,0.69968,-0.67219,343.39,-0.5084,-0.4986,-0.70209,507.91,-0.82639,0.51171,0.23502,347.06,#31,0.71227,0.49124,-0.50135,189.91,0.022018,0.69828,0.71548,327.93,0.70156,-0.52065,0.48655,635.35,#32,0.0076163,0.34462,-0.93871,269.02,0.37001,-0.87308,-0.31753,584.15,-0.929,-0.34491,-0.13416,311.14,#33,0.10925,-0.72117,0.68409,318.38,0.33293,-0.62191,-0.70879,559.95,0.9366,0.30519,0.17215,292.78,#34,0.79046,0.59314,0.15285,317.59,0.41656,-0.70353,0.57578,519.33,0.44905,-0.39146,-0.80319,278.94,#35,-0.86959,-0.46326,0.17086,317.74,-0.39659,0.44918,-0.8006,559.02,0.29414,-0.76395,-0.57433,291.89
> view matrix models
> #25,0.48491,0.64504,-0.59058,264.36,-0.71196,0.68334,0.16178,512.71,0.50792,0.34202,0.7906,133.62,#24,0.30034,-0.75672,-0.58066,559.49,0.95379,0.23289,0.18985,246.55,-0.0084323,-0.61085,0.7917,272.67,#26,0.64964,-0.75219,0.11033,284.18,0.73824,0.65882,0.14476,503.64,-0.18158,-0.012587,0.9833,311.24,#27,0.62819,-0.72051,-0.29367,318.18,-0.22379,-0.52881,0.8187,503.23,-0.74518,-0.44859,-0.49344,333,#28,0.15507,0.95405,0.25641,342.17,0.12514,-0.27643,0.95285,448.01,0.97995,-0.11567,-0.16225,290.36,#29,-0.03546,-0.13522,0.99018,356.15,-0.87015,-0.48312,-0.097137,565.85,0.49151,-0.86505,-0.10053,325.62,#30,0.53437,0.66699,-0.51921,343.34,-0.34598,-0.38786,-0.85432,512.96,-0.7712,0.63616,0.023504,351.61,#31,0.51188,0.41262,-0.75347,177.33,0.097903,0.84336,0.52836,272.24,0.85346,-0.34422,0.3913,583.04,#32,0.12504,0.61164,-0.78119,262.77,0.46553,-0.73148,-0.49821,574.62,-0.87615,-0.30138,-0.3762,303.24,#33,-0.18477,-0.60032,0.77812,319.29,0.24043,-0.79531,-0.55649,564.06,0.95292,0.084257,0.29128,296.02,#34,0.54734,0.8162,0.185,331.36,0.52601,-0.50744,0.68251,526.09,0.65095,-0.27625,-0.70707,280.05,#35,-0.79214,-0.37564,0.48105,319.11,-0.60823,0.42036,-0.67332,563.12,0.050705,-0.82595,-0.56146,294.95
> view matrix models
> #25,0.62413,0.55993,-0.54492,253.09,-0.58658,0.79651,0.14661,486.98,0.51613,0.22813,0.82557,141.89,#24,0.15242,-0.82823,-0.53926,594.69,0.98219,0.06629,0.17579,279.35,-0.10985,-0.55646,0.82358,274.11,#26,0.51555,-0.84112,0.16346,287.79,0.80395,0.54083,0.24732,496.93,-0.29643,0.0039063,0.95505,317.17,#27,0.59482,-0.66576,-0.4505,323.06,-0.19826,-0.66461,0.7204,503.34,-0.77903,-0.33919,-0.52732,335.74,#28,0.21023,0.9728,0.097302,351.67,0.23406,-0.14671,0.96109,448.48,0.94922,-0.17927,-0.25854,295.56,#29,0.13366,-0.12808,0.98272,350.52,-0.81827,-0.57368,0.036526,569.81,0.55908,-0.809,-0.18149,320.11,#30,0.51863,0.76498,-0.38188,347.84,-0.33444,-0.22956,-0.91403,518.2,-0.78688,0.60176,0.13678,351.19,#31,0.55617,0.25355,-0.79144,238.28,0.24672,0.85902,0.44858,278.17,0.7936,-0.44475,0.41521,614.71,#32,-0.014613,0.68908,-0.72454,255.42,0.39749,-0.66089,-0.63657,563.1,-0.91749,-0.29729,-0.26424,305.62,#33,-0.14411,-0.46595,0.873,312.16,0.29674,-0.86196,-0.41107,560.11,0.94402,0.19981,0.26248,294.18,#34,0.51122,0.85908,0.025109,328.5,0.65543,-0.4086,0.63519,522.97,0.55594,-0.30827,-0.77195,280.2,#35,-0.68567,-0.49743,0.53144,312.04,-0.70798,0.28603,-0.64572,559.07,0.16919,-0.819,-0.54829,293.21
> view matrix models
> #25,0.72986,0.45034,-0.5143,250.65,-0.54918,0.83428,-0.048833,502.39,0.40708,0.31808,0.85622,139.96,#24,0.0023112,-0.85836,-0.51305,625.45,0.99972,0.014128,-0.019133,332.95,0.023671,-0.51286,0.85815,229.96,#26,0.37665,-0.90908,0.17805,293.11,0.90486,0.40222,0.13949,493.98,-0.19842,0.10857,0.97409,313.6,#27,0.57363,-0.58008,-0.57832,328.04,-0.00043152,-0.70624,0.70797,503.12,-0.81911,-0.40586,-0.40537,331.67,#28,0.22585,0.97248,-0.057236,362.04,0.13434,0.0271,0.99056,459.06,0.96485,-0.23141,-0.12453,283.23,#29,0.28121,-0.087825,0.95562,344.68,-0.8559,-0.4733,0.20837,574.46,0.43399,-0.87651,-0.20827,324.57,#30,0.51765,0.822,-0.2374,351.21,-0.14427,-0.18964,-0.9712,519.35,-0.84334,0.53699,0.020421,348.19,#31,0.55726,0.10169,-0.82409,292.19,0.21974,0.93903,0.26447,232.53,0.80074,-0.32847,0.50093,579.09,#32,-0.12232,0.76018,-0.6381,250.91,0.50955,-0.50362,-0.69765,555.46,-0.8517,-0.41048,-0.32575,312.56,#33,-0.13357,-0.32454,0.93639,306.77,0.14292,-0.94129,-0.30585,562.62,0.98068,0.092976,0.17212,298.87,#34,0.44063,0.89098,-0.10952,327.53,0.64499,-0.22937,0.72896,530.57,0.62437,-0.39184,-0.67574,279.27,#35,-0.56558,-0.57777,0.58847,306.75,-0.81956,0.31434,-0.47907,561.71,0.091809,-0.75325,-0.6513,297.77
> ui mousemode right zoom
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #4 models
> hide #4 models
> show #3 models
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.72986,0.45034,-0.5143,389.96,-0.54918,0.83428,-0.048833,659.89,0.40708,0.31808,0.85622,62.474,#24,0.0023112,-0.85836,-0.51305,764.76,0.99972,0.014128,-0.019133,490.45,0.023671,-0.51286,0.85815,152.47,#26,0.37665,-0.90908,0.17805,432.42,0.90486,0.40222,0.13949,651.48,-0.19842,0.10857,0.97409,236.12,#27,0.57363,-0.58008,-0.57832,467.35,-0.00043152,-0.70624,0.70797,660.62,-0.81911,-0.40586,-0.40537,254.18,#28,0.22585,0.97248,-0.057236,501.35,0.13434,0.0271,0.99056,616.56,0.96485,-0.23141,-0.12453,205.75,#29,0.28121,-0.087825,0.95562,483.99,-0.8559,-0.4733,0.20837,731.96,0.43399,-0.87651,-0.20827,247.08,#30,0.51765,0.822,-0.2374,490.53,-0.14427,-0.18964,-0.9712,676.85,-0.84334,0.53699,0.020421,270.7,#31,0.55726,0.10169,-0.82409,431.5,0.21974,0.93903,0.26447,390.03,0.80074,-0.32847,0.50093,501.6,#32,-0.12232,0.76018,-0.6381,390.22,0.50955,-0.50362,-0.69765,712.96,-0.8517,-0.41048,-0.32575,235.07,#33,-0.13357,-0.32454,0.93639,446.08,0.14292,-0.94129,-0.30585,720.12,0.98068,0.092976,0.17212,221.38,#34,0.44063,0.89098,-0.10952,466.84,0.64499,-0.22937,0.72896,688.07,0.62437,-0.39184,-0.67574,201.78,#35,-0.56558,-0.57777,0.58847,446.06,-0.81956,0.31434,-0.47907,719.21,0.091809,-0.75325,-0.6513,220.28
> view matrix models
> #25,0.72986,0.45034,-0.5143,267.48,-0.54918,0.83428,-0.048833,664.17,0.40708,0.31808,0.85622,111.09,#24,0.0023112,-0.85836,-0.51305,642.27,0.99972,0.014128,-0.019133,494.73,0.023671,-0.51286,0.85815,201.09,#26,0.37665,-0.90908,0.17805,309.93,0.90486,0.40222,0.13949,655.76,-0.19842,0.10857,0.97409,284.73,#27,0.57363,-0.58008,-0.57832,344.86,-0.00043152,-0.70624,0.70797,664.9,-0.81911,-0.40586,-0.40537,302.8,#28,0.22585,0.97248,-0.057236,378.86,0.13434,0.0271,0.99056,620.84,0.96485,-0.23141,-0.12453,254.37,#29,0.28121,-0.087825,0.95562,361.5,-0.8559,-0.4733,0.20837,736.24,0.43399,-0.87651,-0.20827,295.7,#30,0.51765,0.822,-0.2374,368.04,-0.14427,-0.18964,-0.9712,681.13,-0.84334,0.53699,0.020421,319.32,#31,0.55726,0.10169,-0.82409,309.01,0.21974,0.93903,0.26447,394.31,0.80074,-0.32847,0.50093,550.22,#32,-0.12232,0.76018,-0.6381,267.73,0.50955,-0.50362,-0.69765,717.24,-0.8517,-0.41048,-0.32575,283.69,#33,-0.13357,-0.32454,0.93639,323.59,0.14292,-0.94129,-0.30585,724.4,0.98068,0.092976,0.17212,270,#34,0.44063,0.89098,-0.10952,344.35,0.64499,-0.22937,0.72896,692.35,0.62437,-0.39184,-0.67574,250.4,#35,-0.56558,-0.57777,0.58847,323.57,-0.81956,0.31434,-0.47907,723.49,0.091809,-0.75325,-0.6513,268.9
> view matrix models
> #25,0.72986,0.45034,-0.5143,276.32,-0.54918,0.83428,-0.048833,565,0.40708,0.31808,0.85622,113.98,#24,0.0023112,-0.85836,-0.51305,651.12,0.99972,0.014128,-0.019133,395.56,0.023671,-0.51286,0.85815,203.98,#26,0.37665,-0.90908,0.17805,318.78,0.90486,0.40222,0.13949,556.59,-0.19842,0.10857,0.97409,287.62,#27,0.57363,-0.58008,-0.57832,353.71,-0.00043152,-0.70624,0.70797,565.73,-0.81911,-0.40586,-0.40537,305.69,#28,0.22585,0.97248,-0.057236,387.71,0.13434,0.0271,0.99056,521.67,0.96485,-0.23141,-0.12453,257.25,#29,0.28121,-0.087825,0.95562,370.35,-0.8559,-0.4733,0.20837,637.07,0.43399,-0.87651,-0.20827,298.59,#30,0.51765,0.822,-0.2374,376.89,-0.14427,-0.18964,-0.9712,581.96,-0.84334,0.53699,0.020421,322.21,#31,0.55726,0.10169,-0.82409,317.86,0.21974,0.93903,0.26447,295.14,0.80074,-0.32847,0.50093,553.1,#32,-0.12232,0.76018,-0.6381,276.58,0.50955,-0.50362,-0.69765,618.07,-0.8517,-0.41048,-0.32575,286.58,#33,-0.13357,-0.32454,0.93639,332.44,0.14292,-0.94129,-0.30585,625.23,0.98068,0.092976,0.17212,272.88,#34,0.44063,0.89098,-0.10952,353.2,0.64499,-0.22937,0.72896,593.18,0.62437,-0.39184,-0.67574,253.29,#35,-0.56558,-0.57777,0.58847,332.42,-0.81956,0.31434,-0.47907,624.32,0.091809,-0.75325,-0.6513,271.78
> view matrix models
> #25,0.72986,0.45034,-0.5143,282.76,-0.54918,0.83428,-0.048833,571.39,0.40708,0.31808,0.85622,109.8,#24,0.0023112,-0.85836,-0.51305,657.56,0.99972,0.014128,-0.019133,401.95,0.023671,-0.51286,0.85815,199.8,#26,0.37665,-0.90908,0.17805,325.22,0.90486,0.40222,0.13949,562.98,-0.19842,0.10857,0.97409,283.44,#27,0.57363,-0.58008,-0.57832,360.15,-0.00043152,-0.70624,0.70797,572.11,-0.81911,-0.40586,-0.40537,301.51,#28,0.22585,0.97248,-0.057236,394.15,0.13434,0.0271,0.99056,528.06,0.96485,-0.23141,-0.12453,253.07,#29,0.28121,-0.087825,0.95562,376.79,-0.8559,-0.4733,0.20837,643.45,0.43399,-0.87651,-0.20827,294.41,#30,0.51765,0.822,-0.2374,383.33,-0.14427,-0.18964,-0.9712,588.35,-0.84334,0.53699,0.020421,318.03,#31,0.55726,0.10169,-0.82409,324.3,0.21974,0.93903,0.26447,301.53,0.80074,-0.32847,0.50093,548.92,#32,-0.12232,0.76018,-0.6381,283.02,0.50955,-0.50362,-0.69765,624.46,-0.8517,-0.41048,-0.32575,282.4,#33,-0.13357,-0.32454,0.93639,338.88,0.14292,-0.94129,-0.30585,631.62,0.98068,0.092976,0.17212,268.71,#34,0.44063,0.89098,-0.10952,359.64,0.64499,-0.22937,0.72896,599.57,0.62437,-0.39184,-0.67574,249.11,#35,-0.56558,-0.57777,0.58847,338.86,-0.81956,0.31434,-0.47907,630.71,0.091809,-0.75325,-0.6513,267.6
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.97821,0.20538,-0.030554,234.84,-0.12876,0.71545,0.68669,442.91,0.16289,-0.66779,0.7263,266.43,#24,-0.35202,-0.93516,-0.039506,644.08,0.65166,-0.27517,0.70684,357.33,-0.67188,0.22308,0.70627,216.66,#26,-0.10683,-0.84648,0.52159,348.76,0.37526,0.45147,0.80954,564.79,-0.92074,0.28221,0.26942,331.2,#27,0.11351,-0.39709,-0.91073,382.05,-0.69703,-0.68505,0.21181,580,-0.708,0.61076,-0.35454,314.17,#28,0.55873,0.68844,-0.46246,404.87,0.79326,-0.28092,0.54021,510.85,0.24198,-0.66868,-0.70307,302.28,#29,0.73289,-0.28311,0.61865,366.63,-0.24665,-0.95801,-0.14621,617.73,0.63407,-0.045429,-0.77194,252.89,#30,0.1093,0.97977,0.16763,402.41,-0.79973,0.18683,-0.57055,600,-0.59033,-0.071697,0.80397,298.08,#31,0.7283,-0.40221,-0.5548,559.38,0.68076,0.33204,0.65293,601.72,-0.078402,-0.85321,0.51563,636.34,#32,-0.65874,0.62896,-0.41288,291.21,-0.31157,-0.72756,-0.61121,608.24,-0.68482,-0.27399,0.67524,312.21,#33,0.26702,0.11683,0.95658,328.53,0.85569,-0.48534,-0.17959,595.35,0.44328,0.86649,-0.22956,269.79,#34,0.40032,0.64472,-0.65121,348.71,0.83038,-0.55578,-0.03978,557.48,-0.38758,-0.52482,-0.75786,270.79,#35,-0.12621,-0.919,0.37352,328.36,-0.37893,-0.30331,-0.87431,593.94,0.91678,-0.25188,-0.30995,269.9
> view matrix models
> #25,0.95358,-0.16872,-0.24942,303.05,0.26361,0.86809,0.42063,414.76,0.14555,-0.46686,0.87227,229.82,#24,-0.64749,-0.71353,-0.26763,704.9,0.5772,-0.68848,0.43912,524.53,-0.49759,0.12985,0.85764,168.64,#26,-0.33237,-0.92947,0.16006,361.3,0.49643,-0.028103,0.86762,554.76,-0.80193,0.36783,0.47075,324.85,#27,0.33044,-0.022493,-0.94356,383.67,-0.3988,-0.90942,-0.11798,586.12,-0.85543,0.41528,-0.30948,312.76,#28,0.19808,0.68202,-0.704,431.99,0.87543,0.19997,0.44004,537.96,0.44089,-0.70347,-0.55745,284.67,#29,0.8212,0.13698,0.55396,348.73,-0.052455,-0.94853,0.31231,626.82,0.56823,-0.28553,-0.77174,262.36,#30,0.37944,0.80373,0.45831,392.42,-0.51775,0.59498,-0.61476,615.98,-0.76678,-0.0040255,0.6419,302.5,#31,0.3705,-0.57613,-0.72856,563.26,0.92275,0.31791,0.21786,605.71,0.1061,-0.753,0.64941,633.81,#32,-0.52691,0.84767,-0.061819,289.5,-0.39341,-0.30772,-0.86633,572.86,-0.75339,-0.43216,0.49562,316.01,#33,-0.074558,0.38237,0.921,324.97,0.76008,-0.57607,0.3007,587.18,0.64554,0.72245,-0.24768,272.47,#34,-0.015474,0.76892,-0.63916,359.04,0.98648,-0.092569,-0.13524,562.32,-0.16316,-0.63261,-0.75709,264.52,#35,0.12247,-0.72847,0.67404,325.42,-0.59737,-0.59646,-0.53609,585.84,0.79256,-0.337,-0.50821,272.22
> hide #!25 models
> view matrix models
> #25,0.30995,-0.0019258,-0.95075,448.39,0.90285,0.31401,0.2937,403.27,0.29798,-0.94942,0.099067,350.03,#24,-0.14001,-0.26182,-0.95491,675.41,-0.22961,-0.92953,0.28853,753.38,-0.96316,0.25966,0.070027,406.32,#26,0.29219,-0.77457,-0.56095,360.23,-0.12266,-0.61206,0.78124,557.75,-0.94846,-0.15946,-0.27385,330.37,#27,0.97376,-0.046372,-0.22279,371.59,-0.21628,-0.49313,-0.84264,591.15,-0.07079,0.86872,-0.49022,310.75,#28,-0.5198,0.85059,-0.079367,434.75,0.80692,0.45836,-0.37254,589.35,-0.2805,-0.25769,-0.92462,348.84,#29,0.0094095,0.60008,0.79988,379.42,0.70702,-0.56966,0.41905,579.15,0.70713,0.56159,-0.42963,238.56,#30,0.96849,0.24124,-0.061855,374.74,-0.23434,0.96683,0.10158,614.05,0.08431,-0.083888,0.9929,287.52,#31,-0.18079,0.18103,-0.96672,209.57,0.88293,-0.40316,-0.24062,812.9,-0.43331,-0.89704,-0.086953,556.3,#32,0.43511,0.88878,-0.14405,323.09,-0.81817,0.3235,-0.47534,514.34,-0.37587,0.32468,0.86793,282.44,#33,-0.78852,-0.17781,0.58874,371.52,0.58279,0.089739,0.80765,538.99,-0.19644,0.97997,0.032862,262.29,#34,-0.196,0.93499,0.2956,403.86,0.57487,0.35377,-0.73782,546.34,-0.79443,0.025316,-0.60683,289.54,#35,-0.36445,0.06647,0.92885,372.38,-0.097824,-0.99466,0.032797,538.41,0.92607,-0.07891,0.36901,263.28
> volume #24 level 0.003588
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.30995,-0.0019258,-0.95075,455.19,0.90285,0.31401,0.2937,440.16,0.29798,-0.94942,0.099067,336.3,#24,-0.14001,-0.26182,-0.95491,682.2,-0.22961,-0.92953,0.28853,790.27,-0.96316,0.25966,0.070027,392.59,#26,0.29219,-0.77457,-0.56095,367.02,-0.12266,-0.61206,0.78124,594.64,-0.94846,-0.15946,-0.27385,316.65,#27,0.97376,-0.046372,-0.22279,378.39,-0.21628,-0.49313,-0.84264,628.04,-0.07079,0.86872,-0.49022,297.03,#28,-0.5198,0.85059,-0.079367,441.55,0.80692,0.45836,-0.37254,626.23,-0.2805,-0.25769,-0.92462,335.11,#29,0.0094095,0.60008,0.79988,386.22,0.70702,-0.56966,0.41905,616.03,0.70713,0.56159,-0.42963,224.84,#30,0.96849,0.24124,-0.061855,381.54,-0.23434,0.96683,0.10158,650.94,0.08431,-0.083888,0.9929,273.8,#31,-0.18079,0.18103,-0.96672,216.37,0.88293,-0.40316,-0.24062,849.79,-0.43331,-0.89704,-0.086953,542.57,#32,0.43511,0.88878,-0.14405,329.89,-0.81817,0.3235,-0.47534,551.23,-0.37587,0.32468,0.86793,268.71,#33,-0.78852,-0.17781,0.58874,378.32,0.58279,0.089739,0.80765,575.88,-0.19644,0.97997,0.032862,248.57,#34,-0.196,0.93499,0.2956,410.66,0.57487,0.35377,-0.73782,583.23,-0.79443,0.025316,-0.60683,275.81,#35,-0.36445,0.06647,0.92885,379.18,-0.097824,-0.99466,0.032797,575.3,0.92607,-0.07891,0.36901,249.55
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.57,0.14349,-0.80902,402.3,0.040342,0.97856,0.20198,454.72,0.82065,-0.14777,0.55199,105.5,#24,-0.16153,-0.55902,-0.81327,727.09,0.79684,-0.56004,0.2267,504.14,-0.58219,-0.61143,0.53591,368.84,#26,0.28091,-0.92212,-0.26607,369.6,0.74836,0.036886,0.66227,550.6,-0.60087,-0.38515,0.70043,253.02,#27,0.8544,-0.24309,-0.45924,392.01,-0.20031,-0.9696,0.14056,579.6,-0.47945,-0.028101,-0.87712,269.94,#28,-0.21858,0.96391,-0.15201,449.38,0.67112,0.26158,0.69367,533.25,0.70839,0.049601,-0.70408,268.07,#29,0.2037,0.35782,0.9113,398.91,-0.35108,-0.84221,0.40917,638.1,0.91392,-0.40329,-0.045937,225.81,#30,0.83638,0.5434,-0.071971,403.44,-0.34577,0.42114,-0.8385,609.1,-0.42533,0.72619,0.54012,278.5,#31,0.13358,0.083074,-0.98755,298.8,0.77732,0.60935,0.1564,478.1,0.61476,-0.78854,0.01682,611.59,#32,0.16541,0.92949,-0.32969,322.73,-0.071503,-0.32211,-0.944,582.84,-0.98363,0.17972,0.01318,204.8,#33,-0.54877,-0.18482,0.81529,377.4,0.55413,-0.81064,0.18922,602.07,0.62593,0.55562,0.54727,203.98,#34,0.036777,0.99686,0.070116,409.08,0.97986,-0.049751,0.19337,574.72,0.19625,0.061593,-0.97862,213.51,#35,-0.41921,-0.25383,0.87169,377.98,-0.80402,-0.34214,-0.4863,600.79,0.42168,-0.90472,-0.060654,203.68
> view matrix models
> #25,0.37461,0.60806,-0.69995,351.15,-0.1851,0.78877,0.58616,466.5,0.90852,-0.090026,0.40803,102.5,#24,0.33175,-0.64403,-0.68933,611.49,0.74672,-0.26728,0.60908,373.1,-0.5765,-0.71679,0.39224,419.96,#26,0.69578,-0.71722,-0.038468,342.85,0.49647,0.44155,0.74736,574.53,-0.51904,-0.5391,0.6633,244.92,#27,0.72783,-0.66054,-0.18425,373.02,-0.60187,-0.74408,0.29001,590.6,-0.32866,-0.10018,-0.93912,266.39,#28,0.0055179,0.95,0.3122,401.36,0.73346,-0.21606,0.64448,522.81,0.67971,0.22543,-0.69798,273.14,#29,-0.14221,-0.01648,0.9897,413.87,-0.35461,-0.93265,-0.066482,636.59,0.92414,-0.36041,0.12679,225.98,#30,0.63489,0.546,-0.54663,395.32,-0.71888,0.15827,-0.67688,611.77,-0.28306,0.8227,0.49299,277.72,#31,0.37644,0.49076,-0.78578,186.96,0.65776,0.45572,0.59973,563.31,0.65242,-0.74261,-0.15125,583.17,#32,0.27592,0.62458,-0.73059,325.47,-0.19449,-0.70809,-0.6788,622.19,-0.9413,0.32939,-0.073904,190.27,#33,-0.3217,-0.63403,0.70322,382.02,0.77969,-0.59877,-0.18317,613.61,0.53721,0.48937,0.68697,199.62,#34,0.45809,0.83061,0.31661,395.06,0.85866,-0.5056,0.084068,575.22,0.22991,0.23335,-0.94482,213.69,#35,-0.81154,-0.22776,0.53807,381.97,-0.49096,-0.23347,-0.83931,612.2,0.31679,-0.94531,0.077644,199.39
> view matrix models
> #25,0.25016,0.77249,-0.58367,331.76,-0.24968,0.63392,0.73198,480.46,0.93546,-0.037381,0.35146,97.865,#24,0.53376,-0.62737,-0.56702,538.64,0.64664,-0.1293,0.75176,336.68,-0.54495,-0.76791,0.33667,435.22,#26,0.8277,-0.55623,0.074347,336.1,0.32318,0.58077,0.74717,589.76,-0.45878,-0.5944,0.66046,239.5,#27,0.60092,-0.79833,-0.039501,367.25,-0.75228,-0.58158,0.3096,599.1,-0.27013,-0.15633,-0.95005,263.42,#28,0.11271,0.85752,0.50195,379.27,0.72416,-0.41679,0.54944,526.84,0.68036,0.30156,-0.66796,272.23,#29,-0.29088,-0.19304,0.93708,420.37,-0.30086,-0.91129,-0.28112,634.35,0.90823,-0.3637,0.20699,226.63,#30,0.48107,0.49949,-0.72047,392.69,-0.84524,0.046152,-0.53239,615.01,-0.23267,0.86509,0.44439,276.6,#31,0.45871,0.6374,-0.61912,154.9,0.56817,0.32532,0.75588,618.17,0.68321,-0.69849,-0.21292,563.84,#32,0.30094,0.42418,-0.85411,334.13,-0.2644,-0.82341,-0.50209,639.27,-0.91626,0.37693,-0.13564,183.78,#33,-0.18366,-0.78788,0.58781,386.45,0.83927,-0.437,-0.32351,618.57,0.51176,0.43391,0.7415,197.68,#34,0.61643,0.67688,0.4023,389.51,0.73987,-0.67275,-0.0017449,578.46,0.26947,0.29872,-0.91551,212.64,#35,-0.92273,-0.19692,0.33136,386.11,-0.29528,-0.19145,-0.93603,617.2,0.24776,-0.96155,0.11851,197.44
> view matrix models
> #25,0.54074,0.83707,0.083165,226.88,-0.79606,0.47727,0.37215,599.46,0.27182,-0.26744,0.92444,148.09,#24,0.4121,-0.90597,0.096951,482.91,0.81913,0.41498,0.396,265.24,-0.399,-0.083775,0.91312,143.4,#26,0.52341,-0.44224,0.72833,351.31,0.50042,0.85137,0.15733,594.34,-0.68965,0.28212,0.66692,276.61,#27,-0.038806,-0.92971,-0.36625,390.47,-0.44005,-0.31317,0.8416,584.98,-0.89714,0.19382,-0.39696,273.68,#28,0.75598,0.59053,0.28243,370.74,0.12512,-0.55386,0.82315,522.93,0.64252,-0.58695,-0.4926,238.98,#29,0.10688,-0.7408,0.66317,426.98,-0.79267,-0.46613,-0.39294,632.96,0.60021,-0.48368,-0.63703,231.47,#30,-0.15027,0.82319,-0.54753,423.02,-0.52993,-0.5346,-0.65831,587.74,-0.83462,0.19123,0.51656,271.18,#31,0.93995,0.26407,-0.21625,394.79,-0.013864,0.66258,0.74886,420.07,0.34103,-0.70089,0.62646,603.07,#32,-0.36159,0.12508,-0.92391,344.39,0.35991,-0.89542,-0.26208,667.95,-0.86007,-0.42729,0.27876,266.86,#33,0.50624,-0.5587,0.65694,380.32,0.33482,-0.57468,-0.74675,640.66,0.79474,0.598,-0.10386,230.48,#34,0.92556,0.33978,-0.16697,371.79,0.37284,-0.7415,0.55783,600.03,0.065726,-0.57856,-0.81299,219.6,#35,-0.68667,-0.71621,-0.12459,379.32,-0.341,0.46869,-0.81489,639.77,0.64203,-0.51708,-0.56607,229.97
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.56775,0.81372,0.12456,224.78,-0.70969,0.40715,0.57495,580.66,0.41713,-0.41483,0.80865,162.63,#24,0.37667,-0.91611,0.13733,485.95,0.70757,0.38021,0.59563,255.54,-0.59788,-0.12718,0.79143,220.71,#26,0.47824,-0.44163,0.75911,355.77,0.33116,0.89124,0.30987,605.8,-0.8134,0.1032,0.57248,281.94,#27,-0.077684,-0.91287,-0.40079,394.88,-0.63455,-0.2648,0.72611,596.21,-0.76897,0.31073,-0.55869,279.1,#28,0.78602,0.56876,0.24227,374.45,0.27305,-0.67099,0.68935,527.75,0.55464,-0.47569,-0.68271,260.66,#29,0.15151,-0.75674,0.63592,428.33,-0.63307,-0.56837,-0.52553,633.39,0.75913,-0.32295,-0.56518,225.1,#30,-0.18419,0.84109,-0.50857,427.21,-0.70821,-0.47236,-0.52471,598.48,-0.68156,0.26353,0.68267,274.27,#31,0.95647,0.21591,-0.19635,419.12,0.069427,0.48514,0.87168,511.39,0.28346,-0.84736,0.44903,636.78,#32,-0.41186,0.11817,-0.90355,347.09,0.15095,-0.96901,-0.19553,675.17,-0.89866,-0.21692,0.38126,255.97,#33,0.54093,-0.51695,0.66345,381.55,0.51089,-0.42466,-0.74743,640.43,0.66812,0.74326,0.034395,224.91,#34,0.92116,0.32205,-0.2185,373.17,0.38248,-0.85291,0.35534,598.34,-0.071924,-0.41089,-0.90884,224.11,#35,-0.64647,-0.75004,-0.13971,380.54,-0.18774,0.33388,-0.92373,639.43,0.73948,-0.57093,-0.35666,224.68
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.56775,0.81372,0.12456,158.31,-0.70969,0.40715,0.57495,456.38,0.41713,-0.41483,0.80865,180.62,#24,0.37667,-0.91611,0.13733,419.48,0.70757,0.38021,0.59563,131.26,-0.59788,-0.12718,0.79143,238.7,#26,0.47824,-0.44163,0.75911,289.3,0.33116,0.89124,0.30987,481.52,-0.8134,0.1032,0.57248,299.92,#27,-0.077684,-0.91287,-0.40079,328.41,-0.63455,-0.2648,0.72611,471.93,-0.76897,0.31073,-0.55869,297.09,#28,0.78602,0.56876,0.24227,307.98,0.27305,-0.67099,0.68935,403.47,0.55464,-0.47569,-0.68271,278.65,#29,0.15151,-0.75674,0.63592,361.86,-0.63307,-0.56837,-0.52553,509.11,0.75913,-0.32295,-0.56518,243.09,#30,-0.18419,0.84109,-0.50857,360.74,-0.70821,-0.47236,-0.52471,474.2,-0.68156,0.26353,0.68267,292.26,#31,0.95647,0.21591,-0.19635,352.65,0.069427,0.48514,0.87168,387.11,0.28346,-0.84736,0.44903,654.76,#32,-0.41186,0.11817,-0.90355,280.62,0.15095,-0.96901,-0.19553,550.89,-0.89866,-0.21692,0.38126,273.96,#33,0.54093,-0.51695,0.66345,315.08,0.51089,-0.42466,-0.74743,516.14,0.66812,0.74326,0.034395,242.9,#34,0.92116,0.32205,-0.2185,306.7,0.38248,-0.85291,0.35534,474.06,-0.071924,-0.41089,-0.90884,242.1,#35,-0.64647,-0.75004,-0.13971,314.08,-0.18774,0.33388,-0.92373,515.15,0.73948,-0.57093,-0.35666,242.66
> view matrix models
> #25,0.56775,0.81372,0.12456,157.25,-0.70969,0.40715,0.57495,457.09,0.41713,-0.41483,0.80865,180.37,#24,0.37667,-0.91611,0.13733,418.42,0.70757,0.38021,0.59563,131.97,-0.59788,-0.12718,0.79143,238.45,#26,0.47824,-0.44163,0.75911,288.25,0.33116,0.89124,0.30987,482.23,-0.8134,0.1032,0.57248,299.68,#27,-0.077684,-0.91287,-0.40079,327.36,-0.63455,-0.2648,0.72611,472.64,-0.76897,0.31073,-0.55869,296.84,#28,0.78602,0.56876,0.24227,306.93,0.27305,-0.67099,0.68935,404.18,0.55464,-0.47569,-0.68271,278.41,#29,0.15151,-0.75674,0.63592,360.8,-0.63307,-0.56837,-0.52553,509.82,0.75913,-0.32295,-0.56518,242.84,#30,-0.18419,0.84109,-0.50857,359.69,-0.70821,-0.47236,-0.52471,474.91,-0.68156,0.26353,0.68267,292.01,#31,0.95647,0.21591,-0.19635,351.59,0.069427,0.48514,0.87168,387.82,0.28346,-0.84736,0.44903,654.52,#32,-0.41186,0.11817,-0.90355,279.57,0.15095,-0.96901,-0.19553,551.6,-0.89866,-0.21692,0.38126,273.71,#33,0.54093,-0.51695,0.66345,314.02,0.51089,-0.42466,-0.74743,516.85,0.66812,0.74326,0.034395,242.65,#34,0.92116,0.32205,-0.2185,305.64,0.38248,-0.85291,0.35534,474.77,-0.071924,-0.41089,-0.90884,241.85,#35,-0.64647,-0.75004,-0.13971,313.02,-0.18774,0.33388,-0.92373,515.86,0.73948,-0.57093,-0.35666,242.42
> view matrix models
> #25,0.56775,0.81372,0.12456,121.78,-0.70969,0.40715,0.57495,438.32,0.41713,-0.41483,0.80865,193.07,#24,0.37667,-0.91611,0.13733,382.95,0.70757,0.38021,0.59563,113.21,-0.59788,-0.12718,0.79143,251.15,#26,0.47824,-0.44163,0.75911,252.77,0.33116,0.89124,0.30987,463.47,-0.8134,0.1032,0.57248,312.37,#27,-0.077684,-0.91287,-0.40079,291.88,-0.63455,-0.2648,0.72611,453.87,-0.76897,0.31073,-0.55869,309.53,#28,0.78602,0.56876,0.24227,271.46,0.27305,-0.67099,0.68935,385.42,0.55464,-0.47569,-0.68271,291.1,#29,0.15151,-0.75674,0.63592,325.33,-0.63307,-0.56837,-0.52553,491.05,0.75913,-0.32295,-0.56518,255.53,#30,-0.18419,0.84109,-0.50857,324.21,-0.70821,-0.47236,-0.52471,456.15,-0.68156,0.26353,0.68267,304.71,#31,0.95647,0.21591,-0.19635,316.12,0.069427,0.48514,0.87168,369.06,0.28346,-0.84736,0.44903,667.21,#32,-0.41186,0.11817,-0.90355,244.1,0.15095,-0.96901,-0.19553,532.83,-0.89866,-0.21692,0.38126,286.41,#33,0.54093,-0.51695,0.66345,278.55,0.51089,-0.42466,-0.74743,498.09,0.66812,0.74326,0.034395,255.35,#34,0.92116,0.32205,-0.2185,270.17,0.38248,-0.85291,0.35534,456.01,-0.071924,-0.41089,-0.90884,254.55,#35,-0.64647,-0.75004,-0.13971,277.55,-0.18774,0.33388,-0.92373,497.1,0.73948,-0.57093,-0.35666,255.11
> view matrix models
> #25,0.56775,0.81372,0.12456,100.72,-0.70969,0.40715,0.57495,427.82,0.41713,-0.41483,0.80865,200.35,#24,0.37667,-0.91611,0.13733,361.89,0.70757,0.38021,0.59563,102.71,-0.59788,-0.12718,0.79143,258.43,#26,0.47824,-0.44163,0.75911,231.72,0.33116,0.89124,0.30987,452.97,-0.8134,0.1032,0.57248,319.66,#27,-0.077684,-0.91287,-0.40079,270.83,-0.63455,-0.2648,0.72611,443.37,-0.76897,0.31073,-0.55869,316.82,#28,0.78602,0.56876,0.24227,250.4,0.27305,-0.67099,0.68935,374.92,0.55464,-0.47569,-0.68271,298.39,#29,0.15151,-0.75674,0.63592,304.27,-0.63307,-0.56837,-0.52553,480.55,0.75913,-0.32295,-0.56518,262.82,#30,-0.18419,0.84109,-0.50857,303.16,-0.70821,-0.47236,-0.52471,445.65,-0.68156,0.26353,0.68267,311.99,#31,0.95647,0.21591,-0.19635,295.06,0.069427,0.48514,0.87168,358.56,0.28346,-0.84736,0.44903,674.5,#32,-0.41186,0.11817,-0.90355,223.04,0.15095,-0.96901,-0.19553,522.34,-0.89866,-0.21692,0.38126,293.7,#33,0.54093,-0.51695,0.66345,257.49,0.51089,-0.42466,-0.74743,487.59,0.66812,0.74326,0.034395,262.64,#34,0.92116,0.32205,-0.2185,249.11,0.38248,-0.85291,0.35534,445.51,-0.071924,-0.41089,-0.90884,261.83,#35,-0.64647,-0.75004,-0.13971,256.49,-0.18774,0.33388,-0.92373,486.6,0.73948,-0.57093,-0.35666,262.4
> select subtract #26
31014 atoms, 31550 bonds, 1 pseudobond, 3912 residues, 14 models selected
> select add #26
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 15 models selected
> hide #26 models
> hide #27 models
> hide #28 models
> hide #29 models
> hide #30 models
> hide #31 models
> hide #!32 models
> hide #33 models
> hide #34 models
> hide #35 models
> color #24 #ff2600ff models
> view matrix models
> #25,0.56775,0.81372,0.12456,120.98,-0.70969,0.40715,0.57495,425.68,0.41713,-0.41483,0.80865,198.46,#24,0.37667,-0.91611,0.13733,382.14,0.70757,0.38021,0.59563,100.56,-0.59788,-0.12718,0.79143,256.54,#26,0.47824,-0.44163,0.75911,251.97,0.33116,0.89124,0.30987,450.82,-0.8134,0.1032,0.57248,317.77,#27,-0.077684,-0.91287,-0.40079,291.08,-0.63455,-0.2648,0.72611,441.23,-0.76897,0.31073,-0.55869,314.93,#28,0.78602,0.56876,0.24227,270.65,0.27305,-0.67099,0.68935,372.77,0.55464,-0.47569,-0.68271,296.5,#29,0.15151,-0.75674,0.63592,324.52,-0.63307,-0.56837,-0.52553,478.4,0.75913,-0.32295,-0.56518,260.93,#30,-0.18419,0.84109,-0.50857,323.41,-0.70821,-0.47236,-0.52471,443.5,-0.68156,0.26353,0.68267,310.1,#31,0.95647,0.21591,-0.19635,315.32,0.069427,0.48514,0.87168,356.41,0.28346,-0.84736,0.44903,672.61,#32,-0.41186,0.11817,-0.90355,243.29,0.15095,-0.96901,-0.19553,520.19,-0.89866,-0.21692,0.38126,291.81,#33,0.54093,-0.51695,0.66345,277.75,0.51089,-0.42466,-0.74743,485.44,0.66812,0.74326,0.034395,260.75,#34,0.92116,0.32205,-0.2185,269.36,0.38248,-0.85291,0.35534,443.36,-0.071924,-0.41089,-0.90884,259.94,#35,-0.64647,-0.75004,-0.13971,276.74,-0.18774,0.33388,-0.92373,484.45,0.73948,-0.57093,-0.35666,260.51
> view matrix models
> #25,0.56775,0.81372,0.12456,133.04,-0.70969,0.40715,0.57495,478.96,0.41713,-0.41483,0.80865,180.59,#24,0.37667,-0.91611,0.13733,394.21,0.70757,0.38021,0.59563,153.84,-0.59788,-0.12718,0.79143,238.67,#26,0.47824,-0.44163,0.75911,264.03,0.33116,0.89124,0.30987,504.1,-0.8134,0.1032,0.57248,299.89,#27,-0.077684,-0.91287,-0.40079,303.14,-0.63455,-0.2648,0.72611,494.51,-0.76897,0.31073,-0.55869,297.05,#28,0.78602,0.56876,0.24227,282.71,0.27305,-0.67099,0.68935,426.05,0.55464,-0.47569,-0.68271,278.62,#29,0.15151,-0.75674,0.63592,336.59,-0.63307,-0.56837,-0.52553,531.69,0.75913,-0.32295,-0.56518,243.05,#30,-0.18419,0.84109,-0.50857,335.47,-0.70821,-0.47236,-0.52471,496.78,-0.68156,0.26353,0.68267,292.23,#31,0.95647,0.21591,-0.19635,327.38,0.069427,0.48514,0.87168,409.69,0.28346,-0.84736,0.44903,654.73,#32,-0.41186,0.11817,-0.90355,255.36,0.15095,-0.96901,-0.19553,573.47,-0.89866,-0.21692,0.38126,273.93,#33,0.54093,-0.51695,0.66345,289.81,0.51089,-0.42466,-0.74743,538.72,0.66812,0.74326,0.034395,242.87,#34,0.92116,0.32205,-0.2185,281.43,0.38248,-0.85291,0.35534,496.64,-0.071924,-0.41089,-0.90884,242.07,#35,-0.64647,-0.75004,-0.13971,288.81,-0.18774,0.33388,-0.92373,537.73,0.73948,-0.57093,-0.35666,242.63
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.31393,0.69197,-0.6501,252.34,-0.12626,0.70906,0.69375,361.81,0.94101,-0.13571,0.30997,132.62,#24,0.43359,-0.63792,-0.63644,487.56,0.64472,-0.27382,0.71369,276.12,-0.62955,-0.71977,0.29255,471.16,#26,0.76611,-0.64257,0.013391,249.58,0.36612,0.45344,0.81262,484.42,-0.52824,-0.61765,0.58264,262.95,#27,0.67276,-0.73128,-0.11235,280.36,-0.70383,-0.67939,0.20749,499.49,-0.22806,-0.060516,-0.97176,284.28,#28,0.054909,0.91114,0.40842,301,0.79611,-0.28683,0.53286,430.26,0.60266,0.29588,-0.74112,299.24,#29,-0.21821,-0.10056,0.97071,327.56,-0.23975,-0.95867,-0.1532,536.61,0.94599,-0.26616,0.18508,241.71,#30,0.56603,0.52443,-0.63607,304.29,-0.80537,0.18702,-0.56249,519.36,-0.17603,0.83066,0.52823,294.61,#31,0.41646,0.56756,-0.71024,79.208,0.68063,0.32329,0.65744,524.53,0.60275,-0.75721,-0.25166,591.89,#32,0.29322,0.53101,-0.79502,239.72,-0.31888,-0.72963,-0.60494,527.63,-0.9013,0.4309,-0.044618,202.98,#33,-0.25918,-0.71441,0.64996,294.58,0.86023,-0.47671,-0.18095,514.36,0.43911,0.51222,0.73811,216.12,#34,0.53689,0.76133,0.36349,302.85,0.82691,-0.56031,-0.047804,476.53,0.16727,0.32624,-0.93037,234.61,#35,-0.87195,-0.21112,0.44174,294.39,-0.37004,-0.30661,-0.87696,512.95,0.32059,-0.92812,0.18923,216.03
> view matrix models
> #25,0.23101,0.91523,-0.33013,200.8,-0.83636,0.36017,0.41325,514.99,0.49713,0.18064,0.84867,87.81,#24,0.65679,-0.68759,-0.30961,380.72,0.7409,0.512,0.43464,153.53,-0.14033,-0.51486,0.84571,207.22,#26,0.85306,-0.40862,0.32453,244.97,0.39498,0.91206,0.11014,502.93,-0.341,0.034228,0.93944,260.81,#27,0.3463,-0.93803,-0.01344,279,-0.48415,-0.19097,0.85389,488.92,-0.80354,-0.2892,-0.52028,277.4,#28,0.35611,0.72387,0.59093,270.8,0.073566,-0.65214,0.75452,427.67,0.93154,-0.22522,-0.28549,237.1,#29,-0.30319,-0.46473,0.83193,337.34,-0.76333,-0.40416,-0.50397,529.77,0.57044,-0.78783,-0.2322,258.84,#30,0.20791,0.54819,-0.8101,308.69,-0.55664,-0.6147,-0.55883,487.72,-0.80432,0.56712,0.17735,291.22,#31,0.64378,0.65567,-0.39453,100.82,-0.10325,0.5853,0.80422,344.13,0.75822,-0.477,0.44449,565.5,#32,0.15354,0.19971,-0.96775,253.32,0.34873,-0.9273,-0.13604,576.15,-0.92456,-0.3166,-0.21202,249.39,#33,0.093561,-0.84854,0.52079,298.52,0.31943,-0.46985,-0.82293,542.78,0.94298,0.24335,0.22709,235.14,#34,0.81577,0.47884,0.32441,291.17,0.26577,-0.8085,0.52506,502.85,0.5137,-0.34211,-0.78681,221.21,#35,-0.95011,-0.30565,0.062186,297.8,-0.2207,0.51789,-0.82649,541.98,0.22041,-0.79898,-0.55951,234.2
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.23101,0.91523,-0.33013,208.08,-0.83636,0.36017,0.41325,475.99,0.49713,0.18064,0.84867,105.89,#24,0.65679,-0.68759,-0.30961,388,0.7409,0.512,0.43464,114.53,-0.14033,-0.51486,0.84571,225.31,#26,0.85306,-0.40862,0.32453,252.25,0.39498,0.91206,0.11014,463.93,-0.341,0.034228,0.93944,278.89,#27,0.3463,-0.93803,-0.01344,286.28,-0.48415,-0.19097,0.85389,449.92,-0.80354,-0.2892,-0.52028,295.49,#28,0.35611,0.72387,0.59093,278.08,0.073566,-0.65214,0.75452,388.67,0.93154,-0.22522,-0.28549,255.18,#29,-0.30319,-0.46473,0.83193,344.62,-0.76333,-0.40416,-0.50397,490.78,0.57044,-0.78783,-0.2322,276.93,#30,0.20791,0.54819,-0.8101,315.97,-0.55664,-0.6147,-0.55883,448.72,-0.80432,0.56712,0.17735,309.3,#31,0.64378,0.65567,-0.39453,108.1,-0.10325,0.5853,0.80422,305.13,0.75822,-0.477,0.44449,583.59,#32,0.15354,0.19971,-0.96775,260.6,0.34873,-0.9273,-0.13604,537.15,-0.92456,-0.3166,-0.21202,267.47,#33,0.093561,-0.84854,0.52079,305.8,0.31943,-0.46985,-0.82293,503.78,0.94298,0.24335,0.22709,253.22,#34,0.81577,0.47884,0.32441,298.45,0.26577,-0.8085,0.52506,463.86,0.5137,-0.34211,-0.78681,239.29,#35,-0.95011,-0.30565,0.062186,305.08,-0.2207,0.51789,-0.82649,502.98,0.22041,-0.79898,-0.55951,252.28
> view matrix models
> #25,0.23101,0.91523,-0.33013,212.69,-0.83636,0.36017,0.41325,496.36,0.49713,0.18064,0.84867,105.06,#24,0.65679,-0.68759,-0.30961,392.61,0.7409,0.512,0.43464,134.91,-0.14033,-0.51486,0.84571,224.47,#26,0.85306,-0.40862,0.32453,256.86,0.39498,0.91206,0.11014,484.3,-0.341,0.034228,0.93944,278.05,#27,0.3463,-0.93803,-0.01344,290.89,-0.48415,-0.19097,0.85389,470.29,-0.80354,-0.2892,-0.52028,294.65,#28,0.35611,0.72387,0.59093,282.69,0.073566,-0.65214,0.75452,409.04,0.93154,-0.22522,-0.28549,254.35,#29,-0.30319,-0.46473,0.83193,349.23,-0.76333,-0.40416,-0.50397,511.15,0.57044,-0.78783,-0.2322,276.09,#30,0.20791,0.54819,-0.8101,320.58,-0.55664,-0.6147,-0.55883,469.1,-0.80432,0.56712,0.17735,308.47,#31,0.64378,0.65567,-0.39453,112.71,-0.10325,0.5853,0.80422,325.5,0.75822,-0.477,0.44449,582.75,#32,0.15354,0.19971,-0.96775,265.22,0.34873,-0.9273,-0.13604,557.52,-0.92456,-0.3166,-0.21202,266.63,#33,0.093561,-0.84854,0.52079,310.41,0.31943,-0.46985,-0.82293,524.15,0.94298,0.24335,0.22709,252.38,#34,0.81577,0.47884,0.32441,303.06,0.26577,-0.8085,0.52506,484.23,0.5137,-0.34211,-0.78681,238.46,#35,-0.95011,-0.30565,0.062186,309.69,-0.2207,0.51789,-0.82649,523.36,0.22041,-0.79898,-0.55951,251.45
> view matrix models
> #25,0.23101,0.91523,-0.33013,233.2,-0.83636,0.36017,0.41325,485.63,0.49713,0.18064,0.84867,114.46,#24,0.65679,-0.68759,-0.30961,413.12,0.7409,0.512,0.43464,124.18,-0.14033,-0.51486,0.84571,233.87,#26,0.85306,-0.40862,0.32453,277.37,0.39498,0.91206,0.11014,473.58,-0.341,0.034228,0.93944,287.45,#27,0.3463,-0.93803,-0.01344,311.4,-0.48415,-0.19097,0.85389,459.56,-0.80354,-0.2892,-0.52028,304.05,#28,0.35611,0.72387,0.59093,303.2,0.073566,-0.65214,0.75452,398.32,0.93154,-0.22522,-0.28549,263.75,#29,-0.30319,-0.46473,0.83193,369.73,-0.76333,-0.40416,-0.50397,500.42,0.57044,-0.78783,-0.2322,285.49,#30,0.20791,0.54819,-0.8101,341.09,-0.55664,-0.6147,-0.55883,458.37,-0.80432,0.56712,0.17735,317.87,#31,0.64378,0.65567,-0.39453,133.22,-0.10325,0.5853,0.80422,314.78,0.75822,-0.477,0.44449,592.15,#32,0.15354,0.19971,-0.96775,285.72,0.34873,-0.9273,-0.13604,546.79,-0.92456,-0.3166,-0.21202,276.03,#33,0.093561,-0.84854,0.52079,330.92,0.31943,-0.46985,-0.82293,513.43,0.94298,0.24335,0.22709,261.78,#34,0.81577,0.47884,0.32441,323.57,0.26577,-0.8085,0.52506,473.5,0.5137,-0.34211,-0.78681,247.86,#35,-0.95011,-0.30565,0.062186,330.19,-0.2207,0.51789,-0.82649,512.63,0.22041,-0.79898,-0.55951,260.85
> view matrix models
> #25,0.23101,0.91523,-0.33013,226.85,-0.83636,0.36017,0.41325,478.83,0.49713,0.18064,0.84867,120.73,#24,0.65679,-0.68759,-0.30961,406.77,0.7409,0.512,0.43464,117.38,-0.14033,-0.51486,0.84571,240.14,#26,0.85306,-0.40862,0.32453,271.02,0.39498,0.91206,0.11014,466.77,-0.341,0.034228,0.93944,293.72,#27,0.3463,-0.93803,-0.01344,305.05,-0.48415,-0.19097,0.85389,452.76,-0.80354,-0.2892,-0.52028,310.32,#28,0.35611,0.72387,0.59093,296.85,0.073566,-0.65214,0.75452,391.51,0.93154,-0.22522,-0.28549,270.02,#29,-0.30319,-0.46473,0.83193,363.39,-0.76333,-0.40416,-0.50397,493.62,0.57044,-0.78783,-0.2322,291.76,#30,0.20791,0.54819,-0.8101,334.74,-0.55664,-0.6147,-0.55883,451.57,-0.80432,0.56712,0.17735,324.14,#31,0.64378,0.65567,-0.39453,126.87,-0.10325,0.5853,0.80422,307.97,0.75822,-0.477,0.44449,598.42,#32,0.15354,0.19971,-0.96775,279.38,0.34873,-0.9273,-0.13604,539.99,-0.92456,-0.3166,-0.21202,282.3,#33,0.093561,-0.84854,0.52079,324.57,0.31943,-0.46985,-0.82293,506.62,0.94298,0.24335,0.22709,268.05,#34,0.81577,0.47884,0.32441,317.22,0.26577,-0.8085,0.52506,466.7,0.5137,-0.34211,-0.78681,254.13,#35,-0.95011,-0.30565,0.062186,323.85,-0.2207,0.51789,-0.82649,505.83,0.22041,-0.79898,-0.55951,267.12
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.31872,0.78454,-0.53189,254.04,-0.79899,0.52427,0.29453,464.05,0.50993,0.33111,0.79394,104.36,#24,0.50551,-0.69156,-0.51596,483.68,0.86262,0.39203,0.31969,139.61,-0.01881,-0.60668,0.79473,243.25,#26,0.7962,-0.5863,0.14938,273.07,0.57344,0.81,0.12272,451.91,-0.19295,-0.012046,0.98114,281.88,#27,0.55516,-0.82465,-0.10834,306.32,-0.36309,-0.35748,0.86045,444.06,-0.7483,-0.43835,-0.49788,303.37,#28,0.18857,0.86714,0.46098,316.97,0.093587,-0.48313,0.87053,384.6,0.97759,-0.12102,-0.17226,261.01,#29,-0.22397,-0.24799,0.94252,357.23,-0.83714,-0.44623,-0.31634,496.57,0.49903,-0.85987,-0.10767,295.17,#30,0.43619,0.56976,-0.6965,333.2,-0.46141,-0.5229,-0.71671,448.04,-0.77255,0.63399,0.034808,321.7,#31,0.52907,0.58705,-0.61274,119.91,-0.013408,0.72777,0.68569,251.92,0.84847,-0.35456,0.39291,556.45,#32,0.21727,0.43004,-0.87627,267.95,0.42031,-0.85145,-0.31365,525.82,-0.88099,-0.30016,-0.36574,273.46,#33,-0.11722,-0.76181,0.63711,320.62,0.28165,-0.6407,-0.71427,502.86,0.95233,0.095715,0.28966,265.87,#34,0.6572,0.67968,0.32577,323.76,0.39469,-0.67856,0.6195,463.06,0.64211,-0.27855,-0.71421,250.13,#35,-0.90736,-0.28035,0.31321,320.22,-0.41574,0.48835,-0.76725,501.99,0.062144,-0.82639,-0.55966,264.82
> view matrix models
> #25,0.31322,0.81558,-0.48653,246.12,-0.79151,0.50729,0.34083,461.03,0.52479,0.27834,0.80444,108.77,#24,0.53327,-0.70355,-0.46973,470.4,0.84291,0.39494,0.36541,133.69,-0.071571,-0.5908,0.80364,249.57,#26,0.80611,-0.55837,0.196,272.42,0.53767,0.82942,0.15154,454.44,-0.24718,-0.016777,0.96882,285.66,#27,0.50942,-0.85462,-0.10055,306.29,-0.40853,-0.34303,0.84583,446.16,-0.75736,-0.3898,-0.52389,306,#28,0.23398,0.84412,0.48241,313.06,0.12093,-0.5176,0.84704,384.92,0.96469,-0.13986,-0.22319,265.42,#29,-0.23041,-0.30019,0.92563,358.55,-0.8107,-0.46691,-0.35322,496.52,0.53822,-0.83179,-0.13579,293.74,#30,0.38622,0.57867,-0.71832,334.06,-0.50335,-0.52036,-0.68983,449.83,-0.77296,0.62799,0.090295,323.02,#31,0.5647,0.5955,-0.57139,124.63,-0.002552,0.6936,0.72035,269.74,0.82529,-0.40533,0.3932,573.56,#32,0.19293,0.38736,-0.90152,269.46,0.38127,-0.87617,-0.29488,528.15,-0.90411,-0.28683,-0.31672,274.78,#33,-0.06604,-0.77828,0.62443,320.94,0.31875,-0.60946,-0.72592,503.08,0.94554,0.1511,0.28832,265.81,#34,0.69755,0.64344,0.3153,322.03,0.39327,-0.71162,0.58218,462.67,0.59897,-0.2821,-0.74944,251.41,#35,-0.91742,-0.29924,0.26229,320.47,-0.38078,0.46883,-0.797,502.18,0.11553,-0.83105,-0.54406,264.81
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.31322,0.81558,-0.48653,226.44,-0.79151,0.50729,0.34083,473.07,0.52479,0.27834,0.80444,98.168,#24,0.53327,-0.70355,-0.46973,450.73,0.84291,0.39494,0.36541,145.73,-0.071571,-0.5908,0.80364,238.97,#26,0.80611,-0.55837,0.196,252.74,0.53767,0.82942,0.15154,466.48,-0.24718,-0.016777,0.96882,275.06,#27,0.50942,-0.85462,-0.10055,286.62,-0.40853,-0.34303,0.84583,458.2,-0.75736,-0.3898,-0.52389,295.4,#28,0.23398,0.84412,0.48241,293.38,0.12093,-0.5176,0.84704,396.96,0.96469,-0.13986,-0.22319,254.81,#29,-0.23041,-0.30019,0.92563,338.88,-0.8107,-0.46691,-0.35322,508.56,0.53822,-0.83179,-0.13579,283.14,#30,0.38622,0.57867,-0.71832,314.38,-0.50335,-0.52036,-0.68983,461.87,-0.77296,0.62799,0.090295,312.41,#31,0.5647,0.5955,-0.57139,104.96,-0.002552,0.6936,0.72035,281.78,0.82529,-0.40533,0.3932,562.96,#32,0.19293,0.38736,-0.90152,249.78,0.38127,-0.87617,-0.29488,540.19,-0.90411,-0.28683,-0.31672,264.17,#33,-0.06604,-0.77828,0.62443,301.26,0.31875,-0.60946,-0.72592,515.12,0.94554,0.1511,0.28832,255.21,#34,0.69755,0.64344,0.3153,302.35,0.39327,-0.71162,0.58218,474.71,0.59897,-0.2821,-0.74944,240.81,#35,-0.91742,-0.29924,0.26229,300.79,-0.38078,0.46883,-0.797,514.22,0.11553,-0.83105,-0.54406,254.2
> view matrix models
> #25,0.31322,0.81558,-0.48653,252.03,-0.79151,0.50729,0.34083,484.65,0.52479,0.27834,0.80444,84.922,#24,0.53327,-0.70355,-0.46973,476.32,0.84291,0.39494,0.36541,157.31,-0.071571,-0.5908,0.80364,225.72,#26,0.80611,-0.55837,0.196,278.34,0.53767,0.82942,0.15154,478.05,-0.24718,-0.016777,0.96882,261.81,#27,0.50942,-0.85462,-0.10055,312.21,-0.40853,-0.34303,0.84583,469.78,-0.75736,-0.3898,-0.52389,282.15,#28,0.23398,0.84412,0.48241,318.97,0.12093,-0.5176,0.84704,408.54,0.96469,-0.13986,-0.22319,241.57,#29,-0.23041,-0.30019,0.92563,364.47,-0.8107,-0.46691,-0.35322,520.14,0.53822,-0.83179,-0.13579,269.89,#30,0.38622,0.57867,-0.71832,339.97,-0.50335,-0.52036,-0.68983,473.44,-0.77296,0.62799,0.090295,299.17,#31,0.5647,0.5955,-0.57139,130.55,-0.002552,0.6936,0.72035,293.36,0.82529,-0.40533,0.3932,549.71,#32,0.19293,0.38736,-0.90152,275.38,0.38127,-0.87617,-0.29488,551.76,-0.90411,-0.28683,-0.31672,250.93,#33,-0.06604,-0.77828,0.62443,326.86,0.31875,-0.60946,-0.72592,526.7,0.94554,0.1511,0.28832,241.96,#34,0.69755,0.64344,0.3153,327.95,0.39327,-0.71162,0.58218,486.28,0.59897,-0.2821,-0.74944,227.56,#35,-0.91742,-0.29924,0.26229,326.38,-0.38078,0.46883,-0.797,525.8,0.11553,-0.83105,-0.54406,240.96
> view matrix models
> #25,0.31322,0.81558,-0.48653,254.82,-0.79151,0.50729,0.34083,480.68,0.52479,0.27834,0.80444,104.69,#24,0.53327,-0.70355,-0.46973,479.1,0.84291,0.39494,0.36541,153.33,-0.071571,-0.5908,0.80364,245.49,#26,0.80611,-0.55837,0.196,281.12,0.53767,0.82942,0.15154,474.08,-0.24718,-0.016777,0.96882,281.58,#27,0.50942,-0.85462,-0.10055,315,-0.40853,-0.34303,0.84583,465.8,-0.75736,-0.3898,-0.52389,301.92,#28,0.23398,0.84412,0.48241,321.76,0.12093,-0.5176,0.84704,404.56,0.96469,-0.13986,-0.22319,261.34,#29,-0.23041,-0.30019,0.92563,367.25,-0.8107,-0.46691,-0.35322,516.16,0.53822,-0.83179,-0.13579,289.66,#30,0.38622,0.57867,-0.71832,342.76,-0.50335,-0.52036,-0.68983,469.47,-0.77296,0.62799,0.090295,318.94,#31,0.5647,0.5955,-0.57139,133.34,-0.002552,0.6936,0.72035,289.38,0.82529,-0.40533,0.3932,569.48,#32,0.19293,0.38736,-0.90152,278.16,0.38127,-0.87617,-0.29488,547.79,-0.90411,-0.28683,-0.31672,270.7,#33,-0.06604,-0.77828,0.62443,329.64,0.31875,-0.60946,-0.72592,522.72,0.94554,0.1511,0.28832,261.74,#34,0.69755,0.64344,0.3153,330.73,0.39327,-0.71162,0.58218,482.31,0.59897,-0.2821,-0.74944,247.33,#35,-0.91742,-0.29924,0.26229,329.17,-0.38078,0.46883,-0.797,521.82,0.11553,-0.83105,-0.54406,260.73
> view matrix models
> #25,0.31322,0.81558,-0.48653,13.603,-0.79151,0.50729,0.34083,438.49,0.52479,0.27834,0.80444,-106.13,#24,0.53327,-0.70355,-0.46973,237.89,0.84291,0.39494,0.36541,111.14,-0.071571,-0.5908,0.80364,34.665,#26,0.80611,-0.55837,0.196,39.905,0.53767,0.82942,0.15154,431.89,-0.24718,-0.016777,0.96882,70.756,#27,0.50942,-0.85462,-0.10055,73.781,-0.40853,-0.34303,0.84583,423.62,-0.75736,-0.3898,-0.52389,91.095,#28,0.23398,0.84412,0.48241,80.545,0.12093,-0.5176,0.84704,362.37,0.96469,-0.13986,-0.22319,50.513,#29,-0.23041,-0.30019,0.92563,126.04,-0.8107,-0.46691,-0.35322,473.97,0.53822,-0.83179,-0.13579,78.836,#30,0.38622,0.57867,-0.71832,101.54,-0.50335,-0.52036,-0.68983,427.28,-0.77296,0.62799,0.090295,108.11,#31,0.5647,0.5955,-0.57139,-107.88,-0.002552,0.6936,0.72035,247.2,0.82529,-0.40533,0.3932,358.66,#32,0.19293,0.38736,-0.90152,36.945,0.38127,-0.87617,-0.29488,505.6,-0.90411,-0.28683,-0.31672,59.87,#33,-0.06604,-0.77828,0.62443,88.426,0.31875,-0.60946,-0.72592,480.53,0.94554,0.1511,0.28832,50.907,#34,0.69755,0.64344,0.3153,89.517,0.39327,-0.71162,0.58218,440.12,0.59897,-0.2821,-0.74944,36.506,#35,-0.91742,-0.29924,0.26229,87.953,-0.38078,0.46883,-0.797,479.63,0.11553,-0.83105,-0.54406,49.9
> show #26 models
> view matrix models
> #25,0.31322,0.81558,-0.48653,64.977,-0.79151,0.50729,0.34083,426.13,0.52479,0.27834,0.80444,12.694,#24,0.53327,-0.70355,-0.46973,289.26,0.84291,0.39494,0.36541,98.788,-0.071571,-0.5908,0.80364,153.49,#26,0.80611,-0.55837,0.196,91.279,0.53767,0.82942,0.15154,419.53,-0.24718,-0.016777,0.96882,189.58,#27,0.50942,-0.85462,-0.10055,125.16,-0.40853,-0.34303,0.84583,411.26,-0.75736,-0.3898,-0.52389,209.92,#28,0.23398,0.84412,0.48241,131.92,0.12093,-0.5176,0.84704,350.02,0.96469,-0.13986,-0.22319,169.34,#29,-0.23041,-0.30019,0.92563,177.41,-0.8107,-0.46691,-0.35322,461.62,0.53822,-0.83179,-0.13579,197.66,#30,0.38622,0.57867,-0.71832,152.92,-0.50335,-0.52036,-0.68983,414.92,-0.77296,0.62799,0.090295,226.94,#31,0.5647,0.5955,-0.57139,-56.506,-0.002552,0.6936,0.72035,234.84,0.82529,-0.40533,0.3932,477.48,#32,0.19293,0.38736,-0.90152,88.319,0.38127,-0.87617,-0.29488,493.24,-0.90411,-0.28683,-0.31672,178.7,#33,-0.06604,-0.77828,0.62443,139.8,0.31875,-0.60946,-0.72592,468.17,0.94554,0.1511,0.28832,169.73,#34,0.69755,0.64344,0.3153,140.89,0.39327,-0.71162,0.58218,427.76,0.59897,-0.2821,-0.74944,155.33,#35,-0.91742,-0.29924,0.26229,139.33,-0.38078,0.46883,-0.797,467.28,0.11553,-0.83105,-0.54406,168.73
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.26233,-0.79368,-0.54886,286.65,0.69342,-0.24051,0.67921,315.3,-0.67108,-0.55877,0.48726,286.2,#24,-0.7935,0.20487,-0.57305,406.91,-0.5957,-0.45407,0.66254,508.47,-0.12447,0.86709,0.48235,-68.073,#26,-0.5393,-0.48607,-0.68767,191.25,-0.69411,-0.20579,0.68982,459.24,-0.47682,0.84934,-0.2264,239.24,#27,0.57131,0.73284,-0.36952,177.07,-0.61684,0.086413,-0.78233,469.55,-0.54139,0.67489,0.50142,202.88,#28,-0.67241,0.23445,-0.70206,245.18,0.68803,-0.15172,-0.70964,460.14,-0.2729,-0.96021,-0.059292,176.13,#29,0.43264,0.89827,0.076956,127.77,0.88138,-0.40346,-0.24573,420.91,-0.18968,0.17414,-0.96628,177.95,#30,0.69183,-0.087156,0.71678,156.94,-0.55023,0.57918,0.60149,473.7,-0.46757,-0.81052,0.35274,177.36,#31,-0.59939,-0.51786,-0.61037,231.49,0.52239,-0.83083,0.19191,828.91,-0.60649,-0.20382,0.76852,262.95,#32,0.11293,0.73365,0.67008,139.07,-0.98968,0.023201,0.1414,418.59,0.08819,-0.67913,0.7287,273.68,#33,-0.73065,0.63867,0.24135,148.41,0.6778,0.63601,0.36888,406.12,0.082094,0.43311,-0.8976,217.86,#34,-0.83583,0.52363,-0.16491,187.87,0.11651,-0.12434,-0.98537,411.39,-0.53648,-0.84282,0.042921,201.82,#35,0.51648,0.1515,0.84279,149.8,0.5486,-0.81425,-0.18982,405.81,0.65749,0.56039,-0.50366,218.03
> view matrix models
> #25,0.3957,-0.80395,-0.44394,263.29,0.5777,-0.15788,0.80083,305.14,-0.71392,-0.57335,0.40197,301.17,#24,-0.87698,0.098142,-0.47039,425.47,-0.46748,-0.40077,0.78794,443.21,-0.11119,0.91091,0.39735,-62.027,#26,-0.63131,-0.54097,-0.55569,194.72,-0.6375,-0.046039,0.76907,457.82,-0.44163,0.83978,-0.3158,237.83,#27,0.47821,0.71459,-0.51057,183.64,-0.74812,0.026924,-0.66302,466.95,-0.46004,0.69903,0.54747,200.1,#28,-0.53944,0.23719,-0.80793,250.08,0.76061,-0.27434,-0.58839,444.2,-0.36121,-0.93192,-0.032417,177.48,#29,0.57907,0.81255,0.06654,127.79,0.77836,-0.52673,-0.34164,424.93,-0.24255,0.24963,-0.93747,177.05,#30,0.60564,0.03682,0.79488,165.33,-0.69558,0.50967,0.50637,471.99,-0.38649,-0.85958,0.33429,173.4,#31,-0.48412,-0.64181,-0.59474,295.04,0.55572,-0.75054,0.35759,816.63,-0.67587,-0.15739,0.72001,232.22,#32,-0.056066,0.74907,0.66011,135.41,-0.98273,-0.15819,0.09604,429.49,0.17636,-0.64333,0.745,273.06,#33,-0.61012,0.72102,0.32847,144.37,0.79225,0.56028,0.24171,410.65,-0.0097597,0.4077,-0.91307,218.99,#34,-0.78688,0.52291,-0.3277,184.66,0.20177,-0.28384,-0.9374,407.96,-0.58319,-0.80374,0.11784,204.44,#35,0.57874,-0.0043097,0.8155,145.68,0.51464,-0.77379,-0.36931,410.14,0.63262,0.63342,-0.4456,219.25
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.3957,-0.80395,-0.44394,286.28,0.5777,-0.15788,0.80083,303.44,-0.71392,-0.57335,0.40197,352.12,#24,-0.87698,0.098142,-0.47039,448.47,-0.46748,-0.40077,0.78794,441.5,-0.11119,0.91091,0.39735,-11.079,#26,-0.63131,-0.54097,-0.55569,217.71,-0.6375,-0.046039,0.76907,456.11,-0.44163,0.83978,-0.3158,288.78,#27,0.47821,0.71459,-0.51057,206.64,-0.74812,0.026924,-0.66302,465.25,-0.46004,0.69903,0.54747,251.05,#28,-0.53944,0.23719,-0.80793,273.08,0.76061,-0.27434,-0.58839,442.49,-0.36121,-0.93192,-0.032417,228.42,#29,0.57907,0.81255,0.06654,150.79,0.77836,-0.52673,-0.34164,423.22,-0.24255,0.24963,-0.93747,228,#30,0.60564,0.03682,0.79488,188.33,-0.69558,0.50967,0.50637,470.28,-0.38649,-0.85958,0.33429,224.35,#31,-0.48412,-0.64181,-0.59474,318.04,0.55572,-0.75054,0.35759,814.92,-0.67587,-0.15739,0.72001,283.17,#32,-0.056066,0.74907,0.66011,158.41,-0.98273,-0.15819,0.09604,427.79,0.17636,-0.64333,0.745,324.01,#33,-0.61012,0.72102,0.32847,167.37,0.79225,0.56028,0.24171,408.95,-0.0097597,0.4077,-0.91307,269.94,#34,-0.78688,0.52291,-0.3277,207.65,0.20177,-0.28384,-0.9374,406.25,-0.58319,-0.80374,0.11784,255.39,#35,0.57874,-0.0043097,0.8155,168.67,0.51464,-0.77379,-0.36931,408.43,0.63262,0.63342,-0.4456,270.2
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.41605,-0.76911,-0.48516,280.37,0.77906,0.026297,0.6264,273.77,-0.46901,-0.63858,0.61012,309.75,#24,-0.85734,0.062168,-0.51098,457.14,-0.41537,-0.66987,0.61542,522.1,-0.30403,0.73987,0.60013,19.292,#26,-0.59065,-0.58174,-0.5592,211.06,-0.46868,-0.31679,0.82461,438.06,-0.65686,0.74915,-0.085536,294.54,#27,0.52092,0.67697,-0.51995,201.69,-0.5576,-0.19134,-0.80776,458.67,-0.64632,0.7107,0.2778,261.11,#28,-0.54043,0.29173,-0.78919,269.78,0.83124,0.039904,-0.55448,444.93,-0.13027,-0.95567,-0.26407,236.24,#29,0.56968,0.81254,0.12345,148.23,0.82026,-0.5715,-0.023628,425.7,0.051355,0.11472,-0.99207,222.74,#30,0.64298,0.067035,0.76294,184.64,-0.53015,0.75788,0.3802,471.8,-0.55273,-0.64894,0.52284,236.41,#31,-0.46365,-0.61263,-0.64009,301.91,0.73812,-0.6667,0.10344,780.75,-0.49011,-0.4245,0.76131,409.21,#32,-0.038698,0.78492,0.61839,150.81,-0.98804,0.062399,-0.14103,399.43,-0.14929,-0.61645,0.77311,315.48,#33,-0.62979,0.68401,0.36809,163.02,0.7483,0.40717,0.52369,398.93,0.20833,0.60526,-0.76828,258.82,#34,-0.76118,0.57068,-0.3081,204.06,0.37038,-0.0074568,-0.92885,401.39,-0.53238,-0.82114,-0.20569,246.49,#35,0.53169,-0.015962,0.84679,164.33,0.29078,-0.93561,-0.20021,398.37,0.79546,0.35268,-0.49282,258.98
> view matrix models
> #25,0.33522,-0.78133,-0.52645,295.01,0.83537,-0.01188,0.54955,280.01,-0.43564,-0.624,0.64872,300.35,#24,-0.82295,0.13682,-0.55139,442.94,-0.47554,-0.69694,0.53679,557.16,-0.31084,0.70396,0.63861,20.016,#26,-0.55987,-0.53567,-0.63214,211.04,-0.48729,-0.40418,0.77408,437.94,-0.67015,0.74141,-0.034739,294.58,#27,0.55519,0.70578,-0.44005,199.18,-0.47612,-0.16413,-0.86393,459.23,-0.68197,0.68916,0.24491,262.39,#28,-0.61496,0.26733,-0.74186,267.7,0.78456,0.11273,-0.60973,452.92,-0.079373,-0.95699,-0.27906,235.77,#29,0.49521,0.86244,0.10468,148.1,0.86474,-0.50092,0.036151,423.5,0.083613,0.072616,-0.99385,223.26,#30,0.67621,-0.014144,0.73658,180.52,-0.4424,0.79168,0.42134,471.97,-0.58909,-0.61078,0.52908,238.66,#31,-0.53758,-0.55933,-0.631,273.3,0.71644,-0.6976,0.0079897,781.39,-0.44465,-0.44778,0.77574,424.96,#32,0.046498,0.76341,0.64424,154.92,-0.97901,0.16293,-0.12241,393.06,-0.19842,-0.62503,0.75496,314.5,#33,-0.6896,0.65726,0.30408,165.96,0.67744,0.43703,0.59168,396.43,0.25599,0.61402,-0.74663,257.7,#34,-0.80194,0.5521,-0.22821,206.35,0.32591,0.08416,-0.94165,403.18,-0.50068,-0.82952,-0.24743,244.86,#35,0.51986,0.074768,0.85097,167.31,0.29822,-0.94937,-0.098774,395.99,0.8005,0.30513,-0.51584,257.81
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.33522,-0.78133,-0.52645,292.05,0.83537,-0.01188,0.54955,264.57,-0.43564,-0.624,0.64872,325.87,#24,-0.82295,0.13682,-0.55139,439.98,-0.47554,-0.69694,0.53679,541.72,-0.31084,0.70396,0.63861,45.537,#26,-0.55987,-0.53567,-0.63214,208.08,-0.48729,-0.40418,0.77408,422.49,-0.67015,0.74141,-0.034739,320.1,#27,0.55519,0.70578,-0.44005,196.22,-0.47612,-0.16413,-0.86393,443.78,-0.68197,0.68916,0.24491,287.91,#28,-0.61496,0.26733,-0.74186,264.74,0.78456,0.11273,-0.60973,437.47,-0.079373,-0.95699,-0.27906,261.29,#29,0.49521,0.86244,0.10468,145.14,0.86474,-0.50092,0.036151,408.06,0.083613,0.072616,-0.99385,248.78,#30,0.67621,-0.014144,0.73658,177.56,-0.4424,0.79168,0.42134,456.52,-0.58909,-0.61078,0.52908,264.18,#31,-0.53758,-0.55933,-0.631,270.34,0.71644,-0.6976,0.0079897,765.95,-0.44465,-0.44778,0.77574,450.48,#32,0.046498,0.76341,0.64424,151.95,-0.97901,0.16293,-0.12241,377.61,-0.19842,-0.62503,0.75496,340.02,#33,-0.6896,0.65726,0.30408,162.99,0.67744,0.43703,0.59168,380.99,0.25599,0.61402,-0.74663,283.22,#34,-0.80194,0.5521,-0.22821,203.38,0.32591,0.08416,-0.94165,387.74,-0.50068,-0.82952,-0.24743,270.38,#35,0.51986,0.074768,0.85097,164.35,0.29822,-0.94937,-0.098774,380.54,0.8005,0.30513,-0.51584,283.33
> view matrix models
> #25,0.33522,-0.78133,-0.52645,279.89,0.83537,-0.01188,0.54955,287.42,-0.43564,-0.624,0.64872,316.99,#24,-0.82295,0.13682,-0.55139,427.82,-0.47554,-0.69694,0.53679,564.57,-0.31084,0.70396,0.63861,36.66,#26,-0.55987,-0.53567,-0.63214,195.91,-0.48729,-0.40418,0.77408,445.34,-0.67015,0.74141,-0.034739,311.22,#27,0.55519,0.70578,-0.44005,184.06,-0.47612,-0.16413,-0.86393,466.63,-0.68197,0.68916,0.24491,279.03,#28,-0.61496,0.26733,-0.74186,252.58,0.78456,0.11273,-0.60973,460.32,-0.079373,-0.95699,-0.27906,252.41,#29,0.49521,0.86244,0.10468,132.98,0.86474,-0.50092,0.036151,430.9,0.083613,0.072616,-0.99385,239.9,#30,0.67621,-0.014144,0.73658,165.4,-0.4424,0.79168,0.42134,479.37,-0.58909,-0.61078,0.52908,255.3,#31,-0.53758,-0.55933,-0.631,258.18,0.71644,-0.6976,0.0079897,788.79,-0.44465,-0.44778,0.77574,441.6,#32,0.046498,0.76341,0.64424,139.79,-0.97901,0.16293,-0.12241,400.46,-0.19842,-0.62503,0.75496,331.14,#33,-0.6896,0.65726,0.30408,150.83,0.67744,0.43703,0.59168,403.84,0.25599,0.61402,-0.74663,274.35,#34,-0.80194,0.5521,-0.22821,191.22,0.32591,0.08416,-0.94165,410.58,-0.50068,-0.82952,-0.24743,261.5,#35,0.51986,0.074768,0.85097,152.19,0.29822,-0.94937,-0.098774,403.39,0.8005,0.30513,-0.51584,274.46
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.29841,-0.56669,-0.768,344.37,0.32437,-0.81698,0.47679,454.9,-0.89763,-0.10684,0.42761,313.67,#24,-0.2942,0.55512,-0.778,274.77,-0.87699,0.16678,0.45063,488.68,0.37992,0.81488,0.43777,-100.21,#26,-0.08461,-0.14238,-0.98619,176.76,-0.9964,0.01745,0.082966,495.03,0.0053963,0.98966,-0.14335,265.48,#27,0.74114,0.62627,0.24186,154.22,-0.44522,0.72814,-0.52114,478.89,-0.50249,0.27856,0.81848,236.14,#28,-0.97967,0.13877,-0.1449,209.99,0.066924,-0.45485,-0.88805,491.41,-0.18914,-0.87969,0.43631,189.49,#29,-0.20599,0.97614,0.068686,140.38,0.77162,0.2052,-0.60208,407.64,-0.60181,-0.071022,-0.79548,248.33,#30,0.80779,-0.5278,0.2625,132.16,-0.30393,0.0086464,0.95266,460.46,-0.50508,-0.84932,-0.15343,220.41,#31,-0.87126,0.052324,-0.48803,-6.8934,-0.17924,-0.95955,0.21711,800.69,-0.45692,0.27664,0.84539,157.38,#32,0.6883,0.47114,0.55161,164.37,-0.64273,0.04348,0.76486,456.34,0.33637,-0.88098,0.33275,328.02,#33,-0.96913,0.19158,-0.15516,171.2,0.19907,0.97939,-0.034109,425.15,0.14543,-0.063945,-0.9873,279.65,#34,-0.80838,0.36862,0.45896,197.08,-0.56029,-0.24269,-0.79194,440.14,-0.18054,-0.89734,0.40273,248.86,#35,0.17847,0.68236,0.7089,172.51,0.9623,-0.27132,0.018895,425.66,0.20523,0.6788,-0.70506,279.36
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.29841,-0.56669,-0.768,369.85,0.32437,-0.81698,0.47679,421.84,-0.89763,-0.10684,0.42761,322.69,#24,-0.2942,0.55512,-0.778,300.25,-0.87699,0.16678,0.45063,455.62,0.37992,0.81488,0.43777,-91.192,#26,-0.08461,-0.14238,-0.98619,202.24,-0.9964,0.01745,0.082966,461.97,0.0053963,0.98966,-0.14335,274.5,#27,0.74114,0.62627,0.24186,179.7,-0.44522,0.72814,-0.52114,445.83,-0.50249,0.27856,0.81848,245.15,#28,-0.97967,0.13877,-0.1449,235.47,0.066924,-0.45485,-0.88805,458.35,-0.18914,-0.87969,0.43631,198.5,#29,-0.20599,0.97614,0.068686,165.86,0.77162,0.2052,-0.60208,374.58,-0.60181,-0.071022,-0.79548,257.34,#30,0.80779,-0.5278,0.2625,157.64,-0.30393,0.0086464,0.95266,427.4,-0.50508,-0.84932,-0.15343,229.42,#31,-0.87126,0.052324,-0.48803,18.586,-0.17924,-0.95955,0.21711,767.63,-0.45692,0.27664,0.84539,166.4,#32,0.6883,0.47114,0.55161,189.85,-0.64273,0.04348,0.76486,423.28,0.33637,-0.88098,0.33275,337.03,#33,-0.96913,0.19158,-0.15516,196.68,0.19907,0.97939,-0.034109,392.09,0.14543,-0.063945,-0.9873,288.66,#34,-0.80838,0.36862,0.45896,222.56,-0.56029,-0.24269,-0.79194,407.08,-0.18054,-0.89734,0.40273,257.88,#35,0.17847,0.68236,0.7089,197.99,0.9623,-0.27132,0.018895,392.6,0.20523,0.6788,-0.70506,288.37
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.070975,-0.78164,-0.61967,357.22,0.61024,-0.52544,0.59289,341.22,-0.78903,-0.33607,0.51428,332.66,#24,-0.60203,0.47926,-0.63865,351.35,-0.7885,-0.23083,0.57007,494.14,0.1258,0.84678,0.51686,-59.594,#26,-0.39913,-0.2448,-0.88361,218.18,-0.87917,-0.17139,0.44461,446.14,-0.26029,0.9543,-0.14682,291.6,#27,0.61335,0.78899,-0.035851,195.29,-0.53721,0.38349,-0.75123,446.1,-0.57896,0.48003,0.65907,258.35,#28,-0.87722,0.088441,-0.47187,257.22,0.4387,-0.25155,-0.86271,449.65,-0.195,-0.96379,0.18187,218.41,#29,0.12424,0.99165,-0.034486,158.03,0.91536,-0.12795,-0.38176,383.07,-0.38299,0.015862,-0.92362,250.88,#30,0.72153,-0.39336,0.56978,170.5,-0.43068,0.38937,0.81419,440.57,-0.54213,-0.83286,0.11153,237.64,#31,-0.82258,-0.29055,-0.48882,156.12,0.24165,-0.95674,0.16204,812.38,-0.51475,0.015167,0.85721,262.34,#32,0.40166,0.56056,0.72418,186.79,-0.89871,0.089286,0.42935,400.26,0.17602,-0.82329,0.53964,341.3,#33,-0.86442,0.50114,-0.040511,188.93,0.4757,0.8413,0.25674,381.07,0.16275,0.20266,-0.96563,286.65,#34,-0.918,0.3745,0.1305,221.67,-0.19224,-0.13239,-0.97238,393.25,-0.34688,-0.91773,0.19353,261.72,#35,0.45164,0.47465,0.75546,190.35,0.76612,-0.64028,-0.055731,381.16,0.45726,0.60394,-0.65282,286.54
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.070975,-0.78164,-0.61967,353.15,0.61024,-0.52544,0.59289,343.18,-0.78903,-0.33607,0.51428,329.12,#24,-0.60203,0.47926,-0.63865,347.28,-0.7885,-0.23083,0.57007,496.1,0.1258,0.84678,0.51686,-63.13,#26,-0.39913,-0.2448,-0.88361,214.11,-0.87917,-0.17139,0.44461,448.1,-0.26029,0.9543,-0.14682,288.07,#27,0.61335,0.78899,-0.035851,191.22,-0.53721,0.38349,-0.75123,448.06,-0.57896,0.48003,0.65907,254.82,#28,-0.87722,0.088441,-0.47187,253.14,0.4387,-0.25155,-0.86271,451.61,-0.195,-0.96379,0.18187,214.87,#29,0.12424,0.99165,-0.034486,153.96,0.91536,-0.12795,-0.38176,385.03,-0.38299,0.015862,-0.92362,247.35,#30,0.72153,-0.39336,0.56978,166.43,-0.43068,0.38937,0.81419,442.53,-0.54213,-0.83286,0.11153,234.11,#31,-0.82258,-0.29055,-0.48882,152.05,0.24165,-0.95674,0.16204,814.34,-0.51475,0.015167,0.85721,258.81,#32,0.40166,0.56056,0.72418,182.72,-0.89871,0.089286,0.42935,402.22,0.17602,-0.82329,0.53964,337.76,#33,-0.86442,0.50114,-0.040511,184.85,0.4757,0.8413,0.25674,383.04,0.16275,0.20266,-0.96563,283.11,#34,-0.918,0.3745,0.1305,217.6,-0.19224,-0.13239,-0.97238,395.21,-0.34688,-0.91773,0.19353,258.19,#35,0.45164,0.47465,0.75546,186.28,0.76612,-0.64028,-0.055731,383.12,0.45726,0.60394,-0.65282,283.01
> view matrix models
> #25,-0.070975,-0.78164,-0.61967,355.44,0.61024,-0.52544,0.59289,347.36,-0.78903,-0.33607,0.51428,332.38,#24,-0.60203,0.47926,-0.63865,349.57,-0.7885,-0.23083,0.57007,500.28,0.1258,0.84678,0.51686,-59.87,#26,-0.39913,-0.2448,-0.88361,216.4,-0.87917,-0.17139,0.44461,452.28,-0.26029,0.9543,-0.14682,291.33,#27,0.61335,0.78899,-0.035851,193.51,-0.53721,0.38349,-0.75123,452.24,-0.57896,0.48003,0.65907,258.08,#28,-0.87722,0.088441,-0.47187,255.43,0.4387,-0.25155,-0.86271,455.79,-0.195,-0.96379,0.18187,218.13,#29,0.12424,0.99165,-0.034486,156.25,0.91536,-0.12795,-0.38176,389.21,-0.38299,0.015862,-0.92362,250.6,#30,0.72153,-0.39336,0.56978,168.72,-0.43068,0.38937,0.81419,446.71,-0.54213,-0.83286,0.11153,237.37,#31,-0.82258,-0.29055,-0.48882,154.34,0.24165,-0.95674,0.16204,818.52,-0.51475,0.015167,0.85721,262.07,#32,0.40166,0.56056,0.72418,185.01,-0.89871,0.089286,0.42935,406.4,0.17602,-0.82329,0.53964,341.02,#33,-0.86442,0.50114,-0.040511,187.14,0.4757,0.8413,0.25674,387.21,0.16275,0.20266,-0.96563,286.37,#34,-0.918,0.3745,0.1305,219.89,-0.19224,-0.13239,-0.97238,399.39,-0.34688,-0.91773,0.19353,261.45,#35,0.45164,0.47465,0.75546,188.57,0.76612,-0.64028,-0.055731,387.3,0.45726,0.60394,-0.65282,286.27
> ui mousemode right zoom
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.054026,-0.7666,-0.63985,355.06,0.80471,-0.41281,0.42665,324.31,-0.59121,-0.49184,0.63919,319.25,#24,-0.59787,0.45685,-0.65867,359.04,-0.79322,-0.45562,0.40399,579.82,-0.11554,0.764,0.63479,-15.379,#26,-0.38308,-0.27054,-0.88321,216.28,-0.77325,-0.42913,0.46683,436.34,-0.50531,0.86177,-0.044808,304.63,#27,0.63486,0.77115,-0.047665,194.35,-0.35525,0.23657,-0.90434,445.47,-0.68611,0.59106,0.42414,271.99,#28,-0.87538,0.11855,-0.46868,257.36,0.4745,0.025151,-0.8799,460.02,-0.092528,-0.99263,-0.078271,236.48,#29,0.1265,0.99196,-0.0042326,157.92,0.98575,-0.12618,-0.11124,386.93,-0.11088,0.0098987,-0.99378,246.25,#30,0.74092,-0.3729,0.55856,170.22,-0.26294,0.60422,0.75218,445.86,-0.61798,-0.70417,0.34963,249.82,#31,-0.80968,-0.28175,-0.51482,151.59,0.37372,-0.9239,-0.082136,796.29,-0.4525,-0.2589,0.85335,375.96,#32,0.40497,0.58316,0.70422,183.9,-0.91185,0.31434,0.26406,378.45,-0.067371,-0.74908,0.65905,338.72,#33,-0.87324,0.48706,-0.015124,187.79,0.41105,0.75293,0.51394,375.15,0.26171,0.44258,-0.85769,280.99,#34,-0.90575,0.40202,0.13412,221.13,-0.089794,0.12724,-0.9878,393.79,-0.41419,-0.90674,-0.079152,261.41,#35,0.43097,0.46313,0.77445,189.22,0.61015,-0.78187,0.12803,375.26,0.66481,0.41735,-0.61955,280.95
> view matrix models
> #25,0.35959,-0.72077,-0.59262,297.91,0.76862,-0.13131,0.62608,270.65,-0.52907,-0.68063,0.50678,350.13,#24,-0.78305,0.083593,-0.61632,466.17,-0.54255,-0.5763,0.61116,505.97,-0.30409,0.81295,0.49662,44.2,#26,-0.48809,-0.59432,-0.63918,212.19,-0.60115,-0.30201,0.73987,423.18,-0.63275,0.74537,-0.20987,312.55,#27,0.62304,0.64253,-0.44607,202.97,-0.55776,-0.034868,-0.82927,438.91,-0.54839,0.76546,0.33666,276.54,#28,-0.61817,0.3517,-0.70297,273.73,0.7439,-0.027118,-0.66774,430.7,-0.25391,-0.93572,-0.24487,257.33,#29,0.47097,0.86046,0.19439,156.28,0.88211,-0.4572,-0.11339,396.06,-0.0086885,0.22488,-0.97435,239.11,#30,0.73449,0.028462,0.67802,186.34,-0.50652,0.68792,0.51982,447.29,-0.45163,-0.72523,0.51968,249.57,#31,-0.50663,-0.50435,-0.69926,256.53,0.62302,-0.77479,0.10743,784.3,-0.59596,-0.38123,0.70675,392.94,#32,0.080793,0.81447,0.57455,155.24,-0.99597,0.088545,0.014534,380.18,-0.039036,-0.57341,0.81834,334.21,#33,-0.72133,0.59103,0.36107,171.36,0.68721,0.5459,0.47931,375.15,0.086178,0.59387,-0.79993,278.77,#34,-0.7582,0.62407,-0.18888,212.64,0.2206,-0.027073,-0.97499,381.09,-0.61357,-0.7809,-0.11714,268.62,#35,0.43952,0.062454,0.89606,172.71,0.43316,-0.88866,-0.15053,374.77,0.78689,0.4543,-0.41763,279.07
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.35959,-0.72077,-0.59262,302,0.76862,-0.13131,0.62608,277.81,-0.52907,-0.68063,0.50678,338.55,#24,-0.78305,0.083593,-0.61632,470.26,-0.54255,-0.5763,0.61116,513.13,-0.30409,0.81295,0.49662,32.611,#26,-0.48809,-0.59432,-0.63918,216.27,-0.60115,-0.30201,0.73987,430.34,-0.63275,0.74537,-0.20987,300.96,#27,0.62304,0.64253,-0.44607,207.05,-0.55776,-0.034868,-0.82927,446.07,-0.54839,0.76546,0.33666,264.95,#28,-0.61817,0.3517,-0.70297,277.81,0.7439,-0.027118,-0.66774,437.86,-0.25391,-0.93572,-0.24487,245.74,#29,0.47097,0.86046,0.19439,160.36,0.88211,-0.4572,-0.11339,403.22,-0.0086885,0.22488,-0.97435,227.52,#30,0.73449,0.028462,0.67802,190.43,-0.50652,0.68792,0.51982,454.44,-0.45163,-0.72523,0.51968,237.98,#31,-0.50663,-0.50435,-0.69926,260.62,0.62302,-0.77479,0.10743,791.46,-0.59596,-0.38123,0.70675,381.35,#32,0.080793,0.81447,0.57455,159.32,-0.99597,0.088545,0.014534,387.34,-0.039036,-0.57341,0.81834,322.62,#33,-0.72133,0.59103,0.36107,175.45,0.68721,0.5459,0.47931,382.31,0.086178,0.59387,-0.79993,267.18,#34,-0.7582,0.62407,-0.18888,216.72,0.2206,-0.027073,-0.97499,388.24,-0.61357,-0.7809,-0.11714,257.03,#35,0.43952,0.062454,0.89606,176.79,0.43316,-0.88866,-0.15053,381.93,0.78689,0.4543,-0.41763,267.48
> view matrix models
> #25,0.35959,-0.72077,-0.59262,302.23,0.76862,-0.13131,0.62608,281.18,-0.52907,-0.68063,0.50678,338.86,#24,-0.78305,0.083593,-0.61632,470.48,-0.54255,-0.5763,0.61116,516.49,-0.30409,0.81295,0.49662,32.928,#26,-0.48809,-0.59432,-0.63918,216.5,-0.60115,-0.30201,0.73987,433.7,-0.63275,0.74537,-0.20987,301.28,#27,0.62304,0.64253,-0.44607,207.28,-0.55776,-0.034868,-0.82927,449.43,-0.54839,0.76546,0.33666,265.27,#28,-0.61817,0.3517,-0.70297,278.04,0.7439,-0.027118,-0.66774,441.22,-0.25391,-0.93572,-0.24487,246.06,#29,0.47097,0.86046,0.19439,160.59,0.88211,-0.4572,-0.11339,406.58,-0.0086885,0.22488,-0.97435,227.84,#30,0.73449,0.028462,0.67802,190.65,-0.50652,0.68792,0.51982,457.81,-0.45163,-0.72523,0.51968,238.3,#31,-0.50663,-0.50435,-0.69926,260.84,0.62302,-0.77479,0.10743,794.82,-0.59596,-0.38123,0.70675,381.67,#32,0.080793,0.81447,0.57455,159.55,-0.99597,0.088545,0.014534,390.71,-0.039036,-0.57341,0.81834,322.94,#33,-0.72133,0.59103,0.36107,175.67,0.68721,0.5459,0.47931,385.67,0.086178,0.59387,-0.79993,267.5,#34,-0.7582,0.62407,-0.18888,216.95,0.2206,-0.027073,-0.97499,391.61,-0.61357,-0.7809,-0.11714,257.35,#35,0.43952,0.062454,0.89606,177.02,0.43316,-0.88866,-0.15053,385.29,0.78689,0.4543,-0.41763,267.8
> color #24 #bec8cfff models
> view matrix models
> #25,0.35959,-0.72077,-0.59262,296.57,0.76862,-0.13131,0.62608,277.75,-0.52907,-0.68063,0.50678,339.64,#24,-0.78305,0.083593,-0.61632,464.83,-0.54255,-0.5763,0.61116,513.07,-0.30409,0.81295,0.49662,33.709,#26,-0.48809,-0.59432,-0.63918,210.85,-0.60115,-0.30201,0.73987,430.27,-0.63275,0.74537,-0.20987,302.06,#27,0.62304,0.64253,-0.44607,201.63,-0.55776,-0.034868,-0.82927,446,-0.54839,0.76546,0.33666,266.05,#28,-0.61817,0.3517,-0.70297,272.39,0.7439,-0.027118,-0.66774,437.79,-0.25391,-0.93572,-0.24487,246.84,#29,0.47097,0.86046,0.19439,154.94,0.88211,-0.4572,-0.11339,403.16,-0.0086885,0.22488,-0.97435,228.62,#30,0.73449,0.028462,0.67802,185,-0.50652,0.68792,0.51982,454.38,-0.45163,-0.72523,0.51968,239.08,#31,-0.50663,-0.50435,-0.69926,255.19,0.62302,-0.77479,0.10743,791.4,-0.59596,-0.38123,0.70675,382.45,#32,0.080793,0.81447,0.57455,153.9,-0.99597,0.088545,0.014534,387.28,-0.039036,-0.57341,0.81834,323.72,#33,-0.72133,0.59103,0.36107,170.02,0.68721,0.5459,0.47931,382.25,0.086178,0.59387,-0.79993,268.28,#34,-0.7582,0.62407,-0.18888,211.3,0.2206,-0.027073,-0.97499,388.18,-0.61357,-0.7809,-0.11714,258.13,#35,0.43952,0.062454,0.89606,171.37,0.43316,-0.88866,-0.15053,381.87,0.78689,0.4543,-0.41763,268.58
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.27308,-0.7906,-0.54808,308.72,0.95664,0.16317,0.24127,253.82,-0.10132,-0.5902,0.80087,252.62,#24,-0.7967,0.19415,-0.57234,433.39,-0.38408,-0.89383,0.23142,622.8,-0.46664,0.4042,0.78668,92.642,#26,-0.54022,-0.4948,-0.68069,214.76,-0.24751,-0.67968,0.69049,397.2,-0.80431,0.54149,0.24471,304.02,#27,0.57144,0.72765,-0.37945,200.97,-0.15905,-0.35541,-0.92108,427.86,-0.80508,0.5867,-0.08736,281.67,#28,-0.66506,0.24155,-0.70665,269.24,0.71753,0.46898,-0.51499,436.17,0.20701,-0.84954,-0.48522,254.95,#29,0.44062,0.89381,0.083438,151.54,0.80654,-0.43497,0.40036,405.43,0.39414,-0.10911,-0.91255,231.97,#30,0.6918,-0.076025,0.71808,181.09,-0.15332,0.9563,0.24896,447.06,-0.70562,-0.28233,0.64991,264.07,#31,-0.59039,-0.5221,-0.61551,257.47,0.79157,-0.52353,-0.31518,673.46,-0.15768,-0.6733,0.72236,550.38,#32,0.10501,0.73958,0.66482,162,-0.83538,0.4283,-0.34452,344.54,-0.53955,-0.51921,0.66281,306,#33,-0.7264,0.63953,0.25168,171.73,0.49157,0.22754,0.84058,368.97,0.48031,0.73432,-0.47967,254.36,#34,-0.83035,0.52991,-0.1724,211.36,0.43123,0.41511,-0.80107,382.57,-0.35293,-0.73951,-0.5732,245.05,#35,0.51479,0.1408,0.84567,173.11,0.021873,-0.98826,0.15123,368.61,0.85704,-0.059354,-0.51183,254.31
> show #!25 models
> hide #!24 models
> select subtract #24
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 13 models selected
> hide #26 models
> select subtract #26
31014 atoms, 31550 bonds, 1 pseudobond, 3912 residues, 12 models selected
> select subtract #27
23513 atoms, 23931 bonds, 1 pseudobond, 2959 residues, 11 models selected
> select subtract #28
22056 atoms, 22448 bonds, 1 pseudobond, 2778 residues, 10 models selected
> select subtract #29
20599 atoms, 20965 bonds, 1 pseudobond, 2597 residues, 9 models selected
> select subtract #30
13385 atoms, 13592 bonds, 1 pseudobond, 1692 residues, 8 models selected
> select subtract #31
11923 atoms, 12111 bonds, 1 pseudobond, 1513 residues, 7 models selected
> select subtract #32
5250 atoms, 5325 bonds, 660 residues, 5 models selected
> select subtract #33
3830 atoms, 3884 bonds, 483 residues, 4 models selected
> select subtract #34
1463 atoms, 1486 bonds, 185 residues, 3 models selected
> select subtract #35
2 models selected
> view matrix models
> #25,0.065191,-0.73992,-0.66953,341.05,0.99118,-0.029589,0.12921,286.68,-0.11541,-0.67204,0.73146,272.49
> view matrix models
> #25,0.0066436,-0.72635,-0.68729,348.23,0.9992,-0.022225,0.033147,296.69,-0.039352,-0.68696,0.72563,266.4
> hide #!13 models
> view matrix models
> #25,0.054396,-0.76294,-0.64417,341.9,0.97012,0.19314,-0.14683,296.4,0.23644,-0.61694,0.75066,223.85
> view matrix models
> #25,0.51727,-0.85449,-0.047762,227.32,0.74747,0.4239,0.51147,213.16,-0.41679,-0.30027,0.85798,246.64
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.51727,-0.85449,-0.047762,195.48,0.74747,0.4239,0.51147,193.78,-0.41679,-0.30027,0.85798,230.65
> show #!13 models
> view matrix models
> #25,0.51727,-0.85449,-0.047762,157.88,0.74747,0.4239,0.51147,218.29,-0.41679,-0.30027,0.85798,195.99
> view matrix models
> #25,0.51727,-0.85449,-0.047762,210.94,0.74747,0.4239,0.51147,229.99,-0.41679,-0.30027,0.85798,239.89
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.70293,-0.50682,-0.49902,362.63,0.67229,-0.70249,-0.23353,464.3,-0.2322,-0.49964,0.83453,245.7
> view matrix models
> #25,-0.75868,-0.53578,-0.3706,356.61,0.62434,-0.76043,-0.17875,469.89,-0.18604,-0.36699,0.91143,215.23
> view matrix models
> #25,-0.93586,0.027592,-0.35128,307.05,-0.1268,-0.95652,0.26267,523.84,-0.32876,0.29036,0.89867,154.52
> view matrix models
> #25,-0.87849,0.30691,-0.36616,269.1,-0.42252,-0.85681,0.29556,541.29,-0.22302,0.41435,0.88237,129.8
> fitmap #25 inMap #13
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage1_postprocess.mrc
using 65799 points
correlation = 0.8386, correlation about mean = 0.1168, overlap = 4248
steps = 172, shift = 87.8, angle = 36.5 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage1_postprocess.mrc (#13) coordinates:
Matrix rotation and translation
-0.11325375 0.87368989 -0.47311689 161.39806956
-0.91366114 -0.27867556 -0.29591094 320.66900746
-0.39038051 0.39875549 0.82981754 144.68682489
Axis 0.36192177 -0.04310572 -0.93121132
Axis point 236.23873697 78.94197138 0.00000000
Rotation angle (degrees) 106.32323310
Shift along axis -90.14320499
> view matrix models
> #25,-0.38909,-0.21141,-0.89661,405.72,-0.35776,-0.86223,0.35856,472.47,-0.84889,0.46029,0.25985,263.93
> view matrix models
> #25,-0.32538,-0.59232,-0.73708,424.36,0.85669,-0.51462,0.035371,333.63,-0.40026,-0.61994,0.67488,291.14
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.32538,-0.59232,-0.73708,403.05,0.85669,-0.51462,0.035371,352.56,-0.40026,-0.61994,0.67488,325.57
> view matrix models
> #25,-0.32538,-0.59232,-0.73708,381.37,0.85669,-0.51462,0.035371,349.34,-0.40026,-0.61994,0.67488,303.9
> fitmap #25 inMap #13
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage1_postprocess.mrc
using 65799 points
correlation = 0.933, correlation about mean = 0.1196, overlap = 5896
steps = 116, shift = 38.2, angle = 15 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage1_postprocess.mrc (#13) coordinates:
Matrix rotation and translation
-0.94603206 -0.17522221 -0.27261797 295.24410684
0.28403044 -0.85336477 -0.43714450 266.44938693
-0.15604514 -0.49098451 0.85707885 249.15658630
Axis -0.11290390 -0.24445626 0.96306482
Axis point 143.32181669 184.39107524 0.00000000
Rotation angle (degrees) 166.20593340
Shift along axis 141.48451210
> hide #!13 models
> show #!24 models
> select subtract #25
Nothing selected
> select add #24
2 models selected
> show #26 models
> select add #26
9810 atoms, 10032 bonds, 1233 residues, 3 models selected
> show #27 models
> select add #27
17311 atoms, 17651 bonds, 2186 residues, 4 models selected
> show #28 models
> select add #28
18768 atoms, 19134 bonds, 2367 residues, 5 models selected
> show #29 models
> select add #29
20225 atoms, 20617 bonds, 2548 residues, 6 models selected
> show #30 models
> select add #30
27439 atoms, 27990 bonds, 3453 residues, 7 models selected
> hide #26 models
> hide #27 models
> hide #28 models
> hide #29 models
> hide #30 models
> select add #31
28901 atoms, 29471 bonds, 3632 residues, 8 models selected
> select add #32
35574 atoms, 36257 bonds, 1 pseudobond, 4485 residues, 10 models selected
> select add #33
36994 atoms, 37698 bonds, 1 pseudobond, 4662 residues, 11 models selected
> select add #34
39361 atoms, 40096 bonds, 1 pseudobond, 4960 residues, 12 models selected
> select add #35
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 13 models selected
> view matrix models
> #24,-0.7967,0.19415,-0.57234,611.92,-0.38408,-0.89383,0.23142,805.74,-0.46664,0.4042,0.78668,83.809,#26,-0.54022,-0.4948,-0.68069,393.29,-0.24751,-0.67968,0.69049,580.14,-0.80431,0.54149,0.24471,295.18,#27,0.57144,0.72765,-0.37945,379.5,-0.15905,-0.35541,-0.92108,610.8,-0.80508,0.5867,-0.08736,272.84,#28,-0.66506,0.24155,-0.70665,447.77,0.71753,0.46898,-0.51499,619.1,0.20701,-0.84954,-0.48522,246.12,#29,0.44062,0.89381,0.083438,330.07,0.80654,-0.43497,0.40036,588.37,0.39414,-0.10911,-0.91255,223.14,#30,0.6918,-0.076025,0.71808,359.62,-0.15332,0.9563,0.24896,630,-0.70562,-0.28233,0.64991,255.24,#31,-0.59039,-0.5221,-0.61551,436,0.79157,-0.52353,-0.31518,856.4,-0.15768,-0.6733,0.72236,541.54,#32,0.10501,0.73958,0.66482,340.52,-0.83538,0.4283,-0.34452,527.48,-0.53955,-0.51921,0.66281,297.17,#33,-0.7264,0.63953,0.25168,350.26,0.49157,0.22754,0.84058,551.91,0.48031,0.73432,-0.47967,245.52,#34,-0.83035,0.52991,-0.1724,389.88,0.43123,0.41511,-0.80107,565.51,-0.35293,-0.73951,-0.5732,236.22,#35,0.51479,0.1408,0.84567,351.64,0.021873,-0.98826,0.15123,551.55,0.85704,-0.059354,-0.51183,245.47
> view matrix models
> #24,-0.7967,0.19415,-0.57234,552.53,-0.38408,-0.89383,0.23142,763.66,-0.46664,0.4042,0.78668,47.764,#26,-0.54022,-0.4948,-0.68069,333.9,-0.24751,-0.67968,0.69049,538.06,-0.80431,0.54149,0.24471,259.14,#27,0.57144,0.72765,-0.37945,320.11,-0.15905,-0.35541,-0.92108,568.72,-0.80508,0.5867,-0.08736,236.79,#28,-0.66506,0.24155,-0.70665,388.38,0.71753,0.46898,-0.51499,577.02,0.20701,-0.84954,-0.48522,210.07,#29,0.44062,0.89381,0.083438,270.68,0.80654,-0.43497,0.40036,546.29,0.39414,-0.10911,-0.91255,187.09,#30,0.6918,-0.076025,0.71808,300.23,-0.15332,0.9563,0.24896,587.92,-0.70562,-0.28233,0.64991,219.19,#31,-0.59039,-0.5221,-0.61551,376.61,0.79157,-0.52353,-0.31518,814.32,-0.15768,-0.6733,0.72236,505.5,#32,0.10501,0.73958,0.66482,281.14,-0.83538,0.4283,-0.34452,485.4,-0.53955,-0.51921,0.66281,261.13,#33,-0.7264,0.63953,0.25168,290.87,0.49157,0.22754,0.84058,509.83,0.48031,0.73432,-0.47967,209.48,#34,-0.83035,0.52991,-0.1724,330.5,0.43123,0.41511,-0.80107,523.43,-0.35293,-0.73951,-0.5732,200.18,#35,0.51479,0.1408,0.84567,292.25,0.021873,-0.98826,0.15123,509.47,0.85704,-0.059354,-0.51183,209.43
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.064795,0.61102,-0.78896,326.29,-0.9979,0.039752,-0.051169,765.51,9.7563e-05,0.79062,0.61231,-95.601,#26,0.23127,0.036911,-0.97219,297.56,-0.88769,-0.40093,-0.22639,601.14,-0.39814,0.91536,-0.059957,244.3,#27,0.74139,0.40819,0.53266,276.32,0.066608,0.74506,-0.66367,590.1,-0.66776,0.52751,0.52519,211.79,#28,-0.96923,0.11498,0.21765,316.26,-0.22094,-0.016543,-0.97515,637.9,-0.10852,-0.99323,0.041439,172.24,#29,-0.53853,0.83537,0.11016,287.67,0.81153,0.5494,-0.19897,519.5,-0.22673,-0.017757,-0.9738,194.38,#30,0.75931,-0.64606,-0.077769,258.65,0.21258,0.13332,0.96801,572.24,-0.61503,-0.75155,0.23857,190.75,#31,-0.839,0.39576,-0.37344,11.998,-0.29495,-0.9075,-0.29909,838.24,-0.45726,-0.14079,0.87812,277.18,#32,0.90195,0.27047,0.33666,309.08,-0.43143,0.53,0.73005,540.43,0.019024,-0.80371,0.59472,286.04,#33,-0.94115,-0.13645,-0.30921,316.57,-0.22722,0.93272,0.27999,533.93,0.2502,0.33378,-0.90884,228.94,#34,-0.61301,0.26067,0.74583,330.63,-0.70183,0.25385,-0.66557,567.37,-0.36282,-0.93146,0.027329,206,#35,-0.095711,0.84175,0.53131,317.58,0.81403,-0.241,0.52846,534.94,0.57288,0.48308,-0.66215,228.83
> view matrix models
> #24,-0.079237,0.63095,-0.77176,349.82,-0.99628,-0.023895,0.082754,750.03,0.033772,0.77545,0.6305,-103.62,#26,0.090816,0.0029796,-0.99586,306.72,-0.92395,-0.37286,-0.085374,602.39,-0.37157,0.92788,-0.031108,242.38,#27,0.72546,0.5247,0.44542,283.27,-0.062369,0.69462,-0.71667,593.51,-0.68543,0.49214,0.53664,210.74,#28,-0.99343,0.085273,0.076335,328.6,-0.081952,-0.064437,-0.99455,633.76,-0.07989,-0.99427,0.071002,168.69,#29,-0.42215,0.90487,0.054804,283.9,0.87321,0.42213,-0.24354,521.49,-0.24351,-0.054957,-0.96834,195.59,#30,0.76554,-0.63974,0.068381,262.67,0.081081,0.20137,0.97615,577.73,-0.63825,-0.74175,0.20602,190.73,#31,-0.88439,0.25747,-0.38932,59.14,-0.18501,-0.95915,-0.21404,879.17,-0.42852,-0.11727,0.89589,273.03,#32,0.83081,0.32258,0.45355,310.49,-0.55636,0.45964,0.69223,542,0.01483,-0.82745,0.56135,285.98,#33,-0.95713,0.0077596,-0.28956,315.47,-0.080852,0.95275,0.29278,532.69,0.27815,0.30364,-0.91128,228.99,#34,-0.71679,0.26986,0.64295,333.58,-0.61707,0.1839,-0.76512,562.99,-0.32471,-0.94518,0.034702,204.59,#35,0.037299,0.81081,0.58412,316.61,0.83706,-0.34463,0.42493,533.53,0.54584,0.47309,-0.69155,228.82
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.079237,0.63095,-0.77176,256.54,-0.99628,-0.023895,0.082754,608.43,0.033772,0.77545,0.6305,-54.049,#26,0.090816,0.0029796,-0.99586,213.44,-0.92395,-0.37286,-0.085374,460.79,-0.37157,0.92788,-0.031108,291.96,#27,0.72546,0.5247,0.44542,189.99,-0.062369,0.69462,-0.71667,451.9,-0.68543,0.49214,0.53664,260.32,#28,-0.99343,0.085273,0.076335,235.32,-0.081952,-0.064437,-0.99455,492.15,-0.07989,-0.99427,0.071002,218.26,#29,-0.42215,0.90487,0.054804,190.62,0.87321,0.42213,-0.24354,379.89,-0.24351,-0.054957,-0.96834,245.16,#30,0.76554,-0.63974,0.068381,169.39,0.081081,0.20137,0.97615,436.13,-0.63825,-0.74175,0.20602,240.3,#31,-0.88439,0.25747,-0.38932,-34.139,-0.18501,-0.95915,-0.21404,737.56,-0.42852,-0.11727,0.89589,322.6,#32,0.83081,0.32258,0.45355,217.21,-0.55636,0.45964,0.69223,400.4,0.01483,-0.82745,0.56135,335.55,#33,-0.95713,0.0077596,-0.28956,222.19,-0.080852,0.95275,0.29278,391.08,0.27815,0.30364,-0.91128,278.56,#34,-0.71679,0.26986,0.64295,240.3,-0.61707,0.1839,-0.76512,421.39,-0.32471,-0.94518,0.034702,254.16,#35,0.037299,0.81081,0.58412,223.33,0.83706,-0.34463,0.42493,391.93,0.54584,0.47309,-0.69155,278.4
> view matrix models
> #24,-0.079237,0.63095,-0.77176,248.91,-0.99628,-0.023895,0.082754,603.8,0.033772,0.77545,0.6305,-56.726,#26,0.090816,0.0029796,-0.99586,205.8,-0.92395,-0.37286,-0.085374,456.16,-0.37157,0.92788,-0.031108,289.28,#27,0.72546,0.5247,0.44542,182.36,-0.062369,0.69462,-0.71667,447.28,-0.68543,0.49214,0.53664,257.64,#28,-0.99343,0.085273,0.076335,227.69,-0.081952,-0.064437,-0.99455,487.53,-0.07989,-0.99427,0.071002,215.59,#29,-0.42215,0.90487,0.054804,182.98,0.87321,0.42213,-0.24354,375.26,-0.24351,-0.054957,-0.96834,242.48,#30,0.76554,-0.63974,0.068381,161.76,0.081081,0.20137,0.97615,431.5,-0.63825,-0.74175,0.20602,237.63,#31,-0.88439,0.25747,-0.38932,-41.776,-0.18501,-0.95915,-0.21404,732.94,-0.42852,-0.11727,0.89589,319.92,#32,0.83081,0.32258,0.45355,209.57,-0.55636,0.45964,0.69223,395.77,0.01483,-0.82745,0.56135,332.87,#33,-0.95713,0.0077596,-0.28956,214.55,-0.080852,0.95275,0.29278,386.46,0.27815,0.30364,-0.91128,275.88,#34,-0.71679,0.26986,0.64295,232.66,-0.61707,0.1839,-0.76512,416.76,-0.32471,-0.94518,0.034702,251.48,#35,0.037299,0.81081,0.58412,215.7,0.83706,-0.34463,0.42493,387.3,0.54584,0.47309,-0.69155,275.72
> view matrix models
> #24,-0.079237,0.63095,-0.77176,253.51,-0.99628,-0.023895,0.082754,609.19,0.033772,0.77545,0.6305,-55.25,#26,0.090816,0.0029796,-0.99586,210.41,-0.92395,-0.37286,-0.085374,461.54,-0.37157,0.92788,-0.031108,290.76,#27,0.72546,0.5247,0.44542,186.96,-0.062369,0.69462,-0.71667,452.66,-0.68543,0.49214,0.53664,259.12,#28,-0.99343,0.085273,0.076335,232.3,-0.081952,-0.064437,-0.99455,492.91,-0.07989,-0.99427,0.071002,217.06,#29,-0.42215,0.90487,0.054804,187.59,0.87321,0.42213,-0.24354,380.64,-0.24351,-0.054957,-0.96834,243.96,#30,0.76554,-0.63974,0.068381,166.37,0.081081,0.20137,0.97615,436.88,-0.63825,-0.74175,0.20602,239.1,#31,-0.88439,0.25747,-0.38932,-37.168,-0.18501,-0.95915,-0.21404,738.32,-0.42852,-0.11727,0.89589,321.4,#32,0.83081,0.32258,0.45355,214.18,-0.55636,0.45964,0.69223,401.16,0.01483,-0.82745,0.56135,334.35,#33,-0.95713,0.0077596,-0.28956,219.16,-0.080852,0.95275,0.29278,391.84,0.27815,0.30364,-0.91128,277.36,#34,-0.71679,0.26986,0.64295,237.27,-0.61707,0.1839,-0.76512,422.15,-0.32471,-0.94518,0.034702,252.96,#35,0.037299,0.81081,0.58412,220.3,0.83706,-0.34463,0.42493,392.68,0.54584,0.47309,-0.69155,277.2
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.15955,0.55814,-0.81426,294.69,-0.98245,-0.17053,0.075611,637.6,-0.096654,0.81203,0.57555,-22.917,#26,0.04986,-0.10598,-0.99312,210.58,-0.87816,-0.47832,0.0069562,454.62,-0.47576,0.87177,-0.11692,297.74,#27,0.77459,0.53317,0.34019,189.32,-0.044902,0.58289,-0.81131,451.63,-0.63086,0.61316,0.47545,263.55,#28,-0.98624,0.16513,-0.0080943,241.11,0.01587,0.04582,-0.99882,492.4,-0.16457,-0.98521,-0.04781,230.4,#29,-0.33004,0.93648,0.11863,185.61,0.92958,0.34429,-0.13171,382.12,-0.16419,0.066807,-0.98416,239.64,#30,0.82157,-0.55588,0.12657,169.35,0.087902,0.34288,0.93526,440.2,-0.56329,-0.75726,0.33056,240.23,#31,-0.85602,0.19076,-0.48045,-16.297,-0.054621,-0.95759,-0.2829,746.59,-0.51404,-0.21592,0.83014,343.75,#32,0.78037,0.42749,0.45637,205.86,-0.62526,0.52365,0.57865,389.43,0.00839,-0.73691,0.67594,333.63,#33,-0.98088,0.05614,-0.18635,214.97,-0.028398,0.90596,0.42241,386.48,0.19254,0.41963,-0.88704,276.47,#34,-0.73229,0.36368,0.57575,237.43,-0.50897,0.26941,-0.81753,417.74,-0.45243,-0.89172,-0.012189,257.48,#35,0.055605,0.73768,0.67286,216.19,0.7604,-0.46803,0.45027,387.24,0.64707,0.48661,-0.58695,276.5
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.15955,0.55814,-0.81426,297.63,-0.98245,-0.17053,0.075611,637.24,-0.096654,0.81203,0.57555,-31.774,#26,0.04986,-0.10598,-0.99312,213.52,-0.87816,-0.47832,0.0069562,454.26,-0.47576,0.87177,-0.11692,288.88,#27,0.77459,0.53317,0.34019,192.26,-0.044902,0.58289,-0.81131,451.26,-0.63086,0.61316,0.47545,254.7,#28,-0.98624,0.16513,-0.0080943,244.05,0.01587,0.04582,-0.99882,492.03,-0.16457,-0.98521,-0.04781,221.54,#29,-0.33004,0.93648,0.11863,188.55,0.92958,0.34429,-0.13171,381.76,-0.16419,0.066807,-0.98416,230.78,#30,0.82157,-0.55588,0.12657,172.28,0.087902,0.34288,0.93526,439.83,-0.56329,-0.75726,0.33056,231.37,#31,-0.85602,0.19076,-0.48045,-13.363,-0.054621,-0.95759,-0.2829,746.23,-0.51404,-0.21592,0.83014,334.89,#32,0.78037,0.42749,0.45637,208.79,-0.62526,0.52365,0.57865,389.06,0.00839,-0.73691,0.67594,324.78,#33,-0.98088,0.05614,-0.18635,217.91,-0.028398,0.90596,0.42241,386.12,0.19254,0.41963,-0.88704,267.61,#34,-0.73229,0.36368,0.57575,240.36,-0.50897,0.26941,-0.81753,417.37,-0.45243,-0.89172,-0.012189,248.62,#35,0.055605,0.73768,0.67286,219.12,0.7604,-0.46803,0.45027,386.87,0.64707,0.48661,-0.58695,267.64
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.20627,0.605,-0.76904,288.7,-0.97387,-0.20327,0.10129,636.67,-0.095037,0.76984,0.63112,-35.182,#26,-0.019225,-0.065613,-0.99766,219.29,-0.87338,-0.4846,0.0487,453.21,-0.48666,0.87227,-0.047988,288.71,#27,0.72698,0.59761,0.33819,195.63,-0.068306,0.553,-0.83038,451.52,-0.68326,0.58056,0.44284,256.04,#28,-0.9937,0.098919,-0.052625,246.66,0.057928,0.051525,-0.99699,490.56,-0.09591,-0.99376,-0.05693,219.79,#29,-0.30182,0.95229,0.045299,187.42,0.9442,0.30516,-0.12397,382.52,-0.13188,0.0053536,-0.99125,231.76,#30,0.78393,-0.59187,0.18749,173.65,0.06162,0.37467,0.92511,441.2,-0.61779,-0.71366,0.33019,234.04,#31,-0.89079,0.13577,-0.43366,8.3596,-0.013365,-0.96174,-0.27364,753.54,-0.45422,-0.23796,0.85852,353.13,#32,0.7526,0.39721,0.52518,214.35,-0.65645,0.51515,0.55109,387.82,-0.05165,-0.7595,0.64845,324.2,#33,-0.9657,0.12218,-0.22914,219.39,0.0089735,0.89757,0.44079,385.23,0.25952,0.42361,-0.86787,266.52,#34,-0.78201,0.31248,0.53928,241.76,-0.4731,0.26569,-0.83999,415.78,-0.40576,-0.91201,-0.059934,246.33,#35,0.13124,0.74934,0.64905,220.64,0.74929,-0.50366,0.42999,385.93,0.64911,0.42989,-0.62757,266.47
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.20627,0.605,-0.76904,281.39,-0.97387,-0.20327,0.10129,639.75,-0.095037,0.76984,0.63112,-43.426,#26,-0.019225,-0.065613,-0.99766,211.99,-0.87338,-0.4846,0.0487,456.3,-0.48666,0.87227,-0.047988,280.46,#27,0.72698,0.59761,0.33819,188.33,-0.068306,0.553,-0.83038,454.6,-0.68326,0.58056,0.44284,247.8,#28,-0.9937,0.098919,-0.052625,239.36,0.057928,0.051525,-0.99699,493.65,-0.09591,-0.99376,-0.05693,211.55,#29,-0.30182,0.95229,0.045299,180.12,0.9442,0.30516,-0.12397,385.61,-0.13188,0.0053536,-0.99125,223.52,#30,0.78393,-0.59187,0.18749,166.34,0.06162,0.37467,0.92511,444.28,-0.61779,-0.71366,0.33019,225.8,#31,-0.89079,0.13577,-0.43366,1.0575,-0.013365,-0.96174,-0.27364,756.63,-0.45422,-0.23796,0.85852,344.89,#32,0.7526,0.39721,0.52518,207.04,-0.65645,0.51515,0.55109,390.9,-0.05165,-0.7595,0.64845,315.95,#33,-0.9657,0.12218,-0.22914,212.09,0.0089735,0.89757,0.44079,388.31,0.25952,0.42361,-0.86787,258.28,#34,-0.78201,0.31248,0.53928,234.46,-0.4731,0.26569,-0.83999,418.87,-0.40576,-0.91201,-0.059934,238.08,#35,0.13124,0.74934,0.64905,213.33,0.74929,-0.50366,0.42999,389.02,0.64911,0.42989,-0.62757,258.23
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.23797,0.61098,-0.75503,284.1,-0.964,-0.24351,0.10678,644.68,-0.11862,0.75326,0.64694,-38.254,#26,-0.054368,-0.066273,-0.99632,214.37,-0.85818,-0.50699,0.080554,454.29,-0.51047,0.8594,-0.02931,281.54,#27,0.71316,0.62398,0.31946,190.13,-0.071046,0.51771,-0.8526,454.25,-0.6974,0.58534,0.41354,249.25,#28,-0.99287,0.084099,-0.084515,241.75,0.091016,0.076736,-0.99289,492.73,-0.077016,-0.9935,-0.083843,213.23,#29,-0.27446,0.96127,0.0251,179.38,0.95636,0.2756,-0.097036,386.26,-0.1002,-0.0026286,-0.99496,223.2,#30,0.77519,-0.5916,0.22156,167.48,0.05516,0.41277,0.90916,445.23,-0.62932,-0.69255,0.35261,227.36,#31,-0.89813,0.10188,-0.42776,13.962,0.026834,-0.95828,-0.28457,758.97,-0.4389,-0.26706,0.85793,357.98,#32,0.73089,0.40047,0.55266,207.98,-0.67743,0.52416,0.51608,388.09,-0.083007,-0.75158,0.6544,315.27,#33,-0.96055,0.15698,-0.22958,211.99,0.031131,0.88099,0.47212,386.99,0.27637,0.44634,-0.85112,257.46,#34,-0.80291,0.30553,0.51185,234.97,-0.43721,0.28185,-0.85405,417.41,-0.4052,-0.90951,-0.092718,237.75,#35,0.16513,0.7403,0.65168,213.26,0.72614,-0.53839,0.42762,387.65,0.66742,0.4026,-0.62647,257.41
> view matrix models
> #24,-0.25271,0.58987,-0.76694,294.1,-0.96085,-0.24606,0.12735,640.19,-0.11359,0.7691,0.62896,-38.801,#26,-0.058701,-0.094196,-0.99382,213.96,-0.86265,-0.49623,0.097986,454.61,-0.50239,0.86307,-0.052129,281.38,#27,0.72683,0.62029,0.29488,190.44,-0.09144,0.51291,-0.85356,454.65,-0.6807,0.59343,0.42952,248.57,#28,-0.98914,0.10717,-0.1006,243.52,0.10786,0.064268,-0.99209,491.81,-0.099856,-0.99216,-0.07513,213.29,#29,-0.25488,0.96592,0.045084,179.04,0.95994,0.25836,-0.10843,386.58,-0.11638,0.015642,-0.99308,223.01,#30,0.78963,-0.56877,0.2302,168.12,0.034382,0.4156,0.9089,445.8,-0.61262,-0.70978,0.34772,226.28,#31,-0.88769,0.090349,-0.45148,17.477,0.038012,-0.96283,-0.26742,763.65,-0.45886,-0.25455,0.85126,350.14,#32,0.72016,0.42621,0.54746,205.64,-0.69124,0.50862,0.51332,388.92,-0.059665,-0.7481,0.6609,315.66,#33,-0.96564,0.16308,-0.20235,210.9,0.051306,0.88291,0.46673,387.11,0.25477,0.44031,-0.86094,257.97,#34,-0.80163,0.33038,0.49824,234.85,-0.42726,0.26631,-0.86402,416.89,-0.41814,-0.9055,-0.072326,238.45,#35,0.1636,0.72147,0.67284,212.18,0.73039,-0.54704,0.40899,387.75,0.66315,0.42453,-0.61645,257.94
> surface dust #24 size 25.5
> volume #24 level 0.003298
> view matrix models
> #24,-0.42622,0.5442,-0.72263,332.63,-0.89756,-0.35402,0.26279,617.26,-0.11281,0.7606,0.63934,-39.592,#26,-0.22234,-0.17294,-0.95951,223.78,-0.83467,-0.47485,0.279,447.94,-0.50388,0.86291,-0.038775,281.12,#27,0.68915,0.71126,0.13848,200.26,-0.21986,0.38735,-0.89533,452.45,-0.69046,0.58657,0.42332,248.62,#28,-0.95369,0.10478,-0.28196,258.81,0.28808,0.048508,-0.95638,479.41,-0.086532,-0.99331,-0.076447,212.74,#29,-0.075729,0.99706,0.012037,176.23,0.99099,0.076595,-0.10985,387.76,-0.11045,0.0036097,-0.99387,223.03,#30,0.77483,-0.49159,0.39747,176.41,-0.10805,0.51651,0.84944,447.97,-0.62287,-0.70111,0.34709,226.6,#31,-0.87127,-0.091137,-0.48227,88.242,0.20261,-0.96176,-0.18429,787.43,-0.44703,-0.25828,0.85642,353.28,#32,0.58021,0.503,0.64059,203.97,-0.81137,0.42551,0.40077,384.71,-0.070989,-0.75228,0.655,315.33,#33,-0.93655,0.32788,-0.12393,208.08,0.22639,0.83575,0.50027,382.26,0.26761,0.44048,-0.85695,257.58,#34,-0.87159,0.36235,0.3302,236.84,-0.27075,0.20571,-0.94041,407.24,-0.40869,-0.90906,-0.081188,237.82,#35,0.30316,0.61401,0.72876,209.45,0.6846,-0.67231,0.28165,382.65,0.66288,0.41352,-0.62417,257.53
> view matrix models
> #24,-0.44369,0.54391,-0.71225,334.35,-0.88683,-0.38099,0.2615,620.47,-0.12913,0.74767,0.6514,-36.004,#26,-0.24197,-0.17446,-0.95447,225.07,-0.81888,-0.49094,0.29734,445.97,-0.52046,0.85354,-0.024072,281.78,#27,0.67915,0.72321,0.12542,201.37,-0.21682,0.36092,-0.90704,451.65,-0.70125,0.58882,0.40193,249.6,#28,-0.94888,0.097328,-0.30025,260.11,0.30739,0.068968,-0.94908,478.34,-0.071664,-0.99286,-0.09536,213.82,#29,-0.058289,0.9983,0.0016662,175.93,0.99445,0.058211,-0.087614,388.01,-0.087562,-0.0034501,-0.99615,222.78,#30,0.76744,-0.4878,0.41603,177.26,-0.10815,0.54111,0.83397,448.1,-0.63193,-0.68502,0.36251,227.7,#31,-0.87109,-0.11109,-0.4784,96.455,0.22857,-0.95386,-0.19469,786.18,-0.4347,-0.27894,0.85629,362.72,#32,0.56447,0.50447,0.65337,204.38,-0.82006,0.43308,0.3741,382.36,-0.094243,-0.74696,0.65815,314.75,#33,-0.92993,0.34698,-0.12183,207.96,0.23742,0.81945,0.52166,381.14,0.28084,0.45618,-0.84441,256.91,#34,-0.87985,0.35846,0.31203,237.02,-0.24545,0.21948,-0.94424,406.03,-0.40696,-0.90738,-0.10513,237.46,#35,0.32133,0.6049,0.72859,209.34,0.66381,-0.6926,0.28225,381.51,0.67535,0.39295,-0.62409,256.86
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.44369,0.54391,-0.71225,331.18,-0.88683,-0.38099,0.2615,619.06,-0.12913,0.74767,0.6514,-31.499,#26,-0.24197,-0.17446,-0.95447,221.91,-0.81888,-0.49094,0.29734,444.56,-0.52046,0.85354,-0.024072,286.28,#27,0.67915,0.72321,0.12542,198.2,-0.21682,0.36092,-0.90704,450.24,-0.70125,0.58882,0.40193,254.11,#28,-0.94888,0.097328,-0.30025,256.94,0.30739,0.068968,-0.94908,476.93,-0.071664,-0.99286,-0.09536,218.33,#29,-0.058289,0.9983,0.0016662,172.77,0.99445,0.058211,-0.087614,386.6,-0.087562,-0.0034501,-0.99615,227.29,#30,0.76744,-0.4878,0.41603,174.09,-0.10815,0.54111,0.83397,446.69,-0.63193,-0.68502,0.36251,232.2,#31,-0.87109,-0.11109,-0.4784,93.29,0.22857,-0.95386,-0.19469,784.78,-0.4347,-0.27894,0.85629,367.22,#32,0.56447,0.50447,0.65337,201.22,-0.82006,0.43308,0.3741,380.95,-0.094243,-0.74696,0.65815,319.25,#33,-0.92993,0.34698,-0.12183,204.8,0.23742,0.81945,0.52166,379.73,0.28084,0.45618,-0.84441,261.42,#34,-0.87985,0.35846,0.31203,233.85,-0.24545,0.21948,-0.94424,404.62,-0.40696,-0.90738,-0.10513,241.97,#35,0.32133,0.6049,0.72859,206.18,0.66381,-0.6926,0.28225,380.1,0.67535,0.39295,-0.62409,261.37
> view matrix models
> #24,-0.44369,0.54391,-0.71225,328.37,-0.88683,-0.38099,0.2615,618.57,-0.12913,0.74767,0.6514,-33.493,#26,-0.24197,-0.17446,-0.95447,219.1,-0.81888,-0.49094,0.29734,444.08,-0.52046,0.85354,-0.024072,284.29,#27,0.67915,0.72321,0.12542,195.39,-0.21682,0.36092,-0.90704,449.76,-0.70125,0.58882,0.40193,252.11,#28,-0.94888,0.097328,-0.30025,254.13,0.30739,0.068968,-0.94908,476.44,-0.071664,-0.99286,-0.09536,216.33,#29,-0.058289,0.9983,0.0016662,169.96,0.99445,0.058211,-0.087614,386.11,-0.087562,-0.0034501,-0.99615,225.3,#30,0.76744,-0.4878,0.41603,171.28,-0.10815,0.54111,0.83397,446.2,-0.63193,-0.68502,0.36251,230.21,#31,-0.87109,-0.11109,-0.4784,90.478,0.22857,-0.95386,-0.19469,784.29,-0.4347,-0.27894,0.85629,365.23,#32,0.56447,0.50447,0.65337,198.4,-0.82006,0.43308,0.3741,380.47,-0.094243,-0.74696,0.65815,317.26,#33,-0.92993,0.34698,-0.12183,201.99,0.23742,0.81945,0.52166,379.24,0.28084,0.45618,-0.84441,259.42,#34,-0.87985,0.35846,0.31203,231.04,-0.24545,0.21948,-0.94424,404.13,-0.40696,-0.90738,-0.10513,239.97,#35,0.32133,0.6049,0.72859,203.37,0.66381,-0.6926,0.28225,379.62,0.67535,0.39295,-0.62409,259.37
> select subtract #35
39361 atoms, 40096 bonds, 1 pseudobond, 4960 residues, 12 models selected
> select subtract #34
36994 atoms, 37698 bonds, 1 pseudobond, 4662 residues, 11 models selected
> select subtract #33
35574 atoms, 36257 bonds, 1 pseudobond, 4485 residues, 10 models selected
> select subtract #32
28901 atoms, 29471 bonds, 3632 residues, 8 models selected
> select subtract #31
27439 atoms, 27990 bonds, 3453 residues, 7 models selected
> select subtract #30
20225 atoms, 20617 bonds, 2548 residues, 6 models selected
> select subtract #29
18768 atoms, 19134 bonds, 2367 residues, 5 models selected
> select subtract #28
17311 atoms, 17651 bonds, 2186 residues, 4 models selected
> select subtract #27
9810 atoms, 10032 bonds, 1233 residues, 3 models selected
> select subtract #26
2 models selected
> select subtract #24
Nothing selected
> hide #!25 models
> show #!25 models
> show #!13 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> fitmap #24 inMap #13
Fit map postprocess_20231221.mrc in map COPI_golph_linkage1_postprocess.mrc
using 28339 points
correlation = 0.8323, correlation about mean = 0.2096, overlap = 68.68
steps = 112, shift = 2.95, angle = 9.66 degrees
Position of postprocess_20231221.mrc (#24) relative to
COPI_golph_linkage1_postprocess.mrc (#13) coordinates:
Matrix rotation and translation
0.36066969 0.89499066 -0.26250545 -65.24306892
-0.85377429 0.20350072 -0.47922534 385.94731508
-0.37548216 0.39696246 0.83751655 73.99878724
Axis 0.44720647 0.05766334 -0.89257006
Axis point 253.82839871 217.75653073 0.00000000
Rotation angle (degrees) 78.41371225
Shift along axis -72.97121361
> hide #!13 models
> show #26 models
> fitmap #26 inMap #24
Fit molecule copy of CopA_F8WHL2.pdb (#26) to map postprocess_20231221.mrc
(#24) using 9810 atoms
average map value = 0.002311, steps = 200
shifted from previous position = 33.3
rotated from previous position = 39.3 degrees
atoms outside contour = 8189, contour level = 0.0032978
Position of copy of CopA_F8WHL2.pdb (#26) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.48919129 0.86758904 -0.08933718 173.66417465
-0.80858149 0.41274017 -0.41933461 228.33852434
-0.32693707 0.27737122 0.90342534 208.22971501
Axis 0.38057152 0.12978756 -0.91559844
Axis point 331.49964154 -46.63271772 0.00000000
Rotation angle (degrees) 66.25427443
Shift along axis -94.92766211
> ui mousemode right zoom
> select add #26
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.24197,-0.17446,-0.95447,216.08,-0.81888,-0.49094,0.29734,444.7,-0.52046,0.85354,-0.024072,295.63
> fitmap #26 inMap #24
Fit molecule copy of CopA_F8WHL2.pdb (#26) to map postprocess_20231221.mrc
(#24) using 9810 atoms
average map value = 0.002292, steps = 176
shifted from previous position = 37.9
rotated from previous position = 36.6 degrees
atoms outside contour = 8069, contour level = 0.0032978
Position of copy of CopA_F8WHL2.pdb (#26) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.52204018 0.84544209 0.11270182 168.13915738
-0.70595342 0.50245145 -0.49917162 232.28140646
-0.47864789 0.18102540 0.85914258 210.96232275
Axis 0.37910664 0.32958775 -0.86466761
Axis point 359.09123453 -14.75335760 -0.00000000
Rotation angle (degrees) 63.78012245
Shift along axis -42.11251195
> show #27 models
> select subtract #26
Nothing selected
> select add #27
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> view matrix models
> #27,0.67915,0.72321,0.12542,188.54,-0.21682,0.36092,-0.90704,442.68,-0.70125,0.58882,0.40193,246.42
> fitmap #26 inMap #24
Fit molecule copy of CopA_F8WHL2.pdb (#26) to map postprocess_20231221.mrc
(#24) using 9810 atoms
average map value = 0.002292, steps = 176
shifted from previous position = 37.9
rotated from previous position = 36.6 degrees
atoms outside contour = 8069, contour level = 0.0032978
Position of copy of CopA_F8WHL2.pdb (#26) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.52204018 0.84544209 0.11270182 168.13915738
-0.70595342 0.50245145 -0.49917162 232.28140646
-0.47864789 0.18102540 0.85914258 210.96232275
Axis 0.37910664 0.32958775 -0.86466761
Axis point 359.09123453 -14.75335760 0.00000000
Rotation angle (degrees) 63.78012245
Shift along axis -42.11251195
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002632, steps = 80
shifted from previous position = 7.07
rotated from previous position = 8.79 degrees
atoms outside contour = 5370, contour level = 0.0032978
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.05510091 -0.66182875 0.74762731 172.62310921
-0.01234173 0.74825620 0.66329506 209.73384589
-0.99840451 -0.04577518 0.03306149 233.19971501
Axis -0.35572697 0.87595076 0.32583521
Axis point 217.55626143 0.00000000 -50.28320725
Rotation angle (degrees) 94.69150286
Shift along axis 198.29450426
> select subtract #27
Nothing selected
> hide #26 models
> show #26 models
> show #28 models
> fitmap #28 inMap #24
Fit molecule copy of hArf1_P84078 (#28) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.002587, steps = 88
shifted from previous position = 12.8
rotated from previous position = 9.62 degrees
atoms outside contour = 1280, contour level = 0.0032978
Position of copy of hArf1_P84078 (#28) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.15689372 0.02394020 0.98732528 126.73150289
-0.68693840 -0.71561887 0.12651188 200.57796539
0.70957733 -0.69808057 -0.09583067 178.39248618
Axis -0.73389363 0.24719782 -0.63268742
Axis point 0.00000000 138.28668246 -15.53757163
Rotation angle (degrees) 145.82012059
Shift along axis -156.29169001
> hide #28 models
> show #29 models
> fitmap #28 inMap #24
Fit molecule copy of hArf1_P84078 (#28) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.002587, steps = 44
shifted from previous position = 0.00728
rotated from previous position = 0.0538 degrees
atoms outside contour = 1280, contour level = 0.0032978
Position of copy of hArf1_P84078 (#28) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.15769401 0.02392714 0.98719810 126.73595070
-0.68651507 -0.71593579 0.12701565 200.57436049
0.70980958 -0.69775599 -0.09647245 178.39967908
Axis -0.73420556 0.24692919 -0.63243036
Axis point 0.00000000 138.24458997 -15.45000257
Rotation angle (degrees) 145.82819979
Shift along axis -156.34794935
> fitmap #28 inMap #24
Fit molecule copy of hArf1_P84078 (#28) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.002588, steps = 44
shifted from previous position = 0.0446
rotated from previous position = 0.0231 degrees
atoms outside contour = 1281, contour level = 0.0032978
Position of copy of hArf1_P84078 (#28) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.15760567 0.02370579 0.98721754 126.69653215
-0.68678014 -0.71571476 0.12682820 200.56618010
0.70957274 -0.69799026 -0.09652004 178.41867472
Axis -0.73416533 0.24712976 -0.63239872
Axis point 0.00000000 138.26923718 -15.43472773
Rotation angle (degrees) 145.82385973
Shift along axis -156.28207120
> fitmap #28 inMap #24
Fit molecule copy of hArf1_P84078 (#28) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.002588, steps = 44
shifted from previous position = 0.0351
rotated from previous position = 0.0173 degrees
atoms outside contour = 1279, contour level = 0.0032978
Position of copy of hArf1_P84078 (#28) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.15786530 0.02378436 0.98717417 126.72606327
-0.68665422 -0.71579568 0.12705318 200.57530670
0.70963689 -0.69790460 -0.09666767 178.40234647
Axis -0.73425942 0.24702399 -0.63233081
Axis point 0.00000000 138.26041196 -15.43881299
Rotation angle (degrees) 145.82227451
Shift along axis -156.31219278
> hide #29 models
> show #30 models
> fitmap #29 inMap #24
Fit molecule copy of hArf1_P84078 (#29) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.003766, steps = 88
shifted from previous position = 4.36
rotated from previous position = 9.68 degrees
atoms outside contour = 619, contour level = 0.0032978
Position of copy of hArf1_P84078 (#29) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.84461901 -0.49418276 0.20591772 243.00983013
-0.47653853 0.51868237 -0.70984478 195.93867822
0.24398717 -0.69767613 -0.67358612 220.56719229
Axis 0.27853266 -0.87138535 0.40386523
Axis point 151.40232781 0.00000000 157.23746430
Rotation angle (degrees) 178.74831937
Shift along axis -13.97250052
> show #29 models
> hide #29 models
> fitmap #30 inMap #24
Fit molecule copy of CopBprime_O55029.pdb (#30) to map
postprocess_20231221.mrc (#24) using 7214 atoms
average map value = 0.00312, steps = 76
shifted from previous position = 10.5
rotated from previous position = 9.7 degrees
atoms outside contour = 3971, contour level = 0.0032978
Position of copy of CopBprime_O55029.pdb (#30) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.16363982 -0.17476461 -0.97091675 188.45128193
-0.01368357 -0.98368662 0.17936944 177.45916348
-0.98642525 0.04263759 0.15857889 238.55628903
Axis -0.64539813 0.07320281 0.76033059
Axis point 189.46127810 85.46785517 0.00000000
Rotation angle (degrees) 173.91934795
Shift along axis 72.74604733
> hide #30 models
> show #31 models
> fitmap #30 inMap #24
Fit molecule copy of CopBprime_O55029.pdb (#30) to map
postprocess_20231221.mrc (#24) using 7214 atoms
average map value = 0.00312, steps = 28
shifted from previous position = 0.0174
rotated from previous position = 0.041 degrees
atoms outside contour = 3970, contour level = 0.0032978
Position of copy of CopBprime_O55029.pdb (#30) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.16311521 -0.17470792 -0.97101522 188.46021007
-0.01416285 -0.98368049 0.17936583 177.45082967
-0.98650537 0.04300963 0.15797888 238.54740741
Axis -0.64560973 0.07334164 0.76013754
Axis point 189.53840317 85.41525215 0.00000000
Rotation angle (degrees) 173.93811101
Shift along axis 72.67162994
> fitmap #31 inMap #24
Fit molecule copy of CopD_Q5XJY5 (#31) to map postprocess_20231221.mrc (#24)
using 1462 atoms
average map value = 0.003728, steps = 132
shifted from previous position = 9.68
rotated from previous position = 9.66 degrees
atoms outside contour = 817, contour level = 0.0032978
Position of copy of CopD_Q5XJY5 (#31) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.23963491 0.93119401 0.27468678 -92.88764505
-0.88602605 0.09409261 0.45398725 105.67552374
0.39690421 -0.35217084 0.84761002 472.48286733
Axis -0.40474615 -0.06136146 -0.91236798
Axis point -102.55080352 189.86009943 0.00000000
Rotation angle (degrees) 84.79791770
Shift along axis -399.96672467
> hide #31 models
> show #!32 models
> fitmap #32 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#32) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.003524, steps = 84
shifted from previous position = 5.85
rotated from previous position = 9.62 degrees
atoms outside contour = 4302, contour level = 0.0032978
Position of copy of CopG_Q9QZE5 (#32) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.48942633 -0.51114053 -0.70653890 223.51135443
0.54869313 -0.44922702 0.70507513 282.31373609
-0.67778884 -0.73275537 0.06059576 258.72093709
Axis -0.80485009 -0.01609333 0.59325993
Axis point 0.00000000 244.98810042 103.85799789
Rotation angle (degrees) 116.71818112
Shift along axis -30.94773883
> hide #!32 models
> show #33 models
> fitmap #33 inMap #24
Fit molecule copy of CopZ1_P61924.pdb (#33) to map postprocess_20231221.mrc
(#24) using 1420 atoms
average map value = 0.003933, steps = 72
shifted from previous position = 3.15
rotated from previous position = 9.63 degrees
atoms outside contour = 672, contour level = 0.0032978
Position of copy of CopZ1_P61924.pdb (#33) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.16497815 -0.93975601 -0.29940085 230.48988127
-0.38657680 0.21766036 -0.89620441 241.46049476
0.90738117 0.26359557 -0.32737866 218.20338037
Axis 0.65793032 -0.68458225 0.31380701
Axis point 143.39347613 0.00000000 249.44869489
Rotation angle (degrees) 118.18825327
Shift along axis 54.82046417
> hide #33 models
> show #34 models
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.0031, steps = 68
shifted from previous position = 7.53
rotated from previous position = 9.65 degrees
atoms outside contour = 1385, contour level = 0.0032978
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.66117593 -0.23521496 0.71240459 198.01003745
-0.68849984 -0.56744326 0.45163715 233.20261117
0.29801737 -0.78910207 -0.53712529 191.32274258
Axis -0.89621613 0.29932197 -0.32741870
Axis point 0.00000000 180.07492889 -4.25084707
Rotation angle (degrees) 136.19470870
Shift along axis -170.29976691
> hide #34 models
> show #35 models
> fitmap #35 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#35) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.003943, steps = 60
shifted from previous position = 3.31
rotated from previous position = 9.64 degrees
atoms outside contour = 720, contour level = 0.0032978
Position of copy of CopZ2_Q9CTG7.pdb (#35) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.81858562 0.29511592 -0.49277197 229.58139340
0.42681840 0.88664168 -0.17802420 242.04890220
0.38437439 -0.35605219 -0.85175302 217.25843400
Axis -0.19678808 -0.96957756 0.14558092
Axis point 58.98360344 0.00000000 149.08497815
Rotation angle (degrees) 153.10645180
Shift along axis -248.23538238
> hide #35 models
> show #28 models
> show #29 models
> show #30 models
> show #31 models
> show #!32 models
> show #33 models
> show #34 models
> show #35 models
> show #!25 models
> ui mousemode right zoom
> show #!13 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!24 models
> hide #26 models
> hide #27 models
> hide #28 models
> hide #29 models
> hide #30 models
> hide #31 models
> hide #!32 models
> hide #33 models
> hide #34 models
> hide #35 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_1_fitting.cxs"
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/postprocess_20231221.mrc"
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00309, step 1, values float32
> color #36 #d6d6d6ff models
> color #24 #d6d6d6ff models
> rename #40 id #37
> show #!37 models
> hide #!36 models
> show #!36 models
> hide #!25 models
> hide #!13 models
> hide #!2 models
> select add #36
2 models selected
> surface dust #36 size 25.5
> ui mousemode right "translate selected models"
> view matrix models #36,1,0,0,78.717,0,1,0,120.2,0,0,1,104.78
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.99206,-0.088449,0.089364,77.564,0.10249,0.98057,-0.16725,137.1,-0.072835,0.17508,0.98186,92.496
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.99206,-0.088449,0.089364,88.426,0.10249,0.98057,-0.16725,138.93,-0.072835,0.17508,0.98186,86.082
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 37871
points
correlation = 0.6733, correlation about mean = 0.3886, overlap = 19.59
steps = 164, shift = 29.2, angle = 12.3 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53620047 -0.84400779 -0.01182950 402.28303931
0.84368442 -0.53632452 0.02350819 56.14293471
-0.02618555 0.00262474 0.99965367 -108.56145376
Axis -0.01237257 0.00850536 0.99988728
Axis point 184.78476986 138.64550447 0.00000000
Rotation angle (degrees) 122.44132659
Shift along axis -113.04897788
> view matrix models
> #36,0.99999,0.0017302,-0.0051465,67.07,-0.0017409,1,-0.0020851,109.41,0.0051429,0.002094,0.99998,136.71
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.8447,-0.37364,0.38325,480.73,0.36684,-0.92554,-0.093788,409.39,0.38976,0.06137,0.91887,54.092
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.8447,-0.37364,0.38325,508.21,0.36684,-0.92554,-0.093788,447.32,0.38976,0.06137,0.91887,30.206
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.45066,-0.86467,0.22193,545.55,0.8912,-0.45017,0.055771,202.26,0.05168,0.22291,0.97347,65.992
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.45066,-0.86467,0.22193,544.44,0.8912,-0.45017,0.055771,192.46,0.05168,0.22291,0.97347,68.858
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 37871
points
correlation = 0.1777, correlation about mean = 0.1219, overlap = 4.186
steps = 104, shift = 12.3, angle = 5.94 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53503957 0.80553794 -0.25463958 122.34959261
-0.84147634 -0.48131609 0.24546368 359.54287069
0.07516818 0.34560597 0.93536426 -171.95841740
Axis 0.05951309 -0.19599989 -0.97879632
Axis point 162.00515606 164.59925472 0.00000000
Rotation angle (degrees) 122.71738942
Shift along axis 105.12330341
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.36897,0.92922,0.020184,236.35,-0.92839,-0.36949,0.039514,611.37,0.044175,-0.0041593,0.99902,113.27
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.36897,0.92922,0.020184,215.46,-0.92839,-0.36949,0.039514,603.79,0.044175,-0.0041593,0.99902,122.93
> view matrix models
> #36,-0.36897,0.92922,0.020184,217.55,-0.92839,-0.36949,0.039514,598.81,0.044175,-0.0041593,0.99902,122.86
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.99693,-0.046758,-0.062739,103.84,0.040616,0.99457,-0.095847,144.96,0.06688,0.093005,0.99342,100.39
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.99693,-0.046758,-0.062739,123.22,0.040616,0.99457,-0.095847,130.67,0.06688,0.093005,0.99342,94.744
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 37871
points
correlation = 0.6733, correlation about mean = 0.3887, overlap = 19.59
steps = 128, shift = 21.3, angle = 6.84 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53615526 -0.84403605 -0.01186247 402.30101724
0.84371528 -0.53628046 0.02340589 56.15500330
-0.02611703 0.00254065 0.99965568 -108.55629858
Axis -0.01236136 0.00844494 0.99988793
Axis point 184.79198002 138.66052905 0.00000000
Rotation angle (degrees) 122.43822779
Shift along axis -113.04289552
> volume #36 level 0.004527
> select add #37
4 models selected
> select subtract #37
2 models selected
> select subtract #36
Nothing selected
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_1_fitting.cxs"
——— End of log from Thu Jan 25 16:06:42 2024 ———
opened ChimeraX session
> show #!1 models
> hide #!36 models
> show #!13 models
> show #!2 models
> hide #!2 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!13 models
> hide #!37 models
> show #!37 models
> show #!36 models
> hide #!37 models
> ui tool show "Fit in Map"
> fitmap #36 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 11978
points
correlation = 1, correlation about mean = 0.9999, overlap = 1.04
steps = 40, shift = 0.345, angle = 0.266 degrees
Position of postprocess_20231221.mrc (#36) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00006676 -0.00002236 -0.02989814
-0.00006676 1.00000000 0.00003143 -0.01486284
0.00002236 -0.00003143 1.00000000 -0.00253272
Axis -0.40760935 -0.29001750 -0.86587786
Axis point -141.44494503 333.70790751 0.00000000
Rotation angle (degrees) 0.00441776
Shift along axis 0.01869027
> fitmap #36 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 11978
points
correlation = 1, correlation about mean = 0.9998, overlap = 1.036
steps = 44, shift = 0.0521, angle = 0.0234 degrees
Position of postprocess_20231221.mrc (#36) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99999994 -0.00034062 -0.00000287 0.06768847
0.00034062 0.99999994 0.00002814 -0.06173873
0.00000286 -0.00002814 1.00000000 -0.02901541
Axis -0.08234288 -0.00837393 0.99656888
Axis point 182.12386166 190.47985210 0.00000000
Rotation angle (degrees) 0.01958306
Shift along axis -0.03397252
> fitmap #36 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 11978
points
correlation = 1, correlation about mean = 0.9999, overlap = 1.04
steps = 40, shift = 0.0226, angle = 0.0177 degrees
Position of postprocess_20231221.mrc (#36) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00003169 0.00000147 -0.00541357
0.00003168 1.00000000 0.00002178 -0.01376358
-0.00000147 -0.00002177 1.00000000 -0.02023148
Axis -0.56595470 0.03824516 0.82354877
Axis point 417.33412239 -423.15145428 0.00000000
Rotation angle (degrees) 0.00220436
Shift along axis -0.01412416
> fitmap #36 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 11978
points
correlation = 1, correlation about mean = 0.9998, overlap = 1.039
steps = 48, shift = 0.0416, angle = 0.0236 degrees
Position of postprocess_20231221.mrc (#36) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99999993 -0.00036831 -0.00002113 0.06219646
0.00036830 0.99999991 -0.00021329 -0.04146817
0.00002121 0.00021328 0.99999998 -0.03387551
Axis 0.50051804 -0.04968009 0.86429947
Axis point 112.10560848 163.53476479 0.00000000
Rotation angle (degrees) 0.02441542
Shift along axis 0.00391201
> fitmap #36 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 11978
points
correlation = 1, correlation about mean = 0.9999, overlap = 1.042
steps = 40, shift = 0.00802, angle = 0.0146 degrees
Position of postprocess_20231221.mrc (#36) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00017423 -0.00000387 0.02077895
0.00017423 0.99999998 -0.00004973 -0.03336166
0.00000388 0.00004973 1.00000000 -0.00286359
Axis 0.27440533 -0.02135869 0.96137689
Axis point 191.03788481 113.47555473 0.00000000
Rotation angle (degrees) 0.01038395
Shift along axis 0.00366143
> fitmap #36 inMap #2
Fit map postprocess_20231221.mrc in map emdb 3720 using 11978 points
correlation = 0.7662, correlation about mean = 0.1758, overlap = 15.28
steps = 60, shift = 0.348, angle = 0.345 degrees
Position of postprocess_20231221.mrc (#36) relative to emdb 3720 (#2)
coordinates:
Matrix rotation and translation
-0.53809684 -0.84280212 -0.01167777 402.49453385
0.84254598 -0.53822181 0.02082191 57.41588058
-0.02383398 0.00136515 0.99971499 -108.92729882
Axis -0.01154359 0.00721221 0.99990736
Axis point 184.66596532 139.00563744 0.00000000
Rotation angle (degrees) 122.56811178
Shift along axis -113.14934247
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 11978
points
correlation = 0.7662, correlation about mean = 0.1756, overlap = 15.28
steps = 44, shift = 0.0582, angle = 0.0299 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53805710 -0.84282596 -0.01178946 402.51126030
0.84257100 -0.53818481 0.02076641 57.40218213
-0.02384738 0.00124006 0.99971485 -108.90099824
Axis -0.01158453 0.00715369 0.99990731
Axis point 184.67696824 139.00477342 0.00000000
Rotation angle (degrees) 122.56550718
Shift along axis -113.14317184
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 11978
points
correlation = 0.7662, correlation about mean = 0.1757, overlap = 15.28
steps = 48, shift = 0.0254, angle = 0.00757 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53809630 -0.84280248 -0.01167827 402.48879877
0.84254637 -0.53822128 0.02082053 57.42757559
-0.02383309 0.00136397 0.99971503 -108.92394461
Axis -0.01154346 0.00721138 0.99990737
Axis point 184.65994008 139.00995823 0.00000000
Rotation angle (degrees) 122.56807333
Shift along axis -113.14583660
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!24 models
> show #!24 models
> hide #!25 models
> show #!25 models
> show #!37 models
> hide #!37 models
> color #36 #d6d6d6db models
> color #36 silver models
> combine #3 modelId #38
> combine #4 modelId #39
> combine #5 modelId #40
> combine #6 modelId #41
> combine #7 modelId #42
> combine #8 modelId #43
> combine #9 modelId #44
> combine #10 modelId #45
> combine #11 modelId #46
> combine #12 modelId #47
> hide #47 models
> hide #46 models
> hide #45 models
> hide #!44 models
> hide #43 models
> hide #42 models
> hide #41 models
> hide #40 models
> hide #39 models
> hide #38 models
> hide #!36 models
> show #!37 models
> show #!13 models
> hide #!1 models
> hide #!24 models
> show #!24 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!24 models
> show #!24 models
> hide #!37 models
> show #!37 models
> show #!2 models
> hide #!24 models
> select add #37
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #37,-0.53759,0.84262,-0.031325,296.92,-0.84305,-0.53784,0.00058592,648.61,-0.016354,0.026724,0.99951,144.38
> ui mousemode right "rotate selected models"
> view matrix models
> #37,0.435,0.82685,-0.35651,227.09,-0.64332,0.56242,0.51944,433.29,0.63001,0.0033908,0.77658,100.31
> ui mousemode right "translate selected models"
> view matrix models
> #37,0.435,0.82685,-0.35651,217.55,-0.64332,0.56242,0.51944,437.01,0.63001,0.0033908,0.77658,111.85
> fitmap #37 inMap #13
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage1_postprocess.mrc
using 93502 points
correlation = 0.8275, correlation about mean = 0.0683, overlap = 5387
steps = 128, shift = 23.6, angle = 20.8 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage1_postprocess.mrc (#13) coordinates:
Matrix rotation and translation
0.96497243 -0.24385286 -0.09676759 112.72644718
0.25704999 0.95258237 0.16282538 125.52334262
0.05247366 -0.18199611 0.98189811 157.44320497
Axis -0.55069080 -0.23834299 0.79995766
Axis point -409.53411756 597.77424891 0.00000000
Rotation angle (degrees) 18.24499542
Shift along axis 33.95287092
> view matrix models
> #37,0.70986,0.64624,-0.28014,208.19,-0.43561,0.71535,0.54638,382.22,0.55349,-0.26582,0.7893,122.24
> fitmap #37 inMap #13
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage1_postprocess.mrc
using 93502 points
correlation = 0.8275, correlation about mean = 0.06833, overlap = 5387
steps = 76, shift = 16.5, angle = 0.0111 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage1_postprocess.mrc (#13) coordinates:
Matrix rotation and translation
0.96495984 -0.24383080 -0.09694854 112.75477523
0.25706459 0.95256799 0.16288640 125.51623738
0.05263335 -0.18210087 0.98187014 157.44621713
Axis -0.55080901 -0.23882345 0.79973295
Axis point -409.41627607 597.69294757 0.00000000
Rotation angle (degrees) 18.25002154
Shift along axis 33.83236095
> ui mousemode right "rotate selected models"
> view matrix models
> #37,0.96793,-0.08683,-0.23573,250.2,0.19595,0.84814,0.4922,295.12,0.15719,-0.5226,0.83796,202.52
> view matrix models
> #37,0.99441,-0.10557,-0.003281,222,0.090994,0.84049,0.53414,302.97,-0.053633,-0.53145,0.84539,226.57
> view matrix models
> #37,0.98573,-0.13479,0.10084,214.18,0.029337,0.72743,0.68556,305.58,-0.16577,-0.67281,0.721,270.84
> ui mousemode right "translate selected models"
> view matrix models
> #37,0.98573,-0.13479,0.10084,211.97,0.029337,0.72743,0.68556,326.99,-0.16577,-0.67281,0.721,284.38
> fitmap #37 inMap #13
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage1_postprocess.mrc
using 93502 points
correlation = 0.7947, correlation about mean = 0.07398, overlap = 5015
steps = 132, shift = 15.2, angle = 19.6 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage1_postprocess.mrc (#13) coordinates:
Matrix rotation and translation
0.52297669 -0.84563649 0.10674393 207.17830589
0.50369708 0.40764960 0.76165020 111.36478075
-0.68759334 -0.34455870 0.63913588 309.65795163
Axis -0.57701428 0.41433761 0.70383156
Axis point 181.50515184 241.23904203 0.00000000
Rotation angle (degrees) 73.44825912
Shift along axis 144.54481693
> ui mousemode right "rotate selected models"
> view matrix models
> #37,-0.12571,-0.84024,0.52745,383.52,0.73732,0.27658,0.61633,305.73,-0.66375,0.46637,0.58475,212.99
> view matrix models
> #37,-0.11699,-0.92563,-0.35989,497.48,0.72116,-0.32833,0.61003,380.58,-0.68282,-0.18817,0.70594,279.06
> view matrix models
> #37,-0.44799,-0.85868,-0.24894,513.86,0.50602,-0.47308,0.72121,409.11,-0.73706,0.19713,0.64644,246.18
> view matrix models
> #37,0.94059,0.12144,-0.31709,247.6,0.19754,0.56382,0.80192,310.61,0.27617,-0.81692,0.50634,269.18
> ui mousemode right "translate selected models"
> view matrix models
> #37,0.94059,0.12144,-0.31709,273.94,0.19754,0.56382,0.80192,303.28,0.27617,-0.81692,0.50634,278.37
> fitmap #37 inMap #13
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage1_postprocess.mrc
using 93502 points
correlation = 0.9169, correlation about mean = 0.1628, overlap = 7251
steps = 84, shift = 13.2, angle = 16.2 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage1_postprocess.mrc (#13) coordinates:
Matrix rotation and translation
0.71800307 -0.65223642 -0.24302103 221.33708653
0.67862437 0.57836847 0.45272381 126.52773866
-0.15472725 -0.48997708 0.85789388 248.75308436
Axis -0.57717534 -0.05405849 0.81482901
Axis point 44.46532013 380.39002860 0.00000000
Rotation angle (degrees) 54.75087482
Shift along axis 68.10102134
> fitmap #37 inMap #13
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage1_postprocess.mrc
using 93502 points
correlation = 0.917, correlation about mean = 0.163, overlap = 7251
steps = 36, shift = 0.0525, angle = 0.0264 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage1_postprocess.mrc (#13) coordinates:
Matrix rotation and translation
0.71811713 -0.65224239 -0.24266771 221.27774252
0.67841410 0.57838734 0.45301475 126.48867681
-0.15511949 -0.48994685 0.85784031 248.75619417
Axis -0.57735479 -0.05360386 0.81473190
Axis point 44.52800019 380.32378630 0.00000000
Rotation angle (degrees) 54.74809097
Shift along axis 68.13356175
> select subtract #37
Nothing selected
> hide #!25 models
> hide #!2 models
> hide #!13 models
> show #!36 models
> select add #36
2 models selected
> volume #36 level 0.003803
> select add #38
9810 atoms, 10032 bonds, 1233 residues, 3 models selected
> select add #39
17311 atoms, 17651 bonds, 2186 residues, 4 models selected
> select add #40
18768 atoms, 19134 bonds, 2367 residues, 5 models selected
> select add #41
20225 atoms, 20617 bonds, 2548 residues, 6 models selected
> select add #42
27439 atoms, 27990 bonds, 3453 residues, 7 models selected
> select add #43
28901 atoms, 29471 bonds, 3632 residues, 8 models selected
> select add #44
35574 atoms, 36257 bonds, 1 pseudobond, 4485 residues, 10 models selected
> select add #45
36994 atoms, 37698 bonds, 1 pseudobond, 4662 residues, 11 models selected
> select add #46
39361 atoms, 40096 bonds, 1 pseudobond, 4960 residues, 12 models selected
> select add #47
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 13 models selected
> view matrix models
> #36,0.99997,-0.00047655,-0.0074944,145.76,0.00047082,1,-0.00076704,281.05,0.0074948,0.0007635,0.99997,74.503,#38,0.90148,0.40137,0.16197,305.92,-0.20826,0.7303,-0.65061,525.57,-0.37942,0.55278,0.74194,315.68,#39,-0.016838,-0.71721,0.69665,315.58,-0.071971,0.69581,0.71461,486.46,-0.99726,-0.038106,-0.063335,313.09,#40,0.15679,0.025292,0.98731,270.57,-0.68697,-0.71543,0.12742,481.49,0.70957,-0.69823,-0.094795,254.84,#41,-0.84494,-0.49319,0.20698,386.8,-0.47648,0.51826,-0.7102,476.86,0.24299,-0.6987,-0.67289,297.2,#42,-0.16138,-0.17465,-0.97132,332.27,-0.013588,-0.98373,0.17914,458.33,-0.9868,0.042107,0.15638,315.08,#43,0.23963,0.93175,0.27278,50.506,-0.88592,0.094928,0.45402,386.33,0.39714,-0.35046,0.84821,548.51,#44,0.48985,-0.51006,-0.70703,367.21,0.54942,-0.44906,0.70462,563.22,-0.6769,-0.73361,0.060264,335.37,#45,0.16446,-0.94009,-0.29863,374.26,-0.38651,0.21712,-0.89636,522.41,0.9075,0.26284,-0.32765,294.82,#46,0.6604,-0.235,0.7132,341.85,-0.68915,-0.5669,0.45133,514.18,0.29825,-0.78956,-0.53633,267.91,#47,-0.81927,0.2953,-0.49153,373.32,0.42635,0.88692,-0.17778,522.98,0.38344,-0.35521,-0.85252,293.9
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.17575,-0.9818,-0.071927,606.61,0.82199,-0.18656,0.53808,231.14,-0.5417,0.035445,0.83982,218.11,#38,0.075028,-0.82807,0.55559,320.7,0.56985,0.49282,0.65757,447.75,-0.81831,0.26727,0.50885,340.35,#39,0.1474,-0.55502,-0.81867,357.6,-0.54294,-0.73726,0.40208,461.54,-0.82674,0.38522,-0.41001,331.55,#40,0.59459,0.74967,-0.29061,374.66,0.6425,-0.22571,0.73229,393.95,0.48338,-0.62213,-0.61587,307.37,#41,0.59748,-0.37096,0.71091,355.76,-0.47007,-0.88029,-0.064277,512.95,0.64965,-0.29577,-0.70034,278.91,#42,0.11456,0.99326,-0.017724,382.16,-0.66637,0.063599,-0.7429,481.52,-0.73677,0.096914,0.66917,323.1,#43,0.79857,-0.23009,-0.5562,484.81,0.57741,0.55381,0.59992,391.47,0.16999,-0.80022,0.5751,670.11,#44,-0.57495,0.58431,-0.57273,271.57,-0.070094,-0.73259,-0.67705,501.57,-0.81518,-0.34912,0.46216,324.53,#45,0.2836,-0.068354,0.9565,313.41,0.70041,-0.66652,-0.2553,492.89,0.65498,0.74235,-0.14115,285.37,#46,0.53916,0.65608,-0.52807,329.14,0.83108,-0.51604,0.20739,453.27,-0.13644,-0.55069,-0.82349,280.35,#47,-0.30382,-0.89612,0.32352,313.08,-0.54111,-0.11719,-0.83275,491.52,0.78416,-0.42806,-0.44929,285.13
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.17575,-0.9818,-0.071927,618.94,0.82199,-0.18656,0.53808,234.64,-0.5417,0.035445,0.83982,205.55,#38,0.075028,-0.82807,0.55559,333.02,0.56985,0.49282,0.65757,451.25,-0.81831,0.26727,0.50885,327.79,#39,0.1474,-0.55502,-0.81867,369.93,-0.54294,-0.73726,0.40208,465.04,-0.82674,0.38522,-0.41001,318.98,#40,0.59459,0.74967,-0.29061,386.98,0.6425,-0.22571,0.73229,397.45,0.48338,-0.62213,-0.61587,294.8,#41,0.59748,-0.37096,0.71091,368.09,-0.47007,-0.88029,-0.064277,516.45,0.64965,-0.29577,-0.70034,266.35,#42,0.11456,0.99326,-0.017724,394.49,-0.66637,0.063599,-0.7429,485.02,-0.73677,0.096914,0.66917,310.53,#43,0.79857,-0.23009,-0.5562,497.14,0.57741,0.55381,0.59992,394.97,0.16999,-0.80022,0.5751,657.54,#44,-0.57495,0.58431,-0.57273,283.9,-0.070094,-0.73259,-0.67705,505.07,-0.81518,-0.34912,0.46216,311.96,#45,0.2836,-0.068354,0.9565,325.73,0.70041,-0.66652,-0.2553,496.39,0.65498,0.74235,-0.14115,272.8,#46,0.53916,0.65608,-0.52807,341.46,0.83108,-0.51604,0.20739,456.77,-0.13644,-0.55069,-0.82349,267.78,#47,-0.30382,-0.89612,0.32352,325.4,-0.54111,-0.11719,-0.83275,495.02,0.78416,-0.42806,-0.44929,272.57
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.14175,-0.98979,-0.014596,600.72,0.68361,-0.10855,0.72173,207.01,-0.71595,0.092328,0.69202,263.27,#38,0.085117,-0.78862,0.60896,332.11,0.35833,0.59452,0.71983,464.31,-0.92971,0.15694,0.33319,335.75,#39,0.089987,-0.58688,-0.80466,369.5,-0.72835,-0.58982,0.34873,473.23,-0.67927,0.55469,-0.48053,323.43,#40,0.64622,0.71605,-0.26395,381.73,0.69674,-0.41246,0.58688,400.91,0.31137,-0.56315,-0.76545,315.44,#41,0.58693,-0.43191,0.68481,369.21,-0.34465,-0.89865,-0.27139,511.04,0.73262,-0.076734,-0.6763,260.28,#42,0.052429,0.99771,-0.042766,394.96,-0.82513,0.019158,-0.56462,489.05,-0.56251,0.06489,0.82424,310.19,#43,0.83658,-0.21974,-0.50184,502.17,0.54752,0.36693,0.75206,475.43,0.018878,-0.90392,0.42728,667.1,#44,-0.60188,0.52855,-0.59864,285.87,-0.21946,-0.83024,-0.51238,516.09,-0.76784,-0.17701,0.61571,308.52,#45,0.34448,-0.086523,0.9348,325.94,0.81311,-0.4702,-0.34315,495.84,0.46924,0.87831,-0.09162,271.86,#46,0.58403,0.60728,-0.53863,339.09,0.73962,-0.67153,0.044843,455.2,-0.33447,-0.42457,-0.84135,276,#47,-0.31266,-0.91377,0.25936,325.52,-0.32337,-0.15434,-0.9336,494.48,0.89313,-0.37577,-0.24723,271.96
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.14175,-0.98979,-0.014596,604.48,0.68361,-0.10855,0.72173,211.99,-0.71595,0.092328,0.69202,255.66,#38,0.085117,-0.78862,0.60896,335.87,0.35833,0.59452,0.71983,469.29,-0.92971,0.15694,0.33319,328.13,#39,0.089987,-0.58688,-0.80466,373.27,-0.72835,-0.58982,0.34873,478.21,-0.67927,0.55469,-0.48053,315.81,#40,0.64622,0.71605,-0.26395,385.5,0.69674,-0.41246,0.58688,405.9,0.31137,-0.56315,-0.76545,307.82,#41,0.58693,-0.43191,0.68481,372.98,-0.34465,-0.89865,-0.27139,516.02,0.73262,-0.076734,-0.6763,252.66,#42,0.052429,0.99771,-0.042766,398.73,-0.82513,0.019158,-0.56462,494.04,-0.56251,0.06489,0.82424,302.58,#43,0.83658,-0.21974,-0.50184,505.94,0.54752,0.36693,0.75206,480.41,0.018878,-0.90392,0.42728,659.48,#44,-0.60188,0.52855,-0.59864,289.64,-0.21946,-0.83024,-0.51238,521.07,-0.76784,-0.17701,0.61571,300.9,#45,0.34448,-0.086523,0.9348,329.7,0.81311,-0.4702,-0.34315,500.82,0.46924,0.87831,-0.09162,264.24,#46,0.58403,0.60728,-0.53863,342.86,0.73962,-0.67153,0.044843,460.18,-0.33447,-0.42457,-0.84135,268.38,#47,-0.31266,-0.91377,0.25936,329.28,-0.32337,-0.15434,-0.9336,499.46,0.89313,-0.37577,-0.24723,264.34
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.02392,-0.9965,-0.08006,595.67,0.66786,-0.075519,0.74044,204.41,-0.7439,-0.035757,0.66733,293.1,#38,0.21766,-0.78165,0.5845,328.82,0.33005,0.62253,0.7096,471.72,-0.91853,0.038461,0.39348,323.79,#39,0.15288,-0.67387,-0.72286,367.78,-0.74903,-0.55616,0.36006,479.15,-0.64466,0.4864,-0.58977,316.28,#40,0.62348,0.76886,-0.14184,378.48,0.68479,-0.44948,0.57361,406.3,0.37727,-0.45477,-0.80675,311.63,#41,0.47441,-0.44856,0.75745,377.01,-0.34241,-0.88671,-0.31065,515.21,0.81098,-0.11198,-0.57425,252.79,#42,0.097155,0.98082,-0.16898,395.27,-0.84139,-0.0097478,-0.54034,493.82,-0.53163,0.19467,0.8243,306.14,#43,0.84514,-0.08749,-0.52734,454.54,0.52186,0.34871,0.7785,486.65,0.11578,-0.93314,0.34037,674.24,#44,-0.50383,0.51854,-0.69085,288.31,-0.22173,-0.85061,-0.47675,524.14,-0.83486,-0.087024,0.54354,289.55,#45,0.30788,-0.21617,0.92654,332.1,0.81464,-0.44319,-0.37409,501.67,0.4915,0.86998,0.03965,258.94,#46,0.64746,0.63421,-0.42258,343.22,0.71192,-0.70121,0.038406,460.78,-0.27196,-0.32571,-0.90551,265.7,#47,-0.43718,-0.86175,0.25743,331.63,-0.28912,-0.13638,-0.94753,500.33,0.85164,-0.48867,-0.18953,259.01
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.02392,-0.9965,-0.08006,596.43,0.66786,-0.075519,0.74044,204.57,-0.7439,-0.035757,0.66733,291.78,#38,0.21766,-0.78165,0.5845,329.59,0.33005,0.62253,0.7096,471.88,-0.91853,0.038461,0.39348,322.47,#39,0.15288,-0.67387,-0.72286,368.55,-0.74903,-0.55616,0.36006,479.31,-0.64466,0.4864,-0.58977,314.96,#40,0.62348,0.76886,-0.14184,379.24,0.68479,-0.44948,0.57361,406.46,0.37727,-0.45477,-0.80675,310.31,#41,0.47441,-0.44856,0.75745,377.77,-0.34241,-0.88671,-0.31065,515.37,0.81098,-0.11198,-0.57425,251.47,#42,0.097155,0.98082,-0.16898,396.04,-0.84139,-0.0097478,-0.54034,493.98,-0.53163,0.19467,0.8243,304.82,#43,0.84514,-0.08749,-0.52734,455.31,0.52186,0.34871,0.7785,486.81,0.11578,-0.93314,0.34037,672.92,#44,-0.50383,0.51854,-0.69085,289.08,-0.22173,-0.85061,-0.47675,524.3,-0.83486,-0.087024,0.54354,288.23,#45,0.30788,-0.21617,0.92654,332.87,0.81464,-0.44319,-0.37409,501.83,0.4915,0.86998,0.03965,257.62,#46,0.64746,0.63421,-0.42258,343.98,0.71192,-0.70121,0.038406,460.94,-0.27196,-0.32571,-0.90551,264.38,#47,-0.43718,-0.86175,0.25743,332.39,-0.28912,-0.13638,-0.94753,500.49,0.85164,-0.48867,-0.18953,257.69
> view matrix models
> #36,-0.02392,-0.9965,-0.08006,597.33,0.66786,-0.075519,0.74044,204.9,-0.7439,-0.035757,0.66733,290.48,#38,0.21766,-0.78165,0.5845,330.49,0.33005,0.62253,0.7096,472.21,-0.91853,0.038461,0.39348,321.18,#39,0.15288,-0.67387,-0.72286,369.45,-0.74903,-0.55616,0.36006,479.65,-0.64466,0.4864,-0.58977,313.66,#40,0.62348,0.76886,-0.14184,380.14,0.68479,-0.44948,0.57361,406.8,0.37727,-0.45477,-0.80675,309.01,#41,0.47441,-0.44856,0.75745,378.68,-0.34241,-0.88671,-0.31065,515.7,0.81098,-0.11198,-0.57425,250.17,#42,0.097155,0.98082,-0.16898,396.94,-0.84139,-0.0097478,-0.54034,494.31,-0.53163,0.19467,0.8243,303.52,#43,0.84514,-0.08749,-0.52734,456.21,0.52186,0.34871,0.7785,487.14,0.11578,-0.93314,0.34037,671.62,#44,-0.50383,0.51854,-0.69085,289.98,-0.22173,-0.85061,-0.47675,524.63,-0.83486,-0.087024,0.54354,286.93,#45,0.30788,-0.21617,0.92654,333.77,0.81464,-0.44319,-0.37409,502.17,0.4915,0.86998,0.03965,256.32,#46,0.64746,0.63421,-0.42258,344.88,0.71192,-0.70121,0.038406,461.27,-0.27196,-0.32571,-0.90551,263.08,#47,-0.43718,-0.86175,0.25743,333.29,-0.28912,-0.13638,-0.94753,500.82,0.85164,-0.48867,-0.18953,256.39
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.14104,-0.98937,-0.035348,610.52,0.86225,-0.14031,0.48665,233.65,-0.48644,0.03816,0.87288,175.83,#38,0.093677,-0.79942,0.59342,337.15,0.61622,0.51471,0.59611,455.77,-0.78199,0.30984,0.54083,315.62,#39,0.11063,-0.5864,-0.80243,374.59,-0.49601,-0.73223,0.46671,468.27,-0.86124,0.34638,-0.37186,307.16,#40,0.63133,0.73025,-0.26107,387.99,0.5808,-0.22215,0.78315,401.61,0.51389,-0.64606,-0.56438,278.53,#41,0.58095,-0.41761,0.69864,374.69,-0.53888,-0.84063,-0.054384,522.94,0.61001,-0.34489,-0.7134,257.88,#42,0.072755,0.99625,-0.046771,400.01,-0.62315,0.0087923,-0.78205,487.53,-0.77871,0.086044,0.62145,299.61,#43,0.82816,-0.21163,-0.519,502.1,0.52582,0.61396,0.5887,370.77,0.19406,-0.76044,0.61974,638.74,#44,-0.58717,0.54313,-0.6002,290.58,0.0098331,-0.73664,-0.67622,512.82,-0.8094,-0.40296,0.42719,303.93,#45,0.32562,-0.092693,0.94095,331.47,0.64283,-0.70809,-0.29221,504.61,0.69336,0.70001,-0.17098,263.69,#46,0.57811,0.62321,-0.52669,345.15,0.81075,-0.51151,0.28467,464.67,-0.091999,-0.59158,-0.80098,255.97,#47,-0.32114,-0.90576,0.27654,331.07,-0.57423,-0.045966,-0.8174,503.27,0.75308,-0.4213,-0.50536,263.37
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.14104,-0.98937,-0.035348,600.23,0.86225,-0.14031,0.48665,227.6,-0.48644,0.03816,0.87288,176.83,#38,0.093677,-0.79942,0.59342,326.87,0.61622,0.51471,0.59611,449.73,-0.78199,0.30984,0.54083,316.62,#39,0.11063,-0.5864,-0.80243,364.31,-0.49601,-0.73223,0.46671,462.23,-0.86124,0.34638,-0.37186,308.16,#40,0.63133,0.73025,-0.26107,377.7,0.5808,-0.22215,0.78315,395.56,0.51389,-0.64606,-0.56438,279.53,#41,0.58095,-0.41761,0.69864,364.4,-0.53888,-0.84063,-0.054384,516.9,0.61001,-0.34489,-0.7134,258.88,#42,0.072755,0.99625,-0.046771,389.73,-0.62315,0.0087923,-0.78205,481.48,-0.77871,0.086044,0.62145,300.61,#43,0.82816,-0.21163,-0.519,491.82,0.52582,0.61396,0.5887,364.73,0.19406,-0.76044,0.61974,639.74,#44,-0.58717,0.54313,-0.6002,280.29,0.0098331,-0.73664,-0.67622,506.78,-0.8094,-0.40296,0.42719,304.93,#45,0.32562,-0.092693,0.94095,321.19,0.64283,-0.70809,-0.29221,498.56,0.69336,0.70001,-0.17098,264.69,#46,0.57811,0.62321,-0.52669,334.87,0.81075,-0.51151,0.28467,458.62,-0.091999,-0.59158,-0.80098,256.97,#47,-0.32114,-0.90576,0.27654,320.78,-0.57423,-0.045966,-0.8174,497.23,0.75308,-0.4213,-0.50536,264.37
> view matrix models
> #36,-0.14104,-0.98937,-0.035348,603.93,0.86225,-0.14031,0.48665,224.26,-0.48644,0.03816,0.87288,175.26,#38,0.093677,-0.79942,0.59342,330.57,0.61622,0.51471,0.59611,446.38,-0.78199,0.30984,0.54083,315.05,#39,0.11063,-0.5864,-0.80243,368.01,-0.49601,-0.73223,0.46671,458.88,-0.86124,0.34638,-0.37186,306.58,#40,0.63133,0.73025,-0.26107,381.4,0.5808,-0.22215,0.78315,392.21,0.51389,-0.64606,-0.56438,277.96,#41,0.58095,-0.41761,0.69864,368.1,-0.53888,-0.84063,-0.054384,513.55,0.61001,-0.34489,-0.7134,257.31,#42,0.072755,0.99625,-0.046771,393.43,-0.62315,0.0087923,-0.78205,478.13,-0.77871,0.086044,0.62145,299.04,#43,0.82816,-0.21163,-0.519,495.52,0.52582,0.61396,0.5887,361.38,0.19406,-0.76044,0.61974,638.17,#44,-0.58717,0.54313,-0.6002,283.99,0.0098331,-0.73664,-0.67622,503.43,-0.8094,-0.40296,0.42719,303.36,#45,0.32562,-0.092693,0.94095,324.89,0.64283,-0.70809,-0.29221,495.21,0.69336,0.70001,-0.17098,263.12,#46,0.57811,0.62321,-0.52669,338.57,0.81075,-0.51151,0.28467,455.28,-0.091999,-0.59158,-0.80098,255.39,#47,-0.32114,-0.90576,0.27654,324.48,-0.57423,-0.045966,-0.8174,493.88,0.75308,-0.4213,-0.50536,262.8
> view matrix models
> #36,-0.14104,-0.98937,-0.035348,601.71,0.86225,-0.14031,0.48665,225.16,-0.48644,0.03816,0.87288,175.33,#38,0.093677,-0.79942,0.59342,328.34,0.61622,0.51471,0.59611,447.28,-0.78199,0.30984,0.54083,315.12,#39,0.11063,-0.5864,-0.80243,365.78,-0.49601,-0.73223,0.46671,459.78,-0.86124,0.34638,-0.37186,306.65,#40,0.63133,0.73025,-0.26107,379.18,0.5808,-0.22215,0.78315,393.12,0.51389,-0.64606,-0.56438,278.03,#41,0.58095,-0.41761,0.69864,365.88,-0.53888,-0.84063,-0.054384,514.45,0.61001,-0.34489,-0.7134,257.38,#42,0.072755,0.99625,-0.046771,391.2,-0.62315,0.0087923,-0.78205,479.04,-0.77871,0.086044,0.62145,299.11,#43,0.82816,-0.21163,-0.519,493.29,0.52582,0.61396,0.5887,362.28,0.19406,-0.76044,0.61974,638.24,#44,-0.58717,0.54313,-0.6002,281.77,0.0098331,-0.73664,-0.67622,504.33,-0.8094,-0.40296,0.42719,303.42,#45,0.32562,-0.092693,0.94095,322.66,0.64283,-0.70809,-0.29221,496.12,0.69336,0.70001,-0.17098,263.18,#46,0.57811,0.62321,-0.52669,336.34,0.81075,-0.51151,0.28467,456.18,-0.091999,-0.59158,-0.80098,255.46,#47,-0.32114,-0.90576,0.27654,322.26,-0.57423,-0.045966,-0.8174,494.78,0.75308,-0.4213,-0.50536,262.87
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.22059,-0.97493,0.029062,601.16,0.71752,-0.14202,0.6819,212.54,-0.66068,0.17128,0.73086,216.23,#38,-0.0056811,-0.78578,0.61847,333.87,0.41116,0.56195,0.71775,457.6,-0.91154,0.25837,0.31989,326.29,#39,0.047296,-0.52144,-0.85198,369.81,-0.68704,-0.63612,0.35119,468.26,-0.72508,0.56873,-0.38833,311.32,#40,0.65421,0.67339,-0.34431,383.02,0.69698,-0.36003,0.62016,396.88,0.29364,-0.64569,-0.70488,298.17,#41,0.65725,-0.41529,0.62894,363.06,-0.36725,-0.90519,-0.21392,509.46,0.65814,-0.090383,-0.74745,250.7,#42,0.022496,0.9988,0.043523,393.62,-0.79113,0.044401,-0.61004,485.52,-0.61124,-0.020709,0.79117,296.85,#43,0.82161,-0.30721,-0.48018,532.13,0.56961,0.40952,0.71263,455.42,-0.022283,-0.85902,0.51145,641.78,#44,-0.6617,0.53069,-0.52965,284.19,-0.19427,-0.80364,-0.56252,509.44,-0.72417,-0.26932,0.63486,306.17,#45,0.36483,0.002442,0.93107,321.34,0.79573,-0.52004,-0.31044,492.4,0.48344,0.85414,-0.19167,265.09,#46,0.5344,0.58349,-0.61152,335.79,0.77345,-0.62936,0.075398,451.99,-0.34087,-0.51327,-0.78763,265.74,#47,-0.22497,-0.93933,0.25892,320.97,-0.38084,-0.15982,-0.91073,491.02,0.89686,-0.30349,-0.32178,265.14
> view matrix models
> #36,-0.39651,-0.91731,-0.036286,640.79,0.51918,-0.25666,0.81522,247.92,-0.75712,0.30441,0.57802,243.23,#38,-0.15056,-0.85098,0.50316,343.42,0.20545,0.47092,0.85792,464.75,-0.96702,0.23254,0.10393,333.57,#39,0.11254,-0.353,-0.92883,375.59,-0.80679,-0.57812,0.12195,477.64,-0.58002,0.73565,-0.34986,312.86,#40,0.53987,0.67427,-0.50389,400.29,0.8381,-0.3749,0.39628,408.13,0.078296,-0.63625,-0.7675,312.29,#41,0.76186,-0.25237,0.59655,356.84,-0.11214,-0.95846,-0.26225,503.65,0.63795,0.1329,-0.75852,246.61,#42,0.11577,0.96998,0.21384,394.72,-0.8874,0.19772,-0.41644,495.07,-0.44622,-0.14155,0.88366,292.75,#43,0.70209,-0.44187,-0.55841,562.96,0.67591,0.16676,0.71787,560.14,-0.22408,-0.88144,0.41575,619.13,#44,-0.67091,0.64319,-0.36904,283.84,-0.44415,-0.74706,-0.4946,502.65,-0.59381,-0.16792,0.78688,309.6,#45,0.25326,0.16238,0.95367,320.11,0.92689,-0.323,-0.19115,483.55,0.277,0.93236,-0.23231,268.63,#46,0.35897,0.64467,-0.67493,341.56,0.76027,-0.62144,-0.18921,447,-0.54141,-0.44521,-0.71321,275.4,#47,-0.082224,-0.91641,0.39171,319.99,-0.21602,-0.36731,-0.90466,482.18,0.97292,-0.159,-0.16776,268.99
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.39651,-0.91731,-0.036286,637.92,0.51918,-0.25666,0.81522,250.92,-0.75712,0.30441,0.57802,239.89,#38,-0.15056,-0.85098,0.50316,340.55,0.20545,0.47092,0.85792,467.75,-0.96702,0.23254,0.10393,330.23,#39,0.11254,-0.353,-0.92883,372.71,-0.80679,-0.57812,0.12195,480.64,-0.58002,0.73565,-0.34986,309.52,#40,0.53987,0.67427,-0.50389,397.41,0.8381,-0.3749,0.39628,411.12,0.078296,-0.63625,-0.7675,308.95,#41,0.76186,-0.25237,0.59655,353.97,-0.11214,-0.95846,-0.26225,506.65,0.63795,0.1329,-0.75852,243.27,#42,0.11577,0.96998,0.21384,391.84,-0.8874,0.19772,-0.41644,498.06,-0.44622,-0.14155,0.88366,289.42,#43,0.70209,-0.44187,-0.55841,560.08,0.67591,0.16676,0.71787,563.13,-0.22408,-0.88144,0.41575,615.79,#44,-0.67091,0.64319,-0.36904,280.96,-0.44415,-0.74706,-0.4946,505.65,-0.59381,-0.16792,0.78688,306.26,#45,0.25326,0.16238,0.95367,317.24,0.92689,-0.323,-0.19115,486.55,0.277,0.93236,-0.23231,265.29,#46,0.35897,0.64467,-0.67493,338.68,0.76027,-0.62144,-0.18921,450,-0.54141,-0.44521,-0.71321,272.06,#47,-0.082224,-0.91641,0.39171,317.12,-0.21602,-0.36731,-0.90466,485.17,0.97292,-0.159,-0.16776,265.65
> select subtract #36
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 11 models selected
> select subtract #38
31014 atoms, 31550 bonds, 1 pseudobond, 3912 residues, 10 models selected
> select subtract #39
23513 atoms, 23931 bonds, 1 pseudobond, 2959 residues, 9 models selected
> select subtract #40
22056 atoms, 22448 bonds, 1 pseudobond, 2778 residues, 8 models selected
> select subtract #41
20599 atoms, 20965 bonds, 1 pseudobond, 2597 residues, 7 models selected
> select subtract #42
13385 atoms, 13592 bonds, 1 pseudobond, 1692 residues, 6 models selected
> select subtract #43
11923 atoms, 12111 bonds, 1 pseudobond, 1513 residues, 5 models selected
> select subtract #44
5250 atoms, 5325 bonds, 660 residues, 3 models selected
> select subtract #45
3830 atoms, 3884 bonds, 483 residues, 2 models selected
> select subtract #46
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> select subtract #47
Nothing selected
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 17524
points
correlation = 0.7396, correlation about mean = 0.2452, overlap = 17.26
steps = 92, shift = 10.2, angle = 6.87 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53718104 -0.84338522 -0.01174480 402.36650062
0.84309296 -0.53730541 0.02229769 56.76182007
-0.02511609 0.00207594 0.99968240 -108.75374613
Axis -0.01198928 0.00792771 0.99989670
Axis point 184.71559779 138.80845988 0.00000000
Rotation angle (degrees) 122.50695744
Shift along axis -113.11660621
> hide #!37 models
> volume #36 level 0.003492
> volume #36 color #c0c0c0bd
> volume #36 color #c0c0c0b4
> volume #36 color #c0c0c0b3
> show #38 models
> volume #36 level 0.003026
> select add #38
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> view matrix models
> #38,-0.15056,-0.85098,0.50316,328.48,0.20545,0.47092,0.85792,483.33,-0.96702,0.23254,0.10393,331.97
> fitmap #38 inMap #36
Fit molecule copy of CopA_F8WHL2.pdb (#38) to map postprocess_20231221.mrc
(#36) using 9810 atoms
average map value = 0.001845, steps = 112
shifted from previous position = 14.5
rotated from previous position = 6.9 degrees
atoms outside contour = 7363, contour level = 0.0030265
Position of copy of CopA_F8WHL2.pdb (#38) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.89978186 0.40470537 0.16311391 162.21661696
-0.20990723 0.72919571 -0.65131601 244.62524809
-0.38253306 0.55180355 0.74106767 239.08673404
Axis 0.82572655 0.37448913 -0.42182171
Axis point 0.00000000 -322.99650071 438.18015944
Rotation angle (degrees) 46.76261319
Shift along axis 124.70408997
> select subtract #38
Nothing selected
> hide #38 models
> show #39 models
> fitmap #39 inMap #36
Fit molecule copy of CopB_Q9JIF7.pdb (#39) to map postprocess_20231221.mrc
(#36) using 7501 atoms
average map value = 0.002525, steps = 312
shifted from previous position = 7.47
rotated from previous position = 20.9 degrees
atoms outside contour = 5350, contour level = 0.0030265
Position of copy of CopB_Q9JIF7.pdb (#39) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.06460156 -0.55302768 0.83065457 167.09256288
-0.18845106 0.81065501 0.55436870 200.49543367
-0.97995553 -0.19235083 -0.05184908 229.32041111
Axis -0.37482373 0.90885480 0.18300307
Axis point 225.47316101 0.00000000 -20.15378941
Rotation angle (degrees) 95.06559927
Shift along axis 161.55732002
> hide #39 models
> show #40 models
> fitmap #39 inMap #36
Fit molecule copy of CopB_Q9JIF7.pdb (#39) to map postprocess_20231221.mrc
(#36) using 7501 atoms
average map value = 0.002526, steps = 40
shifted from previous position = 0.0746
rotated from previous position = 0.208 degrees
atoms outside contour = 5341, contour level = 0.0030265
Position of copy of CopB_Q9JIF7.pdb (#39) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.06528128 -0.55023071 0.83245692 167.12871758
-0.18990182 0.81213990 0.55169383 200.50577283
-0.97963037 -0.19410036 -0.05147229 229.37928036
Axis -0.37431722 0.90949419 0.18085058
Axis point 225.69640896 0.00000000 -19.86539156
Rotation angle (degrees) 94.99251240
Shift along axis 161.28305324
> fitmap #39 inMap #36
Fit molecule copy of CopB_Q9JIF7.pdb (#39) to map postprocess_20231221.mrc
(#36) using 7501 atoms
average map value = 0.002525, steps = 40
shifted from previous position = 0.00858
rotated from previous position = 0.053 degrees
atoms outside contour = 5342, contour level = 0.0030265
Position of copy of CopB_Q9JIF7.pdb (#39) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.06525033 -0.55081120 0.83207537 167.12641327
-0.18926120 0.81188569 0.55228781 200.50384422
-0.97975639 -0.19351655 -0.05127138 229.37027211
Axis -0.37432371 0.90936930 0.18146413
Axis point 225.64616418 0.00000000 -19.97146360
Rotation angle (degrees) 94.99493526
Shift along axis 161.39513805
> fitmap #40 inMap #36
Fit molecule copy of hArf1_P84078 (#40) to map postprocess_20231221.mrc (#36)
using 1457 atoms
average map value = 0.002587, steps = 80
shifted from previous position = 10
rotated from previous position = 6.85 degrees
atoms outside contour = 1110, contour level = 0.0030265
Position of copy of hArf1_P84078 (#40) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.15742199 0.02369701 0.98724706 126.73234874
-0.68705342 -0.71547020 0.12672797 200.58268382
0.70934893 -0.69824124 -0.09634963 178.39488616
Axis -0.73407699 0.24728028 -0.63244243
Axis point 0.00000000 138.30427469 -15.50378424
Rotation angle (degrees) 145.81206601
Shift along axis -156.25565426
> hide #40 models
> show #41 models
> fitmap #41 inMap #36
Fit molecule copy of hArf1_P84078 (#41) to map postprocess_20231221.mrc (#36)
using 1457 atoms
average map value = 0.003766, steps = 88
shifted from previous position = 10.7
rotated from previous position = 6.8 degrees
atoms outside contour = 532, contour level = 0.0030265
Position of copy of hArf1_P84078 (#41) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
-0.84461824 -0.49418058 0.20592611 243.00926717
-0.47655890 0.51872551 -0.70979958 195.94109169
0.24395004 -0.69764560 -0.67363118 220.56590457
Axis 0.27853378 -0.87139781 0.40383759
Axis point 151.40382868 0.00000000 157.23174396
Rotation angle (degrees) 178.74983418
Shift along axis -13.98354622
> hide #41 models
> show #42 models
> fitmap #42 inMap #36
Fit molecule copy of CopBprime_O55029.pdb (#42) to map
postprocess_20231221.mrc (#36) using 7214 atoms
average map value = 0.003119, steps = 68
shifted from previous position = 9.07
rotated from previous position = 6.89 degrees
atoms outside contour = 3621, contour level = 0.0030265
Position of copy of CopBprime_O55029.pdb (#42) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.16246064 -0.17528673 -0.97102065 188.51851661
-0.01449850 -0.98356401 0.17997676 177.39518336
-0.98660850 0.04331748 0.15724905 238.53639541
Axis -0.64585918 0.07366904 0.75989393
Axis point 189.62403960 85.35112764 0.00000000
Rotation angle (degrees) 173.92694201
Shift along axis 72.57447712
> hide #42 models
> show #43 models
> fitmap #43 inMap #36
Fit molecule copy of CopD_Q5XJY5 (#43) to map postprocess_20231221.mrc (#36)
using 1462 atoms
average map value = 0.003728, steps = 140
shifted from previous position = 9.62
rotated from previous position = 6.81 degrees
atoms outside contour = 777, contour level = 0.0030265
Position of copy of CopD_Q5XJY5 (#43) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.24062811 0.93088816 0.27485514 -92.64681410
-0.88598994 0.09501323 0.45386598 105.35990271
0.39638359 -0.35273180 0.84762040 472.60767797
Axis -0.40500272 -0.06102094 -0.91227696
Axis point -102.59394014 189.88709015 0.00000000
Rotation angle (degrees) 84.74256338
Shift along axis -400.05604309
> hide #43 models
> show #!44 models
> fitmap #44 inMap #36
Fit molecule copy of CopG_Q9QZE5 (#44) to map postprocess_20231221.mrc (#36)
using 6673 atoms
average map value = 0.002534, steps = 92
shifted from previous position = 9.06
rotated from previous position = 9.53 degrees
atoms outside contour = 4985, contour level = 0.0030265
Position of copy of CopG_Q9QZE5 (#44) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.40005308 -0.55524456 -0.72915088 215.30512143
0.52653340 -0.51194577 0.67872977 279.23758458
-0.75014673 -0.65545023 0.08754932 253.06944842
Axis -0.77669476 0.01222276 0.62975856
Axis point 0.00000000 234.86750685 111.70141084
Rotation angle (degrees) 120.80859332
Shift along axis -4.44065446
> select add #44
6673 atoms, 6786 bonds, 1 pseudobond, 853 residues, 2 models selected
> view matrix models
> #44,-0.54249,0.72294,-0.42786,276.64,-0.52141,-0.68911,-0.50325,508.31,-0.65866,-0.049913,0.75078,290.34
> view matrix models
> #44,-0.54249,0.72294,-0.42786,275.6,-0.52141,-0.68911,-0.50325,508.32,-0.65866,-0.049913,0.75078,293.31
> view matrix models
> #44,-0.54249,0.72294,-0.42786,274.02,-0.52141,-0.68911,-0.50325,508.16,-0.65866,-0.049913,0.75078,290.2
> fitmap #44 inMap #36
Fit molecule copy of CopG_Q9QZE5 (#44) to map postprocess_20231221.mrc (#36)
using 6673 atoms
average map value = 0.003524, steps = 76
shifted from previous position = 4.31
rotated from previous position = 6.7 degrees
atoms outside contour = 4080, contour level = 0.0030265
Position of copy of CopG_Q9QZE5 (#44) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.48873828 -0.51173168 -0.70658728 223.57146441
0.54915305 -0.44888212 0.70493671 282.28090605
-0.67791285 -0.73255411 0.06163313 258.74031676
Axis -0.80450267 -0.01604786 0.59373220
Axis point 0.00000000 245.04131525 103.90846134
Rotation angle (degrees) 116.69591826
Shift along axis -30.77138760
> select subtract #44
Nothing selected
> hide #!44 models
> show #45 models
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.003139, steps = 104
shifted from previous position = 8.48
rotated from previous position = 29.9 degrees
atoms outside contour = 854, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.19312389 -0.97513519 0.10869470 219.27432926
-0.46343472 -0.00698820 -0.88610351 243.25864960
0.86483029 -0.22150066 -0.45056191 224.06719709
Axis 0.58851864 -0.66957264 0.45312062
Axis point 171.87035679 0.00000000 235.79200882
Rotation angle (degrees) 145.62267285
Shift along axis 67.69716150
> show #!44 models
> hide #45 models
> show #46 models
> fitmap #46 inMap #36
Fit molecule copy of Golph3_ Q9CRA5.pdb (#46) to map postprocess_20231221.mrc
(#36) using 2367 atoms
average map value = 0.002823, steps = 76
shifted from previous position = 5.55
rotated from previous position = 14.9 degrees
atoms outside contour = 1509, contour level = 0.0030265
Position of copy of Golph3_ Q9CRA5.pdb (#46) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.79431459 -0.32721850 0.51185192 187.88383847
-0.58325392 -0.64644449 0.49185809 240.20045784
0.16993879 -0.68922969 -0.70433177 189.10441435
Axis -0.94038898 0.27223323 -0.20385690
Axis point 0.00000000 177.06737384 21.42638812
Rotation angle (degrees) 141.09887643
Shift along axis -149.84358522
> show #45 models
> show #42 models
> show #39 models
> select add #46
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> view matrix models
> #46,0.35897,0.64467,-0.67493,336.48,0.76027,-0.62144,-0.18921,453.81,-0.54141,-0.44521,-0.71321,260.42
> fitmap #46 inMap #36
Fit molecule copy of Golph3_ Q9CRA5.pdb (#46) to map postprocess_20231221.mrc
(#36) using 2367 atoms
average map value = 0.0031, steps = 52
shifted from previous position = 4.91
rotated from previous position = 6.88 degrees
atoms outside contour = 1162, contour level = 0.0030265
Position of copy of Golph3_ Q9CRA5.pdb (#46) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.66037595 -0.23675098 0.71263775 198.05026413
-0.68947043 -0.56718583 0.45047837 233.24072072
0.29754684 -0.78882774 -0.53778868 191.34190837
Axis -0.89599540 0.30010305 -0.32730779
Axis point 0.00000000 180.18876170 -4.20452047
Rotation angle (degrees) 136.24464100
Shift along axis -170.08357163
> view matrix models
> #46,0.41891,0.69152,-0.58848,335.36,0.77647,-0.6088,-0.16266,460.88,-0.47076,-0.3888,-0.79198,263.13
> fitmap #46 inMap #36
Fit molecule copy of Golph3_ Q9CRA5.pdb (#46) to map postprocess_20231221.mrc
(#36) using 2367 atoms
average map value = 0.0031, steps = 56
shifted from previous position = 2.95
rotated from previous position = 0.00789 degrees
atoms outside contour = 1162, contour level = 0.0030265
Position of copy of Golph3_ Q9CRA5.pdb (#46) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.66037772 -0.23664993 0.71266968 198.05732277
-0.68946744 -0.56712690 0.45055712 233.24780532
0.29754984 -0.78890043 -0.53768040 191.34677433
Axis -0.89599058 0.30008569 -0.32733693
Axis point 0.00000000 180.19619821 -4.22028621
Rotation angle (degrees) 136.23764146
Shift along axis -170.09803316
> select subtract #46
Nothing selected
> show #47 models
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003008, steps = 216
shifted from previous position = 3.73
rotated from previous position = 28.5 degrees
atoms outside contour = 927, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.75920760 0.13719007 -0.63622538 218.32062358
0.53125651 0.69534164 -0.48401089 247.76162545
0.37599251 -0.70546362 -0.60079177 221.17327703
Axis -0.19976535 -0.91308905 0.35547460
Axis point 34.16127640 0.00000000 188.65130694
Rotation angle (degrees) 146.33871613
Shift along axis -191.21983958
> hide #46 models
> hide #42 models
> hide #39 models
> hide #!44 models
> hide #!36 models
> hide #45 models
> show #45 models
> hide #45 models
> show #45 models
> hide #47 models
> show #47 models
> show #!36 models
> select add #45
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> view matrix models
> #45,0.4074,0.32856,0.8521,316.64,0.70835,-0.70261,-0.067753,494.43,0.57643,0.63118,-0.51898,268.19
> ui mousemode right "rotate selected models"
> view matrix models
> #45,0.79491,0.36438,0.48513,316.27,0.60345,-0.3917,-0.69457,491.62,-0.063061,0.84487,-0.53124,266.32
> hide #!36 models
> view matrix models
> #45,-0.68784,-0.39482,0.60909,305.75,0.71782,-0.24549,0.65151,501.79,-0.1077,0.88535,0.45227,272.76
> view matrix models
> #45,0.50044,0.61601,-0.60835,309.18,-0.77781,0.6285,-0.003429,495.47,0.38023,0.47489,0.79366,274.94
> view matrix models
> #45,0.9407,0.30741,-0.14344,312.53,-0.27614,0.93953,0.20257,500.95,0.19704,-0.15095,0.96871,271.64
> view matrix models
> #45,0.72804,0.66597,-0.1626,313.45,-0.59249,0.73058,0.33941,499.16,0.34484,-0.15076,0.92648,272.07
> ui mousemode right "translate selected models"
> view matrix models
> #45,0.72804,0.66597,-0.1626,316.84,-0.59249,0.73058,0.33941,491.65,0.34484,-0.15076,0.92648,265.94
> view matrix models
> #45,0.72804,0.66597,-0.1626,277.83,-0.59249,0.73058,0.33941,464.15,0.34484,-0.15076,0.92648,270.44
> ui mousemode right "rotate selected models"
> view matrix models
> #45,0.75372,0.077138,-0.65266,271.38,-0.087009,0.99606,0.017242,465.95,0.65141,0.043791,0.75746,271.89
> view matrix models
> #45,0.21111,0.22417,-0.95141,267.72,-0.34854,0.92663,0.14099,465.13,0.91321,0.30184,0.27375,271.44
> ui mousemode right "translate selected models"
> view matrix models
> #45,0.21111,0.22417,-0.95141,317.53,-0.34854,0.92663,0.14099,489.65,0.91321,0.30184,0.27375,262.41
> ui mousemode right "rotate selected models"
> view matrix models
> #45,0.1589,0.17637,-0.97141,316.88,-0.30489,0.94459,0.12163,489.83,0.93904,0.27685,0.20387,261.93
> view matrix models
> #45,0.14542,0.17996,-0.97287,316.83,-0.35891,0.92593,0.11763,489.45,0.92198,0.33206,0.19924,262.14
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.003112, steps = 264
shifted from previous position = 10.9
rotated from previous position = 21 degrees
atoms outside contour = 847, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.97399447 0.16527494 -0.15498057 229.35705387
-0.19245837 -0.24256250 0.95085394 236.35581998
0.11955986 0.95595379 0.26806307 215.40502985
Axis 0.01130869 -0.60878112 -0.79325763
Axis point 119.54809377 18.75677209 0.00000000
Rotation angle (degrees) 166.96867783
Shift along axis -312.16691678
> view matrix models
> #45,-0.016061,-0.046823,-0.99877,317.94,-0.4539,0.89039,-0.034443,493.68,0.89091,0.45279,-0.035553,250.87
> view matrix models
> #45,0.53836,0.34142,-0.77046,324.27,-0.72404,0.6552,-0.21559,489.87,0.43119,0.67391,0.59993,254.12
> ui mousemode right "translate selected models"
> view matrix models
> #45,0.53836,0.34142,-0.77046,311.26,-0.72404,0.6552,-0.21559,488.89,0.43119,0.67391,0.59993,258.16
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.003331, steps = 176
shifted from previous position = 6.2
rotated from previous position = 30.9 degrees
atoms outside contour = 809, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.95696738 0.07482187 -0.28038391 229.42312978
-0.25013758 -0.70250991 0.66626648 241.55633226
-0.14712117 0.70772984 0.69099483 216.75579486
Axis 0.11724008 -0.37680819 -0.91884185
Axis point 135.44318294 63.71073576 0.00000000
Rotation angle (degrees) 169.81477120
Shift along axis -263.28711378
> view matrix models
> #45,0.54529,0.56789,-0.61658,313.54,-0.56934,0.79077,0.22481,490.72,0.61523,0.22846,0.75452,269.69
> view matrix models
> #45,0.54529,0.56789,-0.61658,309.86,-0.56934,0.79077,0.22481,489.44,0.61523,0.22846,0.75452,268.59
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.003341, steps = 124
shifted from previous position = 7.88
rotated from previous position = 26.7 degrees
atoms outside contour = 848, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.79262455 -0.25965120 -0.55165895 225.82439325
-0.24029440 -0.69852575 0.67403292 252.43242993
-0.56036143 0.66681560 0.49127593 221.81898659
Axis -0.32196172 0.38821440 0.86349883
Axis point 153.71958293 77.31257138 0.00000000
Rotation angle (degrees) 179.35779522
Shift along axis 216.83152997
> show #!36 models
> show #!44 models
> select add #47
2883 atoms, 2927 bonds, 362 residues, 2 models selected
> view matrix models
> #45,0.52874,0.67089,-0.51995,316.75,-0.8131,0.5761,-0.083515,491.76,0.24351,0.46693,0.85011,253.88,#47,-0.30922,-0.62631,0.71562,323.54,-0.25028,-0.67238,-0.69661,488.42,0.91746,-0.39451,0.051161,258.49
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.003331, steps = 92
shifted from previous position = 0.699
rotated from previous position = 26.7 degrees
atoms outside contour = 809, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.95696052 0.07496574 -0.28036889 229.41857606
-0.25020565 -0.70260268 0.66614309 241.55647631
-0.14705002 0.70762252 0.69111987 216.76484984
Axis 0.11721334 -0.37673492 -0.91887531
Axis point 135.44275251 63.71231097 0.00000000
Rotation angle (degrees) 169.80843248
Shift along axis -263.29170978
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003943, steps = 116
shifted from previous position = 11.6
rotated from previous position = 25 degrees
atoms outside contour = 662, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.81884158 0.29473455 -0.49257492 229.57710348
0.42640479 0.88680121 -0.17822064 242.04313745
0.38428825 -0.35597078 -0.85182591 217.26590072
Axis -0.19655349 -0.96962243 0.14559902
Axis point 59.02633770 0.00000000 149.08741108
Rotation angle (degrees) 153.11717756
Shift along axis -248.18093319
> hide #!44 models
> hide #!36 models
> hide #45 models
> select subtract #45
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> hide #47 models
> select subtract #47
Nothing selected
> show #!13 models
> color #13 #b2b2b288 models
> color #13 #b2b2b287 models
> hide #!13 models
> show #!13 models
> show #!1 models
> show #!24 models
> color #13 #d6d6d6ff models
> color #13 darkgrey models
> color #13 #a9a9a980 models
> hide #!13 models
> color #1 #c0c0c0e5 models
> color #1 #c0c0c0e6 models
> color #1 #d6d6d6ff models
> color #1 #d6d6d6d8 models
> hide #!1 models
> color #1 #d6d6d6d9 models
> color #24 #d6d6d6db models
> color #24 #d6d6d6d8 models
> hide #!24 models
> color #24 #d6d6d6d9 models
> show #!1 models
> show #!13 models
> show #!24 models
> show #!36 models
> color #36 #d6d6d6ff models
> color #36 #d6d6d6f4 models
> color #36 #d6d6d6d9 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_1_fitting_final.cxs"
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #!24 models
> hide #!13 models
> show #!13 models
> hide #!1 models
> select add #3
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> select subtract #3
Nothing selected
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> show #12 models
> show #26 models
> show #27 models
> show #28 models
> show #29 models
> show #30 models
> show #31 models
> show #!32 models
> show #33 models
> show #34 models
> show #35 models
> show #38 models
> show #39 models
> show #40 models
> show #41 models
> show #42 models
> show #43 models
> show #!44 models
> show #45 models
> show #46 models
> show #47 models
> hide #47 models
> hide #46 models
> hide #45 models
> hide #!44 models
> hide #43 models
> hide #42 models
> hide #41 models
> hide #40 models
> hide #39 models
> hide #38 models
> hide #35 models
> hide #34 models
> hide #33 models
> hide #!32 models
> hide #31 models
> hide #30 models
> hide #29 models
> hide #28 models
> hide #27 models
> hide #26 models
> hide #!13 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> show #!16 models
> show #!13 models
> hide #!13 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!24 models
> show #!25 models
> hide #!25 models
> hide #!24 models
> show #!2 models
> show #!1 models
> hide #!16 models
> show #!16 models
> show #!25 models
> select add #25
2 models selected
> view matrix models
> #25,-0.25541,-0.56476,-0.78473,231.87,0.73989,-0.63665,0.21738,257.28,-0.62236,-0.52509,0.58046,220.85
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.48596,-0.11293,-0.86665,104.37,0.53215,0.82485,0.19091,109.7,0.6933,-0.55396,0.46094,90.472
> view matrix models
> #25,0.82708,0.11158,-0.55089,0.31623,0.081587,0.94589,0.31407,131,0.55613,-0.30471,0.77322,37.878
> view matrix models
> #25,0.82444,0.11315,-0.55453,0.87432,0.082749,0.94518,0.31588,130.73,0.55987,-0.30631,0.76988,38.057
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.82444,0.11315,-0.55453,73.432,0.082749,0.94518,0.31588,93.879,0.55987,-0.30631,0.76988,133.03
> view matrix models
> #25,0.82444,0.11315,-0.55453,67.782,0.082749,0.94518,0.31588,140.35,0.55987,-0.30631,0.76988,162.17
> view matrix models
> #25,0.82444,0.11315,-0.55453,73.036,0.082749,0.94518,0.31588,179.65,0.55987,-0.30631,0.76988,150.63
> view matrix models
> #25,0.82444,0.11315,-0.55453,118.32,0.082749,0.94518,0.31588,163.64,0.55987,-0.30631,0.76988,134.94
> view matrix models
> #25,0.82444,0.11315,-0.55453,117.72,0.082749,0.94518,0.31588,160.75,0.55987,-0.30631,0.76988,146.41
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.82364,0.10196,-0.55788,119.56,0.0021836,0.98313,0.1829,181.65,0.56712,-0.15186,0.80952,122.31
> view matrix models
> #25,0.79503,0.0096224,-0.6065,139.77,0.047196,0.99586,0.077666,187.98,0.60473,-0.090371,0.79128,112.97
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.79503,0.0096224,-0.6065,134.71,0.047196,0.99586,0.077666,199.27,0.60473,-0.090371,0.79128,113.55
> fitmap #25 inMap #16
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage2_postprocess.mrc
using 65799 points
correlation = 0.9339, correlation about mean = 0.1031, overlap = 7611
steps = 84, shift = 13.5, angle = 15.7 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage2_postprocess.mrc (#16) coordinates:
Matrix rotation and translation
-0.62663805 0.62168576 0.46992723 287.56800331
-0.68561197 -0.72646035 0.04681471 442.22538085
0.37048753 -0.29285185 0.88146288 198.63658823
Axis -0.25079502 0.07342195 -0.96525182
Axis point 210.77802438 182.28177259 0.00000000
Rotation angle (degrees) 137.37636026
Shift along axis -231.38590162
> select subtract #25
Nothing selected
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> show #!37 models
> select add #37
2 models selected
> view matrix models
> #37,0.96381,0.24767,-0.098598,239.78,-0.077897,0.61539,0.78437,-105.76,0.25494,-0.7483,0.61241,152.57
> view matrix models
> #37,0.96381,0.24767,-0.098598,206.99,-0.077897,0.61539,0.78437,-72.23,0.25494,-0.7483,0.61241,245.22
> ui mousemode right "rotate selected models"
> view matrix models
> #37,0.62202,0.64809,0.43939,134.33,-0.75268,0.64956,0.10744,79.983,-0.21578,-0.39756,0.89185,223.61
> view matrix models
> #37,0.40997,0.77171,0.4862,138.04,-0.81333,0.55057,-0.18806,133.56,-0.41281,-0.31834,0.85337,240.99
> view matrix models
> #37,-0.84937,0.16887,-0.50006,469.05,-0.46516,-0.6872,0.55802,153.96,-0.24941,0.70657,0.66223,122.6
> view matrix models
> #37,-0.73326,-0.67357,0.092966,486.56,0.66339,-0.73867,-0.11949,112.33,0.14915,-0.025941,0.98847,126.49
> view matrix models
> #37,-0.52084,-0.69936,-0.48951,534.35,0.74653,-0.65127,0.13615,62.304,-0.41402,-0.29452,0.8613,237.35
> view matrix models
> #37,-0.27139,-0.88159,-0.3862,515.69,0.9512,-0.3069,0.032134,10.266,-0.14685,-0.35863,0.92186,207.61
> view matrix models
> #37,-0.34905,-0.82794,-0.43895,524.3,0.93677,-0.29585,-0.18689,36.434,0.024876,-0.47643,0.87886,207.32
> ui mousemode right "translate selected models"
> view matrix models
> #37,-0.34905,-0.82794,-0.43895,470.27,0.93677,-0.29585,-0.18689,114.81,0.024876,-0.47643,0.87886,182.01
> view matrix models
> #37,-0.34905,-0.82794,-0.43895,423.27,0.93677,-0.29585,-0.18689,129.66,0.024876,-0.47643,0.87886,211.07
> view matrix models
> #37,-0.34905,-0.82794,-0.43895,433.73,0.93677,-0.29585,-0.18689,115.37,0.024876,-0.47643,0.87886,224.56
> view matrix models
> #37,-0.34905,-0.82794,-0.43895,431.04,0.93677,-0.29585,-0.18689,123.32,0.024876,-0.47643,0.87886,227.92
> ui mousemode right "rotate selected models"
> view matrix models
> #37,-0.56839,-0.71821,-0.40137,438.32,0.81856,-0.4444,-0.36398,175.35,0.083042,-0.53543,0.84049,232.92
> view matrix models
> #37,-0.63257,-0.6482,-0.4239,439.88,0.77066,-0.47237,-0.42772,191.64,0.077011,-0.59725,0.79835,245.96
> view matrix models
> #37,-0.6202,-0.62664,-0.47188,441.57,0.77532,-0.39822,-0.4902,189.63,0.11926,-0.66988,0.73283,257.59
> ui mousemode right "translate selected models"
> view matrix models
> #37,-0.6202,-0.62664,-0.47188,441.71,0.77532,-0.39822,-0.4902,189.51,0.11926,-0.66988,0.73283,261.88
> fitmap #37 inMap #16
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage2_postprocess.mrc
using 93502 points
correlation = 0.9191, correlation about mean = 0.165, overlap = 9336
steps = 64, shift = 12.5, angle = 7.56 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage2_postprocess.mrc (#16) coordinates:
Matrix rotation and translation
0.90668337 0.31937657 -0.27554284 76.88435031
-0.20060685 0.90112046 0.38436805 189.88270228
0.37105544 -0.29322434 0.88110007 198.61642198
Axis -0.63251755 -0.60358523 -0.48539305
Axis point 0.00000000 255.83888741 -20.46397276
Rotation angle (degrees) 32.38673476
Shift along axis -259.64812684
> fitmap #37 inMap #16
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage2_postprocess.mrc
using 93502 points
correlation = 0.9191, correlation about mean = 0.1652, overlap = 9336
steps = 28, shift = 0.0546, angle = 0.0139 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage2_postprocess.mrc (#16) coordinates:
Matrix rotation and translation
0.90661837 0.31937719 -0.27575590 76.93207441
-0.20050948 0.90111427 0.38443337 189.84318091
0.37126683 -0.29324268 0.88100491 198.55717456
Axis -0.63244084 -0.60383366 -0.48518399
Axis point 0.00000000 255.75993017 -20.24171337
Rotation angle (degrees) 32.39563074
Shift along axis -259.62544933
> fitmap #37 inMap #16
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage2_postprocess.mrc
using 93502 points
correlation = 0.9191, correlation about mean = 0.1652, overlap = 9336
steps = 36, shift = 0.00363, angle = 0.0146 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage2_postprocess.mrc (#16) coordinates:
Matrix rotation and translation
0.90655889 0.31935421 -0.27597798 76.96690804
-0.20038467 0.90111320 0.38450093 189.82105564
0.37147940 -0.29327098 0.88090588 198.55093863
Axis -0.63238191 -0.60409753 -0.48493227
Axis point 0.00000000 255.83552652 -19.98037704
Rotation angle (degrees) 32.40416229
Shift along axis -259.62666700
> fitmap #25 inMap #16
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage2_postprocess.mrc
using 65799 points
correlation = 0.9339, correlation about mean = 0.1028, overlap = 7611
steps = 28, shift = 0.05, angle = 0.00498 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage2_postprocess.mrc (#16) coordinates:
Matrix rotation and translation
-0.62657486 0.62172151 0.46996420 287.57614633
-0.68564315 -0.72642717 0.04687301 442.22267746
0.37053671 -0.29285828 0.88144007 198.67795716
Axis -0.25082801 0.07340860 -0.96524426
Axis point 210.78095647 182.27933421 0.00000000
Rotation angle (degrees) 137.37324782
Shift along axis -231.44196227
> select subtract #37
Nothing selected
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!16 models
> hide #!37 models
> show #!24 models
> select add #24
2 models selected
> select add #26
9810 atoms, 10032 bonds, 1233 residues, 3 models selected
> select add #27
17311 atoms, 17651 bonds, 2186 residues, 4 models selected
> select add #28
18768 atoms, 19134 bonds, 2367 residues, 5 models selected
> select add #29
20225 atoms, 20617 bonds, 2548 residues, 6 models selected
> select add #30
27439 atoms, 27990 bonds, 3453 residues, 7 models selected
> select add #31
28901 atoms, 29471 bonds, 3632 residues, 8 models selected
> select add #32
35574 atoms, 36257 bonds, 1 pseudobond, 4485 residues, 10 models selected
> select add #33
36994 atoms, 37698 bonds, 1 pseudobond, 4662 residues, 11 models selected
> select add #34
39361 atoms, 40096 bonds, 1 pseudobond, 4960 residues, 12 models selected
> select add #35
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 13 models selected
> view matrix models
> #24,-0.30897,0.50832,-0.80384,318.7,-0.9397,-0.29345,0.17562,584.87,-0.14662,0.80963,0.56833,11.434,#26,-0.24197,-0.17446,-0.95447,210.79,-0.81888,-0.49094,0.29734,398.75,-0.52046,0.85354,-0.024072,333.9,#27,0.77926,0.62163,0.079596,184.52,-0.2235,0.39431,-0.89139,402.07,-0.5855,0.67683,0.4462,288.47,#28,-0.96825,0.1898,-0.16272,238.1,0.17778,0.065136,-0.98191,438.26,-0.17577,-0.97966,-0.096811,256.64,#29,-0.1774,0.97716,0.11701,165.92,0.97638,0.18965,-0.10349,337.75,-0.12332,0.095884,-0.98772,259.8,#30,0.83619,-0.48061,0.2642,158.92,-0.015814,0.46039,0.88758,397.6,-0.54822,-0.74636,0.37737,263.05,#31,-0.84347,0.04321,-0.53544,21.318,0.10453,-0.96451,-0.24249,724.13,-0.52691,-0.2605,0.80901,379.14,#32,0.67253,0.51859,0.52799,185.18,-0.73996,0.48346,0.46767,337.43,-0.012731,-0.70521,0.70888,354.27,#33,-0.97686,0.1891,-0.099891,194.83,0.11777,0.86551,0.48685,335.75,0.17852,0.46382,-0.86776,297.15,#34,-0.79381,0.41854,0.44123,222.27,-0.36693,0.24897,-0.89631,363.97,-0.485,-0.87341,-0.044059,279.95,#35,0.1609,0.64572,0.74643,196.17,0.71148,-0.60004,0.36572,336.26,0.68404,0.47223,-0.55596,297.22
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.4842,0.37787,-0.78915,381,-0.74227,-0.65492,0.14183,619.32,-0.46324,0.65444,0.59759,107.42,#26,-0.36722,-0.33228,-0.86876,214.33,-0.51893,-0.70195,0.48783,362.67,-0.77192,0.62996,0.085343,345.39,#27,0.75655,0.63932,-0.13745,192.63,-0.17442,-0.0052913,-0.98466,386.9,-0.63024,0.76892,0.10751,304.07,#28,-0.89592,0.26876,-0.35369,254.64,0.43318,0.35215,-0.82967,419.2,-0.098427,-0.89653,-0.43192,286.59,#29,0.036352,0.98585,0.16363,163.31,0.97363,-0.071837,0.21651,341.9,0.2252,0.15144,-0.96247,254.89,#30,0.85213,-0.32105,0.41327,168.55,-0.0095694,0.78002,0.62569,397.05,-0.52324,-0.53712,0.66161,278.81,#31,-0.76405,-0.13741,-0.63035,93.041,0.4587,-0.80277,-0.381,686.07,-0.45367,-0.58025,0.67639,501.96,#32,0.50523,0.656,0.56071,175.28,-0.81877,0.56968,0.071263,305.21,-0.27268,-0.4951,0.82494,343.25,#33,-0.94202,0.32926,0.064674,188.44,0.25942,0.59238,0.76275,321.04,0.21283,0.7353,-0.64345,289.07,#34,-0.81549,0.52219,0.24959,222.26,0.0024164,0.4343,-0.90076,346.75,-0.57877,-0.73396,-0.35543,282.65,#35,0.25431,0.47312,0.84349,189.84,0.38259,-0.85024,0.36155,321.2,0.88823,0.23077,-0.39724,289.31
> view matrix models
> #24,-0.46887,0.3477,-0.81195,388.56,-0.66386,-0.74509,0.064284,636.62,-0.58263,0.56916,0.58017,155.23,#26,-0.33835,-0.36111,-0.86898,211.08,-0.40032,-0.78048,0.4802,350.66,-0.85162,0.51035,0.11951,347.59,#27,0.78053,0.60765,-0.14676,191.2,-0.091565,-0.1211,-0.98841,380.74,-0.61838,0.78492,-0.038882,309.32,#28,-0.88896,0.30663,-0.34019,254.02,0.45244,0.47268,-0.75623,414.51,-0.071081,-0.82617,-0.55892,299.06,#29,0.032218,0.97853,0.20356,163.65,0.93146,-0.10325,0.3489,343.48,0.36242,0.17836,-0.91479,253.13,#30,0.87255,-0.29503,0.38937,168.2,0.055422,0.85168,0.52113,394.63,-0.48537,-0.43313,0.75948,284.82,#31,-0.7427,-0.11795,-0.65916,85.218,0.5266,-0.71093,-0.46613,649.92,-0.41364,-0.6933,0.59011,543.61,#32,0.51164,0.67842,0.52723,171.85,-0.77731,0.62694,-0.052406,294.52,-0.36609,-0.38301,0.84811,335.79,#33,-0.94852,0.30228,0.094585,187.27,0.23684,0.47863,0.84547,317.72,0.21029,0.82434,-0.52558,284.96,#34,-0.79137,0.5537,0.25913,221.45,0.093224,0.52822,-0.84398,343.71,-0.60418,-0.64374,-0.46964,283.59,#35,0.22012,0.45901,0.86073,188.67,0.25012,-0.87943,0.40502,317.83,0.94286,0.12613,-0.30839,285.28
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.46887,0.3477,-0.81195,385.56,-0.66386,-0.74509,0.064284,827.18,-0.58263,0.56916,0.58017,90.938,#26,-0.33835,-0.36111,-0.86898,208.09,-0.40032,-0.78048,0.4802,541.22,-0.85162,0.51035,0.11951,283.31,#27,0.78053,0.60765,-0.14676,188.2,-0.091565,-0.1211,-0.98841,571.3,-0.61838,0.78492,-0.038882,245.03,#28,-0.88896,0.30663,-0.34019,251.03,0.45244,0.47268,-0.75623,605.07,-0.071081,-0.82617,-0.55892,234.77,#29,0.032218,0.97853,0.20356,160.66,0.93146,-0.10325,0.3489,534.04,0.36242,0.17836,-0.91479,188.84,#30,0.87255,-0.29503,0.38937,165.21,0.055422,0.85168,0.52113,585.18,-0.48537,-0.43313,0.75948,220.53,#31,-0.7427,-0.11795,-0.65916,82.221,0.5266,-0.71093,-0.46613,840.47,-0.41364,-0.6933,0.59011,479.33,#32,0.51164,0.67842,0.52723,168.85,-0.77731,0.62694,-0.052406,485.08,-0.36609,-0.38301,0.84811,271.5,#33,-0.94852,0.30228,0.094585,184.27,0.23684,0.47863,0.84547,508.28,0.21029,0.82434,-0.52558,220.68,#34,-0.79137,0.5537,0.25913,218.46,0.093224,0.52822,-0.84398,534.27,-0.60418,-0.64374,-0.46964,219.3,#35,0.22012,0.45901,0.86073,185.67,0.25012,-0.87943,0.40502,508.38,0.94286,0.12613,-0.30839,220.99
> view matrix models
> #24,-0.46887,0.3477,-0.81195,366.71,-0.66386,-0.74509,0.064284,819.82,-0.58263,0.56916,0.58017,50.664,#26,-0.33835,-0.36111,-0.86898,189.23,-0.40032,-0.78048,0.4802,533.86,-0.85162,0.51035,0.11951,243.03,#27,0.78053,0.60765,-0.14676,169.35,-0.091565,-0.1211,-0.98841,563.94,-0.61838,0.78492,-0.038882,204.76,#28,-0.88896,0.30663,-0.34019,232.17,0.45244,0.47268,-0.75623,597.71,-0.071081,-0.82617,-0.55892,194.49,#29,0.032218,0.97853,0.20356,141.8,0.93146,-0.10325,0.3489,526.68,0.36242,0.17836,-0.91479,148.57,#30,0.87255,-0.29503,0.38937,146.35,0.055422,0.85168,0.52113,577.83,-0.48537,-0.43313,0.75948,180.26,#31,-0.7427,-0.11795,-0.65916,63.368,0.5266,-0.71093,-0.46613,833.12,-0.41364,-0.6933,0.59011,439.05,#32,0.51164,0.67842,0.52723,150,-0.77731,0.62694,-0.052406,477.72,-0.36609,-0.38301,0.84811,231.23,#33,-0.94852,0.30228,0.094585,165.42,0.23684,0.47863,0.84547,500.92,0.21029,0.82434,-0.52558,180.4,#34,-0.79137,0.5537,0.25913,199.6,0.093224,0.52822,-0.84398,526.91,-0.60418,-0.64374,-0.46964,179.03,#35,0.22012,0.45901,0.86073,166.82,0.25012,-0.87943,0.40502,501.03,0.94286,0.12613,-0.30839,180.72
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.08969,-0.67215,-0.73497,465.99,0.93771,-0.30568,0.16512,347.67,-0.33564,-0.67438,0.65769,224.12,#26,0.30196,-0.93294,-0.19607,101.8,0.91571,0.22665,0.33182,458.07,-0.26513,-0.27974,0.92274,150.27,#27,0.73715,-0.40993,-0.53718,138.14,-0.10941,-0.85689,0.50376,483.94,-0.66681,-0.31257,-0.6765,178.12,#28,-0.074188,0.99192,-0.10289,188.69,0.4751,0.12587,0.87088,434.65,0.8768,0.015726,-0.4806,163.66,#29,0.21673,0.20846,0.95371,150.39,-0.60605,-0.73715,0.29885,552.07,0.76533,-0.64277,-0.033426,155.48,#30,0.7492,0.64523,-0.14958,154.49,-0.31151,0.14396,-0.93927,509.54,-0.58452,0.7503,0.30886,198.09,#31,0.28233,0.11207,-0.95275,56.035,0.56108,0.78628,0.25876,306.28,0.77812,-0.60762,0.15911,494.78,#32,0.085455,0.88634,-0.45508,66.038,0.1793,-0.46297,-0.86805,513.69,-0.98008,-0.0074183,-0.19849,128.87,#33,-0.42186,-0.25575,0.86985,122.65,0.42269,-0.90423,-0.060858,526.03,0.8021,0.342,0.48956,127.43,#34,0.18444,0.98246,0.027308,150.87,0.87966,-0.1774,0.44128,493.66,0.43839,-0.057368,-0.89695,126.23,#35,-0.49597,-0.36073,0.78987,123.03,-0.8346,-0.053083,-0.5483,524.84,0.23972,-0.93116,-0.27474,126.72
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.08969,-0.67215,-0.73497,602.78,0.93771,-0.30568,0.16512,196.94,-0.33564,-0.67438,0.65769,286.89,#26,0.30196,-0.93294,-0.19607,238.59,0.91571,0.22665,0.33182,307.33,-0.26513,-0.27974,0.92274,213.04,#27,0.73715,-0.40993,-0.53718,274.93,-0.10941,-0.85689,0.50376,333.2,-0.66681,-0.31257,-0.6765,240.88,#28,-0.074188,0.99192,-0.10289,325.48,0.4751,0.12587,0.87088,283.92,0.8768,0.015726,-0.4806,226.42,#29,0.21673,0.20846,0.95371,287.17,-0.60605,-0.73715,0.29885,401.34,0.76533,-0.64277,-0.033426,218.25,#30,0.7492,0.64523,-0.14958,291.28,-0.31151,0.14396,-0.93927,358.81,-0.58452,0.7503,0.30886,260.86,#31,0.28233,0.11207,-0.95275,192.82,0.56108,0.78628,0.25876,155.55,0.77812,-0.60762,0.15911,557.55,#32,0.085455,0.88634,-0.45508,202.82,0.1793,-0.46297,-0.86805,362.95,-0.98008,-0.0074183,-0.19849,191.64,#33,-0.42186,-0.25575,0.86985,259.44,0.42269,-0.90423,-0.060858,375.29,0.8021,0.342,0.48956,190.2,#34,0.18444,0.98246,0.027308,287.66,0.87966,-0.1774,0.44128,342.92,0.43839,-0.057368,-0.89695,188.99,#35,-0.49597,-0.36073,0.78987,259.82,-0.8346,-0.053083,-0.5483,374.1,0.23972,-0.93116,-0.27474,189.49
> view matrix models
> #24,-0.08969,-0.67215,-0.73497,486.55,0.93771,-0.30568,0.16512,162.52,-0.33564,-0.67438,0.65769,309.88,#26,0.30196,-0.93294,-0.19607,122.36,0.91571,0.22665,0.33182,272.91,-0.26513,-0.27974,0.92274,236.03,#27,0.73715,-0.40993,-0.53718,158.7,-0.10941,-0.85689,0.50376,298.78,-0.66681,-0.31257,-0.6765,263.87,#28,-0.074188,0.99192,-0.10289,209.24,0.4751,0.12587,0.87088,249.5,0.8768,0.015726,-0.4806,249.42,#29,0.21673,0.20846,0.95371,170.94,-0.60605,-0.73715,0.29885,366.92,0.76533,-0.64277,-0.033426,241.24,#30,0.7492,0.64523,-0.14958,175.05,-0.31151,0.14396,-0.93927,324.38,-0.58452,0.7503,0.30886,283.85,#31,0.28233,0.11207,-0.95275,76.588,0.56108,0.78628,0.25876,121.13,0.77812,-0.60762,0.15911,580.54,#32,0.085455,0.88634,-0.45508,86.592,0.1793,-0.46297,-0.86805,328.53,-0.98008,-0.0074183,-0.19849,214.63,#33,-0.42186,-0.25575,0.86985,143.2,0.42269,-0.90423,-0.060858,340.87,0.8021,0.342,0.48956,213.19,#34,0.18444,0.98246,0.027308,171.42,0.87966,-0.1774,0.44128,308.5,0.43839,-0.057368,-0.89695,211.98,#35,-0.49597,-0.36073,0.78987,143.58,-0.8346,-0.053083,-0.5483,339.68,0.23972,-0.93116,-0.27474,212.48
> view matrix models
> #24,-0.08969,-0.67215,-0.73497,487.15,0.93771,-0.30568,0.16512,161.83,-0.33564,-0.67438,0.65769,325.95,#26,0.30196,-0.93294,-0.19607,122.96,0.91571,0.22665,0.33182,272.22,-0.26513,-0.27974,0.92274,252.1,#27,0.73715,-0.40993,-0.53718,159.3,-0.10941,-0.85689,0.50376,298.09,-0.66681,-0.31257,-0.6765,279.95,#28,-0.074188,0.99192,-0.10289,209.85,0.4751,0.12587,0.87088,248.8,0.8768,0.015726,-0.4806,265.49,#29,0.21673,0.20846,0.95371,171.55,-0.60605,-0.73715,0.29885,366.22,0.76533,-0.64277,-0.033426,257.32,#30,0.7492,0.64523,-0.14958,175.65,-0.31151,0.14396,-0.93927,323.69,-0.58452,0.7503,0.30886,299.92,#31,0.28233,0.11207,-0.95275,77.194,0.56108,0.78628,0.25876,120.44,0.77812,-0.60762,0.15911,596.61,#32,0.085455,0.88634,-0.45508,87.198,0.1793,-0.46297,-0.86805,327.84,-0.98008,-0.0074183,-0.19849,230.7,#33,-0.42186,-0.25575,0.86985,143.81,0.42269,-0.90423,-0.060858,340.18,0.8021,0.342,0.48956,229.26,#34,0.18444,0.98246,0.027308,172.03,0.87966,-0.1774,0.44128,307.81,0.43839,-0.057368,-0.89695,228.06,#35,-0.49597,-0.36073,0.78987,144.19,-0.8346,-0.053083,-0.5483,338.99,0.23972,-0.93116,-0.27474,228.55
> view matrix models
> #24,-0.08969,-0.67215,-0.73497,503.57,0.93771,-0.30568,0.16512,159.1,-0.33564,-0.67438,0.65769,333.22,#26,0.30196,-0.93294,-0.19607,139.38,0.91571,0.22665,0.33182,269.5,-0.26513,-0.27974,0.92274,259.37,#27,0.73715,-0.40993,-0.53718,175.72,-0.10941,-0.85689,0.50376,295.37,-0.66681,-0.31257,-0.6765,287.22,#28,-0.074188,0.99192,-0.10289,226.26,0.4751,0.12587,0.87088,246.08,0.8768,0.015726,-0.4806,272.76,#29,0.21673,0.20846,0.95371,187.96,-0.60605,-0.73715,0.29885,363.5,0.76533,-0.64277,-0.033426,264.59,#30,0.7492,0.64523,-0.14958,192.07,-0.31151,0.14396,-0.93927,320.97,-0.58452,0.7503,0.30886,307.19,#31,0.28233,0.11207,-0.95275,93.609,0.56108,0.78628,0.25876,117.71,0.77812,-0.60762,0.15911,603.88,#32,0.085455,0.88634,-0.45508,103.61,0.1793,-0.46297,-0.86805,325.11,-0.98008,-0.0074183,-0.19849,237.97,#33,-0.42186,-0.25575,0.86985,160.22,0.42269,-0.90423,-0.060858,337.46,0.8021,0.342,0.48956,236.53,#34,0.18444,0.98246,0.027308,188.44,0.87966,-0.1774,0.44128,305.09,0.43839,-0.057368,-0.89695,235.33,#35,-0.49597,-0.36073,0.78987,160.61,-0.8346,-0.053083,-0.5483,336.27,0.23972,-0.93116,-0.27474,235.82
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.074452,-0.67754,-0.73171,500.46,0.92674,-0.31796,0.20013,156.27,-0.36825,-0.6632,0.65158,339.74,#26,0.31683,-0.92927,-0.18996,138.09,0.90077,0.23207,0.36709,270,-0.29704,-0.28742,0.91058,262.11,#27,0.7348,-0.42421,-0.52926,174.87,-0.14482,-0.86042,0.48857,296.23,-0.66265,-0.28235,-0.69367,289.03,#28,-0.065762,0.99387,-0.088849,224.59,0.50665,0.10997,0.85511,245.64,0.85964,0.011219,-0.51077,276.3,#29,0.20723,0.19586,0.95849,188.22,-0.58239,-0.76252,0.28173,363.32,0.78605,-0.6166,-0.043953,264.03,#30,0.74357,0.64802,-0.16483,191.65,-0.34409,0.15947,-0.9253,322.24,-0.57333,0.74474,0.34156,308.09,#31,0.29206,0.1246,-0.94825,90.06,0.58323,0.76258,0.27984,131.14,0.75798,-0.63478,0.15005,611.73,#32,0.087741,0.87859,-0.46945,103.24,0.14346,-0.4775,-0.86684,325.42,-0.98576,0.0087077,-0.16794,238.78,#33,-0.4143,-0.27038,0.86905,160.04,0.4574,-0.88737,-0.058026,336.77,0.78686,0.37346,0.49131,236.91,#34,0.1992,0.97937,0.033975,187.72,0.8913,-0.19548,0.40912,303.91,0.40732,-0.051215,-0.91185,236.83,#35,-0.50949,-0.36218,0.78054,160.4,-0.81741,-0.079678,-0.57053,335.55,0.26883,-0.9287,-0.25546,236.23
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.074452,-0.67754,-0.73171,496.69,0.92674,-0.31796,0.20013,159.15,-0.36825,-0.6632,0.65158,339.83,#26,0.31683,-0.92927,-0.18996,134.32,0.90077,0.23207,0.36709,272.88,-0.29704,-0.28742,0.91058,262.2,#27,0.7348,-0.42421,-0.52926,171.1,-0.14482,-0.86042,0.48857,299.11,-0.66265,-0.28235,-0.69367,289.12,#28,-0.065762,0.99387,-0.088849,220.82,0.50665,0.10997,0.85511,248.52,0.85964,0.011219,-0.51077,276.39,#29,0.20723,0.19586,0.95849,184.45,-0.58239,-0.76252,0.28173,366.2,0.78605,-0.6166,-0.043953,264.12,#30,0.74357,0.64802,-0.16483,187.88,-0.34409,0.15947,-0.9253,325.12,-0.57333,0.74474,0.34156,308.18,#31,0.29206,0.1246,-0.94825,86.286,0.58323,0.76258,0.27984,134.02,0.75798,-0.63478,0.15005,611.82,#32,0.087741,0.87859,-0.46945,99.461,0.14346,-0.4775,-0.86684,328.3,-0.98576,0.0087077,-0.16794,238.87,#33,-0.4143,-0.27038,0.86905,156.27,0.4574,-0.88737,-0.058026,339.65,0.78686,0.37346,0.49131,237,#34,0.1992,0.97937,0.033975,183.95,0.8913,-0.19548,0.40912,306.79,0.40732,-0.051215,-0.91185,236.92,#35,-0.50949,-0.36218,0.78054,156.63,-0.81741,-0.079678,-0.57053,338.43,0.26883,-0.9287,-0.25546,236.32
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.015488,-0.70572,-0.70832,476.73,0.75907,-0.45281,0.46774,164.57,-0.65083,-0.54491,0.52867,407.6,#26,0.40246,-0.90261,-0.15273,127.04,0.72182,0.21028,0.65936,279.65,-0.56302,-0.37561,0.73615,286.17,#27,0.71676,-0.50588,-0.47994,166.21,-0.41958,-0.8626,0.28262,309.71,-0.55697,-0.0011933,-0.83053,304.25,#28,-0.015624,0.99986,-0.0059027,210.77,0.76268,0.015735,0.64658,253.39,0.64659,0.0056,-0.76282,310.14,#29,0.1504,0.12048,0.98126,185.98,-0.31122,-0.93631,0.16267,363.48,0.93836,-0.32985,-0.10332,259.28,#30,0.70623,0.66103,-0.25352,185.45,-0.57883,0.33292,-0.74439,338.85,-0.40766,0.67246,0.61775,314.36,#31,0.34786,0.19747,-0.91651,66.042,0.76875,0.49951,0.3994,267.21,0.53667,-0.8435,0.021953,660.26,#32,0.10045,0.82814,-0.55145,97.698,-0.19398,-0.52731,-0.82723,327.41,-0.97585,0.19006,0.10767,245.08,#33,-0.36735,-0.35487,0.85972,155.34,0.7247,-0.6886,0.025417,332.26,0.58298,0.63237,0.51013,241.37,#34,0.28503,0.95575,0.072764,179.7,0.95303,-0.2907,0.08502,298.77,0.10241,0.045112,-0.99372,252.8,#35,-0.58615,-0.36895,0.72132,155.58,-0.63484,-0.34401,-0.69184,330.86,0.50339,-0.86344,-0.032581,241.15
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.015488,-0.70572,-0.70832,485.32,0.75907,-0.45281,0.46774,145.51,-0.65083,-0.54491,0.52867,389.02,#26,0.40246,-0.90261,-0.15273,135.62,0.72182,0.21028,0.65936,260.59,-0.56302,-0.37561,0.73615,267.59,#27,0.71676,-0.50588,-0.47994,174.8,-0.41958,-0.8626,0.28262,290.65,-0.55697,-0.0011933,-0.83053,285.67,#28,-0.015624,0.99986,-0.0059027,219.36,0.76268,0.015735,0.64658,234.33,0.64659,0.0056,-0.76282,291.56,#29,0.1504,0.12048,0.98126,194.57,-0.31122,-0.93631,0.16267,344.42,0.93836,-0.32985,-0.10332,240.7,#30,0.70623,0.66103,-0.25352,194.04,-0.57883,0.33292,-0.74439,319.79,-0.40766,0.67246,0.61775,295.78,#31,0.34786,0.19747,-0.91651,74.629,0.76875,0.49951,0.3994,248.15,0.53667,-0.8435,0.021953,641.68,#32,0.10045,0.82814,-0.55145,106.29,-0.19398,-0.52731,-0.82723,308.35,-0.97585,0.19006,0.10767,226.49,#33,-0.36735,-0.35487,0.85972,163.92,0.7247,-0.6886,0.025417,313.19,0.58298,0.63237,0.51013,222.79,#34,0.28503,0.95575,0.072764,188.29,0.95303,-0.2907,0.08502,279.71,0.10241,0.045112,-0.99372,234.22,#35,-0.58615,-0.36895,0.72132,164.16,-0.63484,-0.34401,-0.69184,311.8,0.50339,-0.86344,-0.032581,222.56
> view matrix models
> #24,0.015488,-0.70572,-0.70832,486.53,0.75907,-0.45281,0.46774,148.75,-0.65083,-0.54491,0.52867,389.15,#26,0.40246,-0.90261,-0.15273,136.84,0.72182,0.21028,0.65936,263.83,-0.56302,-0.37561,0.73615,267.72,#27,0.71676,-0.50588,-0.47994,176.01,-0.41958,-0.8626,0.28262,293.89,-0.55697,-0.0011933,-0.83053,285.8,#28,-0.015624,0.99986,-0.0059027,220.58,0.76268,0.015735,0.64658,237.57,0.64659,0.0056,-0.76282,291.69,#29,0.1504,0.12048,0.98126,195.78,-0.31122,-0.93631,0.16267,347.66,0.93836,-0.32985,-0.10332,240.83,#30,0.70623,0.66103,-0.25352,195.25,-0.57883,0.33292,-0.74439,323.03,-0.40766,0.67246,0.61775,295.91,#31,0.34786,0.19747,-0.91651,75.844,0.76875,0.49951,0.3994,251.4,0.53667,-0.8435,0.021953,641.81,#32,0.10045,0.82814,-0.55145,107.5,-0.19398,-0.52731,-0.82723,311.59,-0.97585,0.19006,0.10767,226.63,#33,-0.36735,-0.35487,0.85972,165.14,0.7247,-0.6886,0.025417,316.44,0.58298,0.63237,0.51013,222.93,#34,0.28503,0.95575,0.072764,189.5,0.95303,-0.2907,0.08502,282.95,0.10241,0.045112,-0.99372,234.35,#35,-0.58615,-0.36895,0.72132,165.38,-0.63484,-0.34401,-0.69184,315.04,0.50339,-0.86344,-0.032581,222.7
> view matrix models
> #24,0.015488,-0.70572,-0.70832,487.92,0.75907,-0.45281,0.46774,150.64,-0.65083,-0.54491,0.52867,386.46,#26,0.40246,-0.90261,-0.15273,138.23,0.72182,0.21028,0.65936,265.72,-0.56302,-0.37561,0.73615,265.03,#27,0.71676,-0.50588,-0.47994,177.4,-0.41958,-0.8626,0.28262,295.78,-0.55697,-0.0011933,-0.83053,283.11,#28,-0.015624,0.99986,-0.0059027,221.96,0.76268,0.015735,0.64658,239.46,0.64659,0.0056,-0.76282,289.01,#29,0.1504,0.12048,0.98126,197.17,-0.31122,-0.93631,0.16267,349.55,0.93836,-0.32985,-0.10332,238.14,#30,0.70623,0.66103,-0.25352,196.64,-0.57883,0.33292,-0.74439,324.92,-0.40766,0.67246,0.61775,293.22,#31,0.34786,0.19747,-0.91651,77.232,0.76875,0.49951,0.3994,253.28,0.53667,-0.8435,0.021953,639.12,#32,0.10045,0.82814,-0.55145,108.89,-0.19398,-0.52731,-0.82723,313.48,-0.97585,0.19006,0.10767,223.94,#33,-0.36735,-0.35487,0.85972,166.53,0.7247,-0.6886,0.025417,318.32,0.58298,0.63237,0.51013,220.24,#34,0.28503,0.95575,0.072764,190.89,0.95303,-0.2907,0.08502,284.84,0.10241,0.045112,-0.99372,231.66,#35,-0.58615,-0.36895,0.72132,166.77,-0.63484,-0.34401,-0.69184,316.93,0.50339,-0.86344,-0.032581,220.01
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.35722,-0.60979,-0.7075,553.12,0.5609,-0.74574,0.35954,277.56,-0.74685,-0.2684,0.60842,335.71,#26,0.029983,-0.97595,-0.21593,168.65,0.65499,-0.144,0.74179,258.66,-0.75504,-0.16368,0.63492,289.88,#27,0.69421,-0.18747,-0.69493,198.57,-0.31886,-0.94568,-0.063411,301.83,-0.64529,0.2656,-0.71628,292.38,#28,-0.13975,0.92175,-0.36172,259.32,0.85575,0.29621,0.4242,263.21,0.49815,-0.25027,-0.83019,295.78,#29,0.41968,0.35385,0.83586,190.78,-0.030652,-0.91483,0.40267,347.05,0.90715,-0.19462,-0.37309,235.83,#30,0.76485,0.63182,0.12572,208.82,-0.43562,0.65104,-0.6216,336.71,-0.47459,0.42067,0.77318,292.47,#31,0.17388,-0.14086,-0.97464,187.58,0.93786,0.32552,0.12027,316.53,0.30032,-0.93498,0.18871,664.19,#32,-0.029887,0.97495,-0.22043,118.08,-0.37835,-0.21515,-0.90031,285.42,-0.92518,0.056491,0.3753,250.42,#33,-0.46517,0.016482,0.88507,169.16,0.70706,-0.59465,0.38269,305.23,0.53261,0.80381,0.26496,231.52,#34,-0.027194,0.98833,-0.14988,204.82,0.99144,0.0075153,-0.13033,283.51,-0.12769,-0.15214,-0.98008,241.64,#35,-0.2398,-0.39418,0.8872,169.8,-0.63924,-0.62369,-0.44988,303.95,0.73066,-0.67501,-0.10242,231.47
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.35722,-0.60979,-0.7075,552.21,0.5609,-0.74574,0.35954,297.3,-0.74685,-0.2684,0.60842,331.38,#26,0.029983,-0.97595,-0.21593,167.74,0.65499,-0.144,0.74179,278.39,-0.75504,-0.16368,0.63492,285.55,#27,0.69421,-0.18747,-0.69493,197.66,-0.31886,-0.94568,-0.063411,321.56,-0.64529,0.2656,-0.71628,288.05,#28,-0.13975,0.92175,-0.36172,258.41,0.85575,0.29621,0.4242,282.95,0.49815,-0.25027,-0.83019,291.45,#29,0.41968,0.35385,0.83586,189.87,-0.030652,-0.91483,0.40267,366.79,0.90715,-0.19462,-0.37309,231.5,#30,0.76485,0.63182,0.12572,207.91,-0.43562,0.65104,-0.6216,356.44,-0.47459,0.42067,0.77318,288.14,#31,0.17388,-0.14086,-0.97464,186.67,0.93786,0.32552,0.12027,336.27,0.30032,-0.93498,0.18871,659.86,#32,-0.029887,0.97495,-0.22043,117.17,-0.37835,-0.21515,-0.90031,305.16,-0.92518,0.056491,0.3753,246.09,#33,-0.46517,0.016482,0.88507,168.25,0.70706,-0.59465,0.38269,324.97,0.53261,0.80381,0.26496,227.19,#34,-0.027194,0.98833,-0.14988,203.91,0.99144,0.0075153,-0.13033,303.25,-0.12769,-0.15214,-0.98008,237.31,#35,-0.2398,-0.39418,0.8872,168.89,-0.63924,-0.62369,-0.44988,323.68,0.73066,-0.67501,-0.10242,227.14
> view matrix models
> #24,-0.35722,-0.60979,-0.7075,543.3,0.5609,-0.74574,0.35954,277.35,-0.74685,-0.2684,0.60842,339.23,#26,0.029983,-0.97595,-0.21593,158.83,0.65499,-0.144,0.74179,258.44,-0.75504,-0.16368,0.63492,293.39,#27,0.69421,-0.18747,-0.69493,188.75,-0.31886,-0.94568,-0.063411,301.61,-0.64529,0.2656,-0.71628,295.89,#28,-0.13975,0.92175,-0.36172,249.5,0.85575,0.29621,0.4242,263,0.49815,-0.25027,-0.83019,299.29,#29,0.41968,0.35385,0.83586,180.96,-0.030652,-0.91483,0.40267,346.84,0.90715,-0.19462,-0.37309,239.34,#30,0.76485,0.63182,0.12572,199,-0.43562,0.65104,-0.6216,336.49,-0.47459,0.42067,0.77318,295.98,#31,0.17388,-0.14086,-0.97464,177.76,0.93786,0.32552,0.12027,316.32,0.30032,-0.93498,0.18871,667.7,#32,-0.029887,0.97495,-0.22043,108.26,-0.37835,-0.21515,-0.90031,285.2,-0.92518,0.056491,0.3753,253.94,#33,-0.46517,0.016482,0.88507,159.35,0.70706,-0.59465,0.38269,305.02,0.53261,0.80381,0.26496,235.04,#34,-0.027194,0.98833,-0.14988,195,0.99144,0.0075153,-0.13033,283.29,-0.12769,-0.15214,-0.98008,245.16,#35,-0.2398,-0.39418,0.8872,159.98,-0.63924,-0.62369,-0.44988,303.73,0.73066,-0.67501,-0.10242,234.98
> view matrix models
> #24,-0.35722,-0.60979,-0.7075,532.66,0.5609,-0.74574,0.35954,267.9,-0.74685,-0.2684,0.60842,340.62,#26,0.029983,-0.97595,-0.21593,148.19,0.65499,-0.144,0.74179,249,-0.75504,-0.16368,0.63492,294.79,#27,0.69421,-0.18747,-0.69493,178.11,-0.31886,-0.94568,-0.063411,292.17,-0.64529,0.2656,-0.71628,297.29,#28,-0.13975,0.92175,-0.36172,238.86,0.85575,0.29621,0.4242,253.55,0.49815,-0.25027,-0.83019,300.69,#29,0.41968,0.35385,0.83586,170.32,-0.030652,-0.91483,0.40267,337.39,0.90715,-0.19462,-0.37309,240.74,#30,0.76485,0.63182,0.12572,188.36,-0.43562,0.65104,-0.6216,327.05,-0.47459,0.42067,0.77318,297.38,#31,0.17388,-0.14086,-0.97464,167.12,0.93786,0.32552,0.12027,306.87,0.30032,-0.93498,0.18871,669.1,#32,-0.029887,0.97495,-0.22043,97.622,-0.37835,-0.21515,-0.90031,275.76,-0.92518,0.056491,0.3753,255.33,#33,-0.46517,0.016482,0.88507,148.71,0.70706,-0.59465,0.38269,295.57,0.53261,0.80381,0.26496,236.43,#34,-0.027194,0.98833,-0.14988,184.36,0.99144,0.0075153,-0.13033,273.85,-0.12769,-0.15214,-0.98008,246.55,#35,-0.2398,-0.39418,0.8872,149.34,-0.63924,-0.62369,-0.44988,294.28,0.73066,-0.67501,-0.10242,236.38
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.21904,-0.50768,-0.83323,508.98,0.63559,-0.72217,0.27293,265.5,-0.7403,-0.46981,0.48086,407.33,#26,0.15696,-0.91362,-0.37506,143.55,0.73781,-0.14397,0.65948,244.21,-0.6565,-0.38024,0.65148,279.74,#27,0.8261,-0.19677,-0.52805,170.38,-0.22856,-0.97352,0.0051966,287.4,-0.51509,0.1164,-0.8492,293.14,#28,-0.27727,0.93971,-0.20019,230.74,0.7899,0.34156,0.5093,249.89,0.54697,-0.016913,-0.83698,305.07,#29,0.22364,0.42625,0.87653,172.49,-0.1261,-0.87909,0.45967,338.66,0.96648,-0.21333,-0.14285,241.44,#30,0.86491,0.50183,-0.010004,178.84,-0.36269,0.61108,-0.70358,322.24,-0.34697,0.61217,0.71054,299.16,#31,0.066618,0.041704,-0.99691,81.986,0.9005,0.42779,0.078071,259.1,0.42972,-0.90292,-0.0090558,653.65,#32,0.17899,0.95058,-0.25369,101.12,-0.27016,-0.20045,-0.94172,274.3,-0.94603,0.2371,0.22094,233.64,#33,-0.59594,-0.1243,0.79335,154.09,0.63169,-0.68255,0.36756,297.18,0.49581,0.7202,0.48527,228.19,#34,-0.043601,0.99711,0.062218,187.8,0.99879,0.04492,-0.019959,275.16,-0.022696,0.061272,-0.99786,243.18,#35,-0.35766,-0.2181,0.90803,154.78,-0.72361,-0.54991,-0.41711,295.92,0.59031,-0.80624,0.038861,228.13
> view matrix models
> #24,-0.041943,-0.22419,-0.97364,443.77,0.57541,-0.80209,0.1599,320.02,-0.81679,-0.55353,0.16264,511.75,#26,0.2682,-0.70861,-0.65264,147.47,0.73441,-0.28804,0.61455,241.37,-0.62347,-0.64413,0.44316,274.49,#27,0.97255,-0.09542,-0.21225,162.46,-0.11804,-0.98831,-0.096544,288.41,-0.20055,0.11895,-0.97243,292.59,#28,-0.54362,0.83898,0.024231,219.79,0.75506,0.47622,0.45066,260.58,0.36656,0.26328,-0.89237,326.23,#29,-0.095298,0.58373,0.80633,174.9,-0.064762,-0.81194,0.58014,337.96,0.99334,0.0030664,0.11518,240.68,#30,0.97052,0.18598,-0.1533,163.82,-0.24024,0.69535,-0.67733,324.27,-0.019374,0.6942,0.71953,298.39,#31,-0.19786,0.28274,-0.93857,-36.055,0.91202,0.40403,-0.070551,257.36,0.35927,-0.86995,-0.3378,605.97,#32,0.51639,0.83559,-0.18743,119.2,-0.26686,-0.050959,-0.96239,263.56,-0.81371,0.54698,0.19667,215,#33,-0.80372,-0.26603,0.53222,167.52,0.55008,-0.67318,0.49421,293.86,0.22681,0.68997,0.68738,225.32,#34,-0.16354,0.90538,0.39184,196.9,0.98033,0.19362,-0.038214,277.5,-0.11047,0.37788,-0.91924,252.05,#35,-0.4356,0.13552,0.88988,168.34,-0.7519,-0.59828,-0.27694,292.72,0.49487,-0.78974,0.36251,225.58
> view matrix models
> #24,-0.27058,-0.62226,-0.73456,521.51,0.65435,-0.67854,0.33377,239.13,-0.70612,-0.39035,0.59078,359.49,#26,0.12017,-0.96605,-0.22871,141.31,0.7269,-0.071283,0.68303,246.67,-0.67614,-0.24833,0.69366,284.21,#27,0.72616,-0.25291,-0.63932,172.99,-0.28881,-0.95607,0.050177,287.6,-0.62392,0.14821,-0.7673,293.49,#28,-0.13671,0.95163,-0.27516,231.36,0.80608,0.26832,0.52749,245.5,0.5758,-0.14969,-0.80377,297.11,#29,0.34584,0.32344,0.88078,171.81,-0.14789,-0.90818,0.39158,338.81,0.92656,-0.26569,-0.26625,241.72,#30,0.7776,0.62779,0.035077,184.87,-0.42639,0.5675,-0.70437,321.66,-0.4621,0.53276,0.70897,298.07,#31,0.19495,-0.051819,-0.97944,133.82,0.89049,0.42794,0.1546,264.34,0.41113,-0.90232,0.12957,662.96,#32,0.024019,0.95609,-0.29208,95.312,-0.27828,-0.27422,-0.92052,280.17,-0.9602,0.10339,0.25947,244.31,#33,-0.47061,-0.074793,0.87916,148.61,0.67312,-0.67464,0.30293,298.94,0.57047,0.73434,0.36784,231.39,#34,0.030616,0.99638,-0.079245,182.28,0.99929,-0.032262,-0.019566,274.32,-0.022051,-0.07859,-0.99666,241.67,#35,-0.32645,-0.37003,0.86977,149.18,-0.69697,-0.52735,-0.48594,297.63,0.63849,-0.76484,-0.085747,231.24
> view matrix models
> #24,-0.24658,-0.47056,-0.84721,510.95,0.81148,-0.57817,0.084954,238.76,-0.52981,-0.66655,0.52442,389.02,#26,0.12375,-0.90419,-0.40882,147.45,0.90202,-0.069212,0.42612,238.73,-0.41358,-0.42149,0.80703,254.34,#27,0.83808,-0.15013,-0.52448,172.12,-0.032969,-0.97357,0.226,277.39,-0.54455,-0.17211,-0.82088,280.06,#28,-0.31702,0.92224,-0.2213,234.18,0.58539,0.37386,0.7194,240.79,0.7462,0.098518,-0.6584,281.75,#29,0.2258,0.46886,0.85392,171.96,-0.38914,-0.76018,0.52029,341.41,0.89307,-0.44978,0.010809,245.34,#30,0.88266,0.46953,0.021185,178.88,-0.20798,0.43062,-0.87824,309.36,-0.42148,0.77079,0.47774,296,#31,0.021581,0.024476,-0.99947,83.835,0.74045,0.67133,0.032428,142.43,0.67176,-0.74076,-0.0036349,615.58,#32,0.19535,0.95823,-0.2089,103.8,0.022341,-0.2173,-0.97585,278.89,-0.98048,0.18597,-0.063859,218.11,#33,-0.62752,-0.094022,0.77291,155.63,0.43447,-0.86605,0.24739,304.73,0.64611,0.49104,0.58431,220.39,#34,-0.091532,0.99355,0.066872,190.3,0.95992,0.07017,0.27135,280.87,0.26491,0.089029,-0.96016,229.01,#35,-0.32465,-0.18834,0.92689,156.38,-0.87839,-0.3034,-0.36931,303.58,0.35077,-0.93407,-0.066937,219.99
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.24658,-0.47056,-0.84721,517.77,0.81148,-0.57817,0.084954,256.64,-0.52981,-0.66655,0.52442,390.48,#26,0.12375,-0.90419,-0.40882,154.27,0.90202,-0.069212,0.42612,256.61,-0.41358,-0.42149,0.80703,255.79,#27,0.83808,-0.15013,-0.52448,178.95,-0.032969,-0.97357,0.226,295.27,-0.54455,-0.17211,-0.82088,281.52,#28,-0.31702,0.92224,-0.2213,241,0.58539,0.37386,0.7194,258.66,0.7462,0.098518,-0.6584,283.2,#29,0.2258,0.46886,0.85392,178.78,-0.38914,-0.76018,0.52029,359.29,0.89307,-0.44978,0.010809,246.8,#30,0.88266,0.46953,0.021185,185.7,-0.20798,0.43062,-0.87824,327.24,-0.42148,0.77079,0.47774,297.45,#31,0.021581,0.024476,-0.99947,90.656,0.74045,0.67133,0.032428,160.3,0.67176,-0.74076,-0.0036349,617.03,#32,0.19535,0.95823,-0.2089,110.62,0.022341,-0.2173,-0.97585,296.76,-0.98048,0.18597,-0.063859,219.56,#33,-0.62752,-0.094022,0.77291,162.45,0.43447,-0.86605,0.24739,322.61,0.64611,0.49104,0.58431,221.85,#34,-0.091532,0.99355,0.066872,197.12,0.95992,0.07017,0.27135,298.74,0.26491,0.089029,-0.96016,230.46,#35,-0.32465,-0.18834,0.92689,163.2,-0.87839,-0.3034,-0.36931,321.45,0.35077,-0.93407,-0.066937,221.44
> view matrix models
> #24,-0.24658,-0.47056,-0.84721,512.22,0.81148,-0.57817,0.084954,255.44,-0.52981,-0.66655,0.52442,387.71,#26,0.12375,-0.90419,-0.40882,148.72,0.90202,-0.069212,0.42612,255.41,-0.41358,-0.42149,0.80703,253.02,#27,0.83808,-0.15013,-0.52448,173.39,-0.032969,-0.97357,0.226,294.07,-0.54455,-0.17211,-0.82088,278.75,#28,-0.31702,0.92224,-0.2213,235.44,0.58539,0.37386,0.7194,257.47,0.7462,0.098518,-0.6584,280.43,#29,0.2258,0.46886,0.85392,173.23,-0.38914,-0.76018,0.52029,358.09,0.89307,-0.44978,0.010809,244.03,#30,0.88266,0.46953,0.021185,180.14,-0.20798,0.43062,-0.87824,326.04,-0.42148,0.77079,0.47774,294.68,#31,0.021581,0.024476,-0.99947,85.101,0.74045,0.67133,0.032428,159.1,0.67176,-0.74076,-0.0036349,614.26,#32,0.19535,0.95823,-0.2089,105.07,0.022341,-0.2173,-0.97585,295.57,-0.98048,0.18597,-0.063859,216.79,#33,-0.62752,-0.094022,0.77291,156.9,0.43447,-0.86605,0.24739,321.41,0.64611,0.49104,0.58431,219.08,#34,-0.091532,0.99355,0.066872,191.56,0.95992,0.07017,0.27135,297.54,0.26491,0.089029,-0.96016,227.69,#35,-0.32465,-0.18834,0.92689,157.64,-0.87839,-0.3034,-0.36931,320.25,0.35077,-0.93407,-0.066937,218.67
> view matrix models
> #24,-0.24658,-0.47056,-0.84721,518.26,0.81148,-0.57817,0.084954,261.35,-0.52981,-0.66655,0.52442,391.38,#26,0.12375,-0.90419,-0.40882,154.76,0.90202,-0.069212,0.42612,261.32,-0.41358,-0.42149,0.80703,256.69,#27,0.83808,-0.15013,-0.52448,179.43,-0.032969,-0.97357,0.226,299.98,-0.54455,-0.17211,-0.82088,282.42,#28,-0.31702,0.92224,-0.2213,241.48,0.58539,0.37386,0.7194,263.38,0.7462,0.098518,-0.6584,284.1,#29,0.2258,0.46886,0.85392,179.27,-0.38914,-0.76018,0.52029,364,0.89307,-0.44978,0.010809,247.7,#30,0.88266,0.46953,0.021185,186.19,-0.20798,0.43062,-0.87824,331.95,-0.42148,0.77079,0.47774,298.35,#31,0.021581,0.024476,-0.99947,91.143,0.74045,0.67133,0.032428,165.02,0.67176,-0.74076,-0.0036349,617.93,#32,0.19535,0.95823,-0.2089,111.11,0.022341,-0.2173,-0.97585,301.48,-0.98048,0.18597,-0.063859,220.46,#33,-0.62752,-0.094022,0.77291,162.94,0.43447,-0.86605,0.24739,327.32,0.64611,0.49104,0.58431,222.75,#34,-0.091532,0.99355,0.066872,197.61,0.95992,0.07017,0.27135,303.46,0.26491,0.089029,-0.96016,231.36,#35,-0.32465,-0.18834,0.92689,163.69,-0.87839,-0.3034,-0.36931,326.17,0.35077,-0.93407,-0.066937,222.34
> view matrix models
> #24,-0.24658,-0.47056,-0.84721,520.55,0.81148,-0.57817,0.084954,256.18,-0.52981,-0.66655,0.52442,395.97,#26,0.12375,-0.90419,-0.40882,157.06,0.90202,-0.069212,0.42612,256.15,-0.41358,-0.42149,0.80703,261.28,#27,0.83808,-0.15013,-0.52448,181.73,-0.032969,-0.97357,0.226,294.81,-0.54455,-0.17211,-0.82088,287,#28,-0.31702,0.92224,-0.2213,243.78,0.58539,0.37386,0.7194,258.2,0.7462,0.098518,-0.6584,288.69,#29,0.2258,0.46886,0.85392,181.57,-0.38914,-0.76018,0.52029,358.83,0.89307,-0.44978,0.010809,252.28,#30,0.88266,0.46953,0.021185,188.48,-0.20798,0.43062,-0.87824,326.78,-0.42148,0.77079,0.47774,302.94,#31,0.021581,0.024476,-0.99947,93.438,0.74045,0.67133,0.032428,159.84,0.67176,-0.74076,-0.0036349,622.52,#32,0.19535,0.95823,-0.2089,113.4,0.022341,-0.2173,-0.97585,296.31,-0.98048,0.18597,-0.063859,225.05,#33,-0.62752,-0.094022,0.77291,165.23,0.43447,-0.86605,0.24739,322.15,0.64611,0.49104,0.58431,227.33,#34,-0.091532,0.99355,0.066872,199.9,0.95992,0.07017,0.27135,298.28,0.26491,0.089029,-0.96016,235.95,#35,-0.32465,-0.18834,0.92689,165.98,-0.87839,-0.3034,-0.36931,320.99,0.35077,-0.93407,-0.066937,226.93
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.31794,-0.62339,-0.71435,537.58,0.87687,-0.47988,0.028498,234.39,-0.36057,-0.61733,0.6992,309.16,#26,0.071957,-0.97447,-0.21266,154.27,0.94616,-0.00077428,0.32369,257.12,-0.31559,-0.22451,0.92195,256.03,#27,0.70339,-0.22333,-0.67481,185.37,0.025786,-0.94072,0.33821,291.76,-0.71034,-0.25529,-0.65593,280.5,#28,-0.12907,0.93721,-0.32401,244.81,0.48816,0.34447,0.8019,254.34,0.86315,-0.05467,-0.50197,264.39,#29,0.39132,0.33217,0.85822,180.61,-0.50498,-0.70212,0.50201,359.74,0.76933,-0.62983,-0.10701,254.8,#30,0.7654,0.63804,0.084061,196.64,-0.16435,0.32008,-0.93303,321.29,-0.62221,0.70033,0.34985,298.46,#31,0.19262,-0.10315,-0.97584,163.72,0.64663,0.76135,0.047159,115.69,0.73809,-0.64009,0.21335,607.78,#32,-0.013478,0.966,-0.25818,105.71,0.14654,-0.25351,-0.95617,302.27,-0.98911,-0.050721,-0.13814,235.19,#33,-0.45966,-0.025197,0.88774,157.9,0.35603,-0.92098,0.15821,326.84,0.81361,0.38879,0.43231,229.56,#34,0.0060954,0.99222,-0.12435,192.58,0.91866,0.043566,0.39265,301.56,0.39501,-0.11663,-0.91124,227.57,#35,-0.28039,-0.3922,0.8761,158.5,-0.91166,-0.17685,-0.37094,325.74,0.30043,-0.90272,-0.30797,228.86
> view matrix models
> #24,-0.318,-0.66115,-0.67953,537.37,0.89087,-0.4536,0.024438,226.91,-0.32439,-0.5976,0.73324,289.52,#26,0.074854,-0.98391,-0.16225,152.46,0.95205,0.022113,0.30513,257.79,-0.29663,-0.17731,0.93839,255.44,#27,0.66908,-0.25314,-0.69875,185.34,0.030287,-0.93013,0.36597,291.26,-0.74257,-0.26603,-0.61467,279.17,#28,-0.078436,0.93993,-0.33223,243.23,0.46945,0.32882,0.81945,253.18,0.87947,-0.091692,-0.46704,259.36,#29,0.41786,0.28831,0.86155,180.67,-0.53032,-0.69258,0.48897,359.91,0.73767,-0.66122,-0.1365,255.32,#30,0.73159,0.67669,0.082843,198.02,-0.163,0.29161,-0.94255,320.14,-0.66197,0.67606,0.32364,297.25,#31,0.23989,-0.11902,-0.96348,175.98,0.62509,0.77828,0.059493,107.77,0.74278,-0.61653,0.2611,602.94,#32,-0.05783,0.95748,-0.28266,103.83,0.17056,-0.26949,-0.94778,304.29,-0.98365,-0.10302,-0.14772,238,#33,-0.41347,-0.024186,0.9102,156.16,0.3445,-0.92949,0.1318,328.05,0.84283,0.36806,0.39264,230.45,#34,0.042438,0.98618,-0.16015,190.21,0.90861,0.028565,0.41667,302.2,0.41548,-0.1632,-0.89484,226.21,#35,-0.28307,-0.4381,0.85319,156.7,-0.91347,-0.14798,-0.37906,326.95,0.29232,-0.88666,-0.3583,229.7
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.318,-0.66115,-0.67953,534.65,0.89087,-0.4536,0.024438,225.83,-0.32439,-0.5976,0.73324,288.89,#26,0.074854,-0.98391,-0.16225,149.74,0.95205,0.022113,0.30513,256.71,-0.29663,-0.17731,0.93839,254.81,#27,0.66908,-0.25314,-0.69875,182.62,0.030287,-0.93013,0.36597,290.18,-0.74257,-0.26603,-0.61467,278.55,#28,-0.078436,0.93993,-0.33223,240.51,0.46945,0.32882,0.81945,252.11,0.87947,-0.091692,-0.46704,258.73,#29,0.41786,0.28831,0.86155,177.94,-0.53032,-0.69258,0.48897,358.83,0.73767,-0.66122,-0.1365,254.7,#30,0.73159,0.67669,0.082843,195.3,-0.163,0.29161,-0.94255,319.06,-0.66197,0.67606,0.32364,296.62,#31,0.23989,-0.11902,-0.96348,173.25,0.62509,0.77828,0.059493,106.69,0.74278,-0.61653,0.2611,602.32,#32,-0.05783,0.95748,-0.28266,101.11,0.17056,-0.26949,-0.94778,303.22,-0.98365,-0.10302,-0.14772,237.38,#33,-0.41347,-0.024186,0.9102,153.44,0.3445,-0.92949,0.1318,326.97,0.84283,0.36806,0.39264,229.82,#34,0.042438,0.98618,-0.16015,187.49,0.90861,0.028565,0.41667,301.13,0.41548,-0.1632,-0.89484,225.58,#35,-0.28307,-0.4381,0.85319,153.98,-0.91347,-0.14798,-0.37906,325.87,0.29232,-0.88666,-0.3583,229.07
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 156, shift = 9.24, angle = 13 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53654733 -0.84379164 -0.01151613 402.23913730
0.84348563 -0.53666482 0.02286592 56.40575565
-0.02547438 0.00255495 0.99967221 -108.72343203
Axis -0.01203643 0.00827176 0.99989335
Axis point 184.72256227 138.71080164 0.00000000
Rotation angle (degrees) 122.46402662
Shift along axis -113.08678508
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 156, shift = 9.24, angle = 13 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53654733 -0.84379164 -0.01151613 402.23913730
0.84348563 -0.53666482 0.02286592 56.40575565
-0.02547438 0.00255495 0.99967221 -108.72343203
Axis -0.01203643 0.00827176 0.99989335
Axis point 184.72256227 138.71080164 0.00000000
Rotation angle (degrees) 122.46402662
Shift along axis -113.08678508
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.034061,-0.79091,-0.61099,480.89,0.82668,-0.36585,0.4275,133.68,-0.56164,-0.49053,0.66629,336.22,#26,0.3589,-0.93305,-0.024816,124.1,0.76749,0.27987,0.57674,272.77,-0.53118,-0.22604,0.81655,275.99,#27,0.6179,-0.54129,-0.57027,166.65,-0.37675,-0.84044,0.38952,299.34,-0.69012,-0.025833,-0.72323,291.76,#28,0.10412,0.99173,-0.075049,208.94,0.68508,-0.016817,0.72827,241.33,0.72098,-0.12724,-0.68117,285.52,#29,0.25659,0.032874,0.96596,182.88,-0.41959,-0.89654,0.14197,357.18,0.87069,-0.44173,-0.21625,250.58,#30,0.6195,0.75767,-0.20531,188.38,-0.55139,0.23384,-0.80081,326.53,-0.55874,0.60931,0.56264,302.27,#31,0.4501,0.10904,-0.8863,111.8,0.69193,0.58482,0.42334,220.21,0.56449,-0.8038,0.18778,651.36,#32,-0.036515,0.82041,-0.57061,91.92,-0.085892,-0.57145,-0.81613,325.77,-0.99564,0.019209,0.091333,244.59,#33,-0.25427,-0.30119,0.91904,148.75,0.66572,-0.74382,-0.059587,329.16,0.70155,0.59667,0.38964,233.71,#34,0.33993,0.93894,-0.053291,172.81,0.92587,-0.32419,0.19408,293.84,0.16495,-0.11532,-0.97954,238.09,#35,-0.54454,-0.49376,0.678,148.89,-0.66854,-0.23262,-0.70636,327.79,0.50649,-0.83791,-0.20343,233.3
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.034061,-0.79091,-0.61099,485.46,0.82668,-0.36585,0.4275,136.38,-0.56164,-0.49053,0.66629,336.67,#26,0.3589,-0.93305,-0.024816,128.67,0.76749,0.27987,0.57674,275.48,-0.53118,-0.22604,0.81655,276.44,#27,0.6179,-0.54129,-0.57027,171.22,-0.37675,-0.84044,0.38952,302.05,-0.69012,-0.025833,-0.72323,292.22,#28,0.10412,0.99173,-0.075049,213.51,0.68508,-0.016817,0.72827,244.03,0.72098,-0.12724,-0.68117,285.97,#29,0.25659,0.032874,0.96596,187.45,-0.41959,-0.89654,0.14197,359.88,0.87069,-0.44173,-0.21625,251.03,#30,0.6195,0.75767,-0.20531,192.95,-0.55139,0.23384,-0.80081,329.24,-0.55874,0.60931,0.56264,302.72,#31,0.4501,0.10904,-0.8863,116.36,0.69193,0.58482,0.42334,222.92,0.56449,-0.8038,0.18778,651.81,#32,-0.036515,0.82041,-0.57061,96.489,-0.085892,-0.57145,-0.81613,328.47,-0.99564,0.019209,0.091333,245.04,#33,-0.25427,-0.30119,0.91904,153.32,0.66572,-0.74382,-0.059587,331.87,0.70155,0.59667,0.38964,234.16,#34,0.33993,0.93894,-0.053291,177.38,0.92587,-0.32419,0.19408,296.55,0.16495,-0.11532,-0.97954,238.54,#35,-0.54454,-0.49376,0.678,153.46,-0.66854,-0.23262,-0.70636,330.5,0.50649,-0.83791,-0.20343,233.75
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6995, correlation about mean = 0.3478, overlap = 18.84
steps = 144, shift = 9.38, angle = 14.3 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53634514 -0.84391968 -0.01155224 402.24655069
0.84361383 -0.53646365 0.02285743 56.32369233
-0.02548720 0.00251385 0.99967199 -108.69945864
Axis -0.01205393 0.00825671 0.99989326
Axis point 184.74404153 138.70156827 0.00000000
Rotation angle (degrees) 122.45033940
Shift along axis -113.07146080
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6995, correlation about mean = 0.3478, overlap = 18.84
steps = 144, shift = 9.38, angle = 14.3 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53634514 -0.84391968 -0.01155224 402.24655069
0.84361383 -0.53646365 0.02285743 56.32369233
-0.02548720 0.00251385 0.99967199 -108.69945864
Axis -0.01205393 0.00825671 0.99989326
Axis point 184.74404153 138.70156827 0.00000000
Rotation angle (degrees) 122.45033940
Shift along axis -113.07146080
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 136, shift = 9.38, angle = 14.3 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650770 -0.84381651 -0.01154089 402.24931528
0.84350890 -0.53662568 0.02292619 56.35897325
-0.02553863 0.00256523 0.99967054 -108.70393002
Axis -0.01206571 0.00829493 0.99989280
Axis point 184.73746046 138.69652445 0.00000000
Rotation angle (degrees) 122.46140825
Shift along axis -113.07820510
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 136, shift = 9.38, angle = 14.3 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650770 -0.84381651 -0.01154089 402.24931528
0.84350890 -0.53662568 0.02292619 56.35897325
-0.02553863 0.00256523 0.99967054 -108.70393002
Axis -0.01206571 0.00829493 0.99989280
Axis point 184.73746046 138.69652445 0.00000000
Rotation angle (degrees) 122.46140825
Shift along axis -113.07820510
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.098015,-0.80866,-0.58006,496.61,0.89947,-0.3214,0.29607,140.2,-0.42585,-0.49272,0.75886,285.85,#26,0.29784,-0.95457,0.0093976,132.24,0.85319,0.2706,0.44592,271.42,-0.4282,-0.12479,0.89503,268.87,#27,0.58371,-0.51366,-0.62883,174.82,-0.24207,-0.84933,0.46908,297.11,-0.77504,-0.12158,-0.62011,285.96,#28,0.12817,0.98133,-0.14343,218.51,0.57279,0.044817,0.81848,242.54,0.80962,-0.18705,-0.55635,268.43,#29,0.32662,0.033692,0.94456,186.4,-0.53431,-0.81777,0.21393,361.11,0.77964,-0.57456,-0.24909,253.2,#30,0.59967,0.78764,-0.14151,196.27,-0.43424,0.17174,-0.88427,323.31,-0.67218,0.59172,0.44501,299.18,#31,0.46278,0.03692,-0.88571,146.19,0.61782,0.70307,0.35212,162.58,0.63571,-0.71016,0.30256,631.88,#32,-0.09852,0.83841,-0.53606,96.336,0.063201,-0.53232,-0.84418,327.11,-0.99313,-0.11705,-0.00054379,247.9,#33,-0.22989,-0.2368,0.94397,152.19,0.54129,-0.83719,-0.078192,334.52,0.8088,0.49298,0.32064,234.31,#34,0.31909,0.93965,-0.12348,177.64,0.90422,-0.26283,0.3366,300,0.28383,-0.21906,-0.93351,231.81,#35,-0.48788,-0.53939,0.68632,152.35,-0.75967,-0.12493,-0.6382,333.23,0.42998,-0.83274,-0.3488,233.69
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 132, shift = 8.49, angle = 13.4 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648110 -0.84383349 -0.01153520 402.24959292
0.84352783 -0.53659914 0.02285101 56.36886561
-0.02547223 0.00252887 0.99967233 -108.70832497
Axis -0.01204245 0.00825878 0.99989338
Axis point 184.73665226 138.70451360 0.00000000
Rotation angle (degrees) 122.45954332
Shift along axis -113.07526848
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 132, shift = 8.49, angle = 13.4 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648110 -0.84383349 -0.01153520 402.24959292
0.84352783 -0.53659914 0.02285101 56.36886561
-0.02547223 0.00252887 0.99967233 -108.70832497
Axis -0.01204245 0.00825878 0.99989338
Axis point 184.73665226 138.70451360 0.00000000
Rotation angle (degrees) 122.45954332
Shift along axis -113.07526848
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.098015,-0.80866,-0.58006,495.95,0.89947,-0.3214,0.29607,143.51,-0.42585,-0.49272,0.75886,283.31,#26,0.29784,-0.95457,0.0093976,131.58,0.85319,0.2706,0.44592,274.73,-0.4282,-0.12479,0.89503,266.33,#27,0.58371,-0.51366,-0.62883,174.16,-0.24207,-0.84933,0.46908,300.42,-0.77504,-0.12158,-0.62011,283.42,#28,0.12817,0.98133,-0.14343,217.85,0.57279,0.044817,0.81848,245.85,0.80962,-0.18705,-0.55635,265.9,#29,0.32662,0.033692,0.94456,185.74,-0.53431,-0.81777,0.21393,364.42,0.77964,-0.57456,-0.24909,250.66,#30,0.59967,0.78764,-0.14151,195.61,-0.43424,0.17174,-0.88427,326.62,-0.67218,0.59172,0.44501,296.64,#31,0.46278,0.03692,-0.88571,145.53,0.61782,0.70307,0.35212,165.89,0.63571,-0.71016,0.30256,629.35,#32,-0.09852,0.83841,-0.53606,95.675,0.063201,-0.53232,-0.84418,330.42,-0.99313,-0.11705,-0.00054379,245.36,#33,-0.22989,-0.2368,0.94397,151.53,0.54129,-0.83719,-0.078192,337.83,0.8088,0.49298,0.32064,231.77,#34,0.31909,0.93965,-0.12348,176.98,0.90422,-0.26283,0.3366,303.31,0.28383,-0.21906,-0.93351,229.27,#35,-0.48788,-0.53939,0.68632,151.69,-0.75967,-0.12493,-0.6382,336.54,0.42998,-0.83274,-0.3488,231.15
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 132, shift = 4.59, angle = 13.4 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53645819 -0.84384808 -0.01153365 402.24487372
0.84354345 -0.53657630 0.02281051 56.39512313
-0.02543729 0.00250775 0.99967327 -108.72632673
Axis -0.01203076 0.00823885 0.99989369
Axis point 184.72768613 138.71922847 0.00000000
Rotation angle (degrees) 122.45795837
Shift along axis -113.08944854
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 132, shift = 4.59, angle = 13.4 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53645819 -0.84384808 -0.01153365 402.24487372
0.84354345 -0.53657630 0.02281051 56.39512313
-0.02543729 0.00250775 0.99967327 -108.72632673
Axis -0.01203076 0.00823885 0.99989369
Axis point 184.72768613 138.71922847 0.00000000
Rotation angle (degrees) 122.45795837
Shift along axis -113.08944854
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 132, shift = 4.59, angle = 13.4 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53645819 -0.84384808 -0.01153365 402.24487372
0.84354345 -0.53657630 0.02281051 56.39512313
-0.02543729 0.00250775 0.99967327 -108.72632673
Axis -0.01203076 0.00823885 0.99989369
Axis point 184.72768613 138.71922847 0.00000000
Rotation angle (degrees) 122.45795837
Shift along axis -113.08944854
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.11006,-0.73831,-0.66542,503.64,0.9284,-0.31542,0.19642,157.85,-0.35491,-0.59615,0.72017,296.32,#26,0.28628,-0.95278,-0.10125,135.42,0.90243,0.23262,0.36263,271.63,-0.32196,-0.19519,0.92642,254.61,#27,0.6674,-0.44915,-0.594,174.62,-0.14106,-0.85945,0.49137,297.77,-0.73122,-0.24415,-0.63695,277.97,#28,0.017389,0.99026,-0.13813,222.89,0.50254,0.11078,0.85743,247.28,0.86438,-0.084325,-0.49572,260.25,#29,0.28244,0.13568,0.94964,185.46,-0.58591,-0.75944,0.28277,364.98,0.75956,-0.63627,-0.135,252.11,#30,0.68485,0.71688,-0.13068,193.15,-0.34074,0.15652,-0.92704,323.7,-0.64411,0.6794,0.35146,295.44,#31,0.36369,0.062382,-0.92943,121.44,0.57991,0.76567,0.27831,131.09,0.729,-0.6402,0.24229,606.56,#32,-0.0079636,0.87551,-0.48313,98.447,0.14818,-0.47677,-0.86645,327.13,-0.98893,-0.07849,-0.12594,235.02,#33,-0.33653,-0.23267,0.91248,154.8,0.45333,-0.88935,-0.059584,338.54,0.82537,0.3936,0.40477,227.72,#34,0.23725,0.96992,-0.054447,182.36,0.88954,-0.19438,0.41344,305.71,0.39042,-0.14652,-0.9089,224.81,#35,-0.4808,-0.45018,0.75244,155.1,-0.8191,-0.075618,-0.56864,337.32,0.31289,-0.88973,-0.33239,227.01
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 124, shift = 4.61, angle = 10.3 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650604 -0.84381756 -0.01154095 402.24895802
0.84351159 -0.53662418 0.02286203 56.37899591
-0.02548454 0.00253069 0.99967201 -108.71380566
Axis -0.01204813 0.00826282 0.99989328
Axis point 184.73362348 138.70556850 0.00000000
Rotation angle (degrees) 122.46125127
Shift along axis -113.08270294
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 124, shift = 4.61, angle = 10.3 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650604 -0.84381756 -0.01154095 402.24895802
0.84351159 -0.53662418 0.02286203 56.37899591
-0.02548454 0.00253069 0.99967201 -108.71380566
Axis -0.01204813 0.00826282 0.99989328
Axis point 184.73362348 138.70556850 0.00000000
Rotation angle (degrees) 122.46125127
Shift along axis -113.08270294
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 124, shift = 4.61, angle = 10.3 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650604 -0.84381756 -0.01154095 402.24895802
0.84351159 -0.53662418 0.02286203 56.37899591
-0.02548454 0.00253069 0.99967201 -108.71380566
Axis -0.01204813 0.00826282 0.99989328
Axis point 184.73362348 138.70556850 0.00000000
Rotation angle (degrees) 122.46125127
Shift along axis -113.08270294
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.11762,-0.74001,-0.66223,504.98,0.93224,-0.31207,0.18315,159.26,-0.3422,-0.59582,0.72657,291.96,#26,0.27906,-0.95528,-0.097826,135.86,0.9082,0.22946,0.35003,271.38,-0.31193,-0.18652,0.93162,253.9,#27,0.66383,-0.44556,-0.60067,175.04,-0.12764,-0.85888,0.49602,297.44,-0.73691,-0.25261,-0.62702,277.36,#28,0.019617,0.98907,-0.14612,223.51,0.49143,0.11773,0.86293,247.48,0.8707,-0.088732,-0.48375,258.71,#29,0.29041,0.13632,0.94714,185.34,-0.59398,-0.75034,0.29012,365.05,0.75023,-0.64684,-0.13693,252.32,#30,0.68296,0.72,-0.12314,193.53,-0.32832,0.15199,-0.93226,323.26,-0.65251,0.67713,0.34019,295.06,#31,0.36464,0.054063,-0.92958,124.81,0.5726,0.77423,0.26964,126.22,0.73428,-0.63059,0.25136,604.08,#32,-0.014749,0.87781,-0.47879,98.446,0.16089,-0.47052,-0.8676,326.91,-0.98686,-0.089829,-0.13429,235.25,#33,-0.33423,-0.2251,0.91522,154.69,0.44063,-0.89572,-0.059389,338.74,0.83315,0.38342,0.39856,227.76,#34,0.23437,0.97015,-0.062306,182.42,0.88582,-0.18672,0.42481,306.12,0.4005,-0.15476,-0.90314,224.27,#35,-0.47411,-0.45504,0.75376,154.99,-0.82592,-0.066791,-0.55982,337.54,0.30509,-0.88796,-0.34416,227.04
> view matrix models
> #24,-0.087024,-0.76284,-0.64071,497.81,0.92608,-0.29899,0.23019,147.64,-0.36716,-0.57331,0.73246,291.85,#26,0.30889,-0.94878,-0.066387,132.77,0.88702,0.26219,0.38007,273.35,-0.3432,-0.17629,0.92257,257.03,#27,0.64431,-0.48387,-0.59223,173.38,-0.17511,-0.84716,0.50165,298.47,-0.74445,-0.21952,-0.63056,279.03,#28,0.055396,0.99112,-0.12089,219.47,0.51485,0.075387,0.85396,246.09,0.85549,-0.10955,-0.5061,261,#29,0.2807,0.094343,0.95515,185.88,-0.58354,-0.77333,0.24787,364.87,0.76203,-0.62694,-0.16202,251.85,#30,0.65706,0.73803,-0.15354,193.21,-0.37391,0.14221,-0.9165,324.02,-0.65457,0.65961,0.3694,295.64,#31,0.40074,0.072825,-0.91329,122.56,0.57819,0.75316,0.31376,138.78,0.7107,-0.6538,0.25971,611.44,#32,-0.02689,0.85665,-0.5152,97.237,0.13317,-0.50772,-0.85117,329.77,-0.99073,-0.091498,-0.10043,237.43,#33,-0.30083,-0.25315,0.91947,153.75,0.47724,-0.87469,-0.084676,339.13,0.82568,0.41333,0.38394,228.61,#34,0.27673,0.95892,-0.062381,180.1,0.88675,-0.22981,0.40107,305.33,0.37025,-0.1663,-0.91392,225.58,#35,-0.50063,-0.47392,0.72441,153.99,-0.79721,-0.073754,-0.59919,337.89,0.33739,-0.87747,-0.34089,227.92
> view matrix models
> #24,-0.065451,-0.65849,-0.74974,496.39,0.8672,-0.40923,0.28372,170.97,-0.49364,-0.6316,0.59783,361.87,#26,0.32374,-0.92125,-0.21559,136.16,0.85322,0.18579,0.48734,271.15,-0.40891,-0.34172,0.84618,259.54,#27,0.75306,-0.41508,-0.51049,172.15,-0.23043,-0.89313,0.38628,301,-0.61628,-0.17326,-0.76823,283.6,#28,-0.090217,0.99303,-0.0758,222.26,0.61924,0.11554,0.77666,249.4,0.78,0.02313,-0.62535,279.28,#29,0.18615,0.21387,0.95896,186.09,-0.46822,-0.83876,0.27795,364.11,0.86378,-0.50074,-0.055999,250.02,#30,0.75962,0.62693,-0.173,188.36,-0.41555,0.26325,-0.87064,329.47,-0.5003,0.73325,0.46049,299.37,#31,0.27018,0.14113,-0.95241,78.647,0.68301,0.66911,0.29291,181.23,0.6786,-0.72964,0.08439,623.44,#32,0.11482,0.87864,-0.46347,101.89,0.0075881,-0.46732,-0.88406,322.67,-0.99336,0.09799,-0.060325,227.9,#33,-0.43654,-0.27945,0.85519,158.71,0.55871,-0.82924,0.014229,333.95,0.70518,0.48401,0.51812,226.03,#34,0.18666,0.98067,0.058675,186.43,0.93968,-0.19565,0.28058,301.53,0.28664,0.0027619,-0.95804,231.21,#35,-0.51566,-0.33622,0.78807,159.09,-0.77549,-0.20793,-0.59614,332.65,0.3643,-0.91854,-0.15351,225.55
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 5.85, angle = 5.5 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650540 -0.84381796 -0.01154137 402.25060611
0.84351214 -0.53662357 0.02285614 56.38038132
-0.02547979 0.00252715 0.99967214 -108.71183289
Axis -0.01204673 0.00825976 0.99989332
Axis point 184.73424112 138.70669247 0.00000000
Rotation angle (degrees) 122.46120430
Shift along axis -113.08035258
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 5.85, angle = 5.5 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650540 -0.84381796 -0.01154137 402.25060611
0.84351214 -0.53662357 0.02285614 56.38038132
-0.02547979 0.00252715 0.99967214 -108.71183289
Axis -0.01204673 0.00825976 0.99989332
Axis point 184.73424112 138.70669247 0.00000000
Rotation angle (degrees) 122.46120430
Shift along axis -113.08035258
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 5.85, angle = 5.5 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650540 -0.84381796 -0.01154137 402.25060611
0.84351214 -0.53662357 0.02285614 56.38038132
-0.02547979 0.00252715 0.99967214 -108.71183289
Axis -0.01204673 0.00825976 0.99989332
Axis point 184.73424112 138.70669247 0.00000000
Rotation angle (degrees) 122.46120430
Shift along axis -113.08035258
> view matrix models
> #24,-0.072731,-0.72339,-0.6866,496.92,0.89048,-0.35714,0.28195,155.76,-0.44917,-0.5909,0.67014,327.71,#26,0.3213,-0.9385,-0.12644,133.58,0.85925,0.23279,0.45552,272.86,-0.39807,-0.25501,0.8812,260.32,#27,0.69042,-0.46171,-0.5569,172.53,-0.22803,-0.86949,0.43818,300.33,-0.68653,-0.17554,-0.7056,282.52,#28,-0.0020009,0.99525,-0.097335,220.12,0.58589,0.080046,0.80643,247.28,0.81039,-0.055414,-0.58327,271.82,#29,0.23863,0.13976,0.961,186.06,-0.51313,-0.82201,0.24696,364.37,0.82447,-0.55205,-0.12444,250.59,#30,0.69944,0.69476,-0.1676,191.06,-0.41834,0.20787,-0.88419,327.47,-0.57946,0.68855,0.43603,298.06,#31,0.351,0.10601,-0.93036,102.83,0.64173,0.69631,0.32145,168.53,0.68189,-0.70987,0.17637,623.62,#32,0.032855,0.86525,-0.50026,98.804,0.048761,-0.50132,-0.86389,326.92,-0.99827,0.0039902,-0.058661,233.88,#33,-0.35536,-0.27009,0.89486,155.67,0.54081,-0.84025,-0.038842,336.3,0.76239,0.47014,0.44466,227.73,#34,0.24535,0.96939,-0.0097327,182.46,0.91868,-0.22928,0.32164,302.75,0.30956,-0.087855,-0.94681,229.18,#35,-0.51313,-0.41838,0.74943,155.96,-0.77299,-0.15425,-0.61537,335.01,0.37306,-0.89508,-0.24426,227.16
> view matrix models
> #24,-0.088031,-0.70512,-0.7036,500.53,0.89357,-0.36806,0.25705,162.75,-0.44022,-0.60609,0.66247,330.39,#26,0.30583,-0.94,-0.15125,135.45,0.87151,0.21243,0.44198,271.58,-0.38333,-0.26698,0.88418,258.66,#27,0.70633,-0.43714,-0.55678,173.37,-0.20286,-0.87855,0.43242,299.75,-0.67819,-0.19248,-0.70923,281.77,#28,-0.029027,0.99368,-0.10847,222.42,0.5762,0.10531,0.81049,248.02,0.81679,-0.038977,-0.57562,271.23,#29,0.2387,0.16866,0.95634,185.79,-0.51661,-0.81183,0.27212,364.47,0.82227,-0.55901,-0.10665,250.78,#30,0.71845,0.67873,-0.15215,190.97,-0.39412,0.21699,-0.89307,327.15,-0.57314,0.7016,0.4234,297.91,#31,0.3244,0.099468,-0.94068,101.75,0.64226,0.70693,0.29624,162.3,0.69446,-0.70026,0.16544,620.24,#32,0.046915,0.87732,-0.4776,99.752,0.061159,-0.47975,-0.87527,325.06,-0.99702,0.011854,-0.076164,232.29,#33,-0.38038,-0.25622,0.88863,156.45,0.52294,-0.85209,-0.021834,335.92,0.76279,0.4564,0.4581,227.14,#34,0.21758,0.97604,-0.0032491,184.05,0.92082,-0.20417,0.33228,303.03,0.32366,-0.075292,-0.94317,228.63,#35,-0.49934,-0.40065,0.7682,156.78,-0.78975,-0.15415,-0.59374,334.65,0.3563,-0.90317,-0.23944,226.55
> view matrix models
> #24,-0.084825,-0.6944,-0.71457,500.11,0.8491,-0.42564,0.31283,171.88,-0.52138,-0.5802,0.62572,351.78,#26,0.30821,-0.93666,-0.16637,135.74,0.83441,0.18217,0.52017,271.77,-0.45691,-0.29914,0.8377,265.01,#27,0.71733,-0.43074,-0.54764,173.19,-0.2603,-0.89477,0.36282,302.13,-0.64629,-0.11772,-0.75396,286.01,#28,-0.043661,0.99373,-0.10289,222.6,0.64831,0.10654,0.75389,249.92,0.76012,-0.033788,-0.6489,280.97,#29,0.22821,0.18028,0.95678,185.82,-0.438,-0.85864,0.26626,363.82,0.86953,-0.47983,-0.11699,249.41,#30,0.7286,0.66716,-0.15507,190.44,-0.44108,0.28381,-0.85141,330.99,-0.52401,0.68873,0.50105,299.83,#31,0.31132,0.10732,-0.94423,96.984,0.70477,0.64045,0.30516,195.83,0.63748,-0.76046,0.12375,634.54,#32,0.061797,0.87891,-0.47297,100.24,-0.030012,-0.47203,-0.88107,322.43,-0.99764,0.068642,-0.0027922,233.34,#33,-0.39394,-0.25979,0.88166,156.96,0.58849,-0.80813,0.024826,333.07,0.70604,0.52862,0.47123,228.05,#34,0.20906,0.97785,0.0097648,184.66,0.94769,-0.20505,0.24463,300.6,0.24122,-0.041889,-0.96957,232.95,#35,-0.50161,-0.3863,0.77406,157.31,-0.75648,-0.23819,-0.60909,331.75,0.41967,-0.89109,-0.17275,227.59
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 5.82, angle = 5.72 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648914 -0.84382819 -0.01154928 402.25077995
0.84352286 -0.53660757 0.02283615 56.38489869
-0.02546722 0.00250926 0.99967251 -108.71256506
Axis -0.01204534 0.00824751 0.99989344
Axis point 184.73317849 138.71088501 0.00000000
Rotation angle (degrees) 122.46009692
Shift along axis -113.08119373
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 5.82, angle = 5.72 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648914 -0.84382819 -0.01154928 402.25077995
0.84352286 -0.53660757 0.02283615 56.38489869
-0.02546722 0.00250926 0.99967251 -108.71256506
Axis -0.01204534 0.00824751 0.99989344
Axis point 184.73317849 138.71088501 0.00000000
Rotation angle (degrees) 122.46009692
Shift along axis -113.08119373
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 5.82, angle = 5.72 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648914 -0.84382819 -0.01154928 402.25077995
0.84352286 -0.53660757 0.02283615 56.38489869
-0.02546722 0.00250926 0.99967251 -108.71256506
Axis -0.01204534 0.00824751 0.99989344
Axis point 184.73317849 138.71088501 0.00000000
Rotation angle (degrees) 122.46009692
Shift along axis -113.08119373
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 5.82, angle = 5.72 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648914 -0.84382819 -0.01154928 402.25077995
0.84352286 -0.53660757 0.02283615 56.38489869
-0.02546722 0.00250926 0.99967251 -108.71256506
Axis -0.01204534 0.00824751 0.99989344
Axis point 184.73317849 138.71088501 0.00000000
Rotation angle (degrees) 122.46009692
Shift along axis -113.08119373
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 5.82, angle = 5.72 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648914 -0.84382819 -0.01154928 402.25077995
0.84352286 -0.53660757 0.02283615 56.38489869
-0.02546722 0.00250926 0.99967251 -108.71256506
Axis -0.01204534 0.00824751 0.99989344
Axis point 184.73317849 138.71088501 0.00000000
Rotation angle (degrees) 122.46009692
Shift along axis -113.08119373
> view matrix models
> #24,-0.0884,-0.65051,-0.75434,501.02,0.86741,-0.42256,0.26275,178.21,-0.48967,-0.63109,0.60162,360.03,#26,0.30132,-0.92673,-0.22446,138.09,0.86261,0.16461,0.47834,269.97,-0.40634,-0.33775,0.84901,259.37,#27,0.75629,-0.39371,-0.52251,173.42,-0.20932,-0.90229,0.37691,300.6,-0.61985,-0.17568,-0.7648,283.44,#28,-0.10258,0.98998,-0.096996,224.77,0.61354,0.13972,0.7772,250.26,0.78297,0.020217,-0.62173,278.73,#29,0.20061,0.23256,0.95167,185.7,-0.46716,-0.83115,0.30158,364.16,0.86111,-0.50508,-0.058093,250.08,#30,0.76779,0.62289,-0.15001,188.99,-0.39471,0.27542,-0.87656,329.38,-0.50469,0.73222,0.45733,299.27,#31,0.25579,0.12213,-0.95899,84.082,0.68655,0.67544,0.26914,177.13,0.68061,-0.72723,0.08892,623.08,#32,0.11108,0.89015,-0.44191,102.46,0.014591,-0.44608,-0.89488,320.77,-0.9937,0.092959,-0.06254,228.07,#33,-0.44758,-0.25736,0.85641,158.98,0.54487,-0.83787,0.032978,333.44,0.70908,0.48139,0.51524,226.06,#34,0.16462,0.98517,0.048402,187.5,0.94275,-0.17159,0.28598,301.7,0.29004,-0.0014478,-0.95701,231,#35,-0.49523,-0.33427,0.80188,159.39,-0.78941,-0.21222,-0.57601,332.16,0.36272,-0.91827,-0.15878,225.56
> view matrix models
> #24,-0.10425,-0.66336,-0.741,504.21,0.87838,-0.41085,0.24422,177.51,-0.46645,-0.62542,0.62552,348.35,#26,0.28737,-0.93532,-0.20641,138.54,0.87369,0.16765,0.45669,269.69,-0.39254,-0.31157,0.86535,258.58,#27,0.74226,-0.39345,-0.54245,174.28,-0.19037,-0.89994,0.39226,299.92,-0.6425,-0.1879,-0.74289,282.53,#28,-0.086797,0.9895,-0.11557,225.75,0.59409,0.14453,0.79131,249.99,0.7997,2.684e-05,-0.6004,275.39,#29,0.22338,0.22442,0.94855,185.46,-0.48653,-0.81757,0.30801,364.33,0.84463,-0.53029,-0.073439,250.43,#30,0.7574,0.63888,-0.13482,190.08,-0.37839,0.26119,-0.88803,328.4,-0.53214,0.72361,0.43957,298.68,#31,0.26867,0.10146,-0.95787,93.681,0.67145,0.69328,0.26177,167.89,0.69063,-0.71349,0.11814,621.14,#32,0.087235,0.89426,-0.43897,101.92,0.038941,-0.44337,-0.89549,321.04,-0.99543,0.061025,-0.0735,229.37,#33,-0.43313,-0.24174,0.86831,158.31,0.52534,-0.85051,0.025262,334.05,0.7324,0.4671,0.49538,226.32,#34,0.16697,0.98567,0.024141,187.1,0.93642,-0.16619,0.30903,302.35,0.30861,-0.028992,-0.95075,229.82,#35,-0.48262,-0.3551,0.80062,158.72,-0.80052,-0.19201,-0.56772,332.78,0.35532,-0.9149,-0.19159,225.78
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.10425,-0.66336,-0.741,503.09,0.87838,-0.41085,0.24422,177.35,-0.46645,-0.62542,0.62552,349.53,#26,0.28737,-0.93532,-0.20641,137.42,0.87369,0.16765,0.45669,269.53,-0.39254,-0.31157,0.86535,259.76,#27,0.74226,-0.39345,-0.54245,173.16,-0.19037,-0.89994,0.39226,299.76,-0.6425,-0.1879,-0.74289,283.71,#28,-0.086797,0.9895,-0.11557,224.63,0.59409,0.14453,0.79131,249.83,0.7997,2.684e-05,-0.6004,276.57,#29,0.22338,0.22442,0.94855,184.33,-0.48653,-0.81757,0.30801,364.17,0.84463,-0.53029,-0.073439,251.61,#30,0.7574,0.63888,-0.13482,188.96,-0.37839,0.26119,-0.88803,328.24,-0.53214,0.72361,0.43957,299.86,#31,0.26867,0.10146,-0.95787,92.56,0.67145,0.69328,0.26177,167.73,0.69063,-0.71349,0.11814,622.32,#32,0.087235,0.89426,-0.43897,100.8,0.038941,-0.44337,-0.89549,320.88,-0.99543,0.061025,-0.0735,230.55,#33,-0.43313,-0.24174,0.86831,157.19,0.52534,-0.85051,0.025262,333.9,0.7324,0.4671,0.49538,227.5,#34,0.16697,0.98567,0.024141,185.98,0.93642,-0.16619,0.30903,302.19,0.30861,-0.028992,-0.95075,231,#35,-0.48262,-0.3551,0.80062,157.6,-0.80052,-0.19201,-0.56772,332.62,0.35532,-0.9149,-0.19159,226.96
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.348, overlap = 18.84
steps = 68, shift = 5.69, angle = 3.52 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53640743 -0.84387973 -0.01157876 402.25402221
0.84357694 -0.53652689 0.02273415 56.39638517
-0.02539720 0.00242719 0.99967449 -108.72602321
Axis -0.01203279 0.00818805 0.99989408
Axis point 184.73226063 138.72732910 0.00000000
Rotation angle (degrees) 122.45451567
Shift along axis -113.09296706
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.348, overlap = 18.84
steps = 68, shift = 5.69, angle = 3.52 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53640743 -0.84387973 -0.01157876 402.25402221
0.84357694 -0.53652689 0.02273415 56.39638517
-0.02539720 0.00242719 0.99967449 -108.72602321
Axis -0.01203279 0.00818805 0.99989408
Axis point 184.73226063 138.72732910 0.00000000
Rotation angle (degrees) 122.45451567
Shift along axis -113.09296706
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.348, overlap = 18.84
steps = 68, shift = 5.69, angle = 3.52 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53640743 -0.84387973 -0.01157876 402.25402221
0.84357694 -0.53652689 0.02273415 56.39638517
-0.02539720 0.00242719 0.99967449 -108.72602321
Axis -0.01203279 0.00818805 0.99989408
Axis point 184.73226063 138.72732910 0.00000000
Rotation angle (degrees) 122.45451567
Shift along axis -113.09296706
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.348, overlap = 18.84
steps = 68, shift = 5.69, angle = 3.52 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53640743 -0.84387973 -0.01157876 402.25402221
0.84357694 -0.53652689 0.02273415 56.39638517
-0.02539720 0.00242719 0.99967449 -108.72602321
Axis -0.01203279 0.00818805 0.99989408
Axis point 184.73226063 138.72732910 0.00000000
Rotation angle (degrees) 122.45451567
Shift along axis -113.09296706
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.348, overlap = 18.84
steps = 68, shift = 5.69, angle = 3.52 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53640743 -0.84387973 -0.01157876 402.25402221
0.84357694 -0.53652689 0.02273415 56.39638517
-0.02539720 0.00242719 0.99967449 -108.72602321
Axis -0.01203279 0.00818805 0.99989408
Axis point 184.73226063 138.72732910 0.00000000
Rotation angle (degrees) 122.45451567
Shift along axis -113.09296706
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.348, overlap = 18.84
steps = 68, shift = 5.69, angle = 3.52 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53640743 -0.84387973 -0.01157876 402.25402221
0.84357694 -0.53652689 0.02273415 56.39638517
-0.02539720 0.00242719 0.99967449 -108.72602321
Axis -0.01203279 0.00818805 0.99989408
Axis point 184.73226063 138.72732910 0.00000000
Rotation angle (degrees) 122.45451567
Shift along axis -113.09296706
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.091059,-0.67112,-0.73573,500.47,0.87121,-0.41156,0.2676,173.94,-0.48239,-0.61661,0.62217,352.14,#26,0.30058,-0.93312,-0.19732,136.15,0.86157,0.17692,0.47581,270.33,-0.40908,-0.31302,0.85713,261.31,#27,0.73782,-0.40823,-0.53756,172.42,-0.21409,-0.8968,0.3872,300.41,-0.64014,-0.1706,-0.74907,284.63,#28,-0.075647,0.99169,-0.10404,223.06,0.61003,0.12856,0.78188,249.53,0.78876,-0.0043199,-0.61469,278.33,#29,0.21722,0.2102,0.95322,184.57,-0.47442,-0.8307,0.29129,364.03,0.85308,-0.51551,-0.080719,251.32,#30,0.75016,0.64444,-0.14819,188.71,-0.40026,0.26415,-0.8775,328.93,-0.52635,0.71758,0.4561,300.23,#31,0.2808,0.11116,-0.95331,90.388,0.67964,0.6783,0.27928,175.96,0.67767,-0.72633,0.11492,625.75,#32,0.085863,0.88714,-0.45344,100.3,0.019196,-0.45651,-0.88951,321.71,-0.99612,0.067671,-0.056227,231.21,#33,-0.42317,-0.25444,0.86959,156.89,0.54564,-0.83777,0.020399,333.76,0.72333,0.48312,0.49335,227.82,#34,0.1826,0.98281,0.027205,185.17,0.93913,-0.18254,0.29104,301.67,0.29101,-0.027596,-0.95632,231.86,#35,-0.49471,-0.35996,0.79101,157.28,-0.78597,-0.20308,-0.58397,332.47,0.37084,-0.9106,-0.18245,227.31
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.091059,-0.67112,-0.73573,497.46,0.87121,-0.41156,0.2676,171.48,-0.48239,-0.61661,0.62217,352.28,#26,0.30058,-0.93312,-0.19732,133.14,0.86157,0.17692,0.47581,267.87,-0.40908,-0.31302,0.85713,261.45,#27,0.73782,-0.40823,-0.53756,169.41,-0.21409,-0.8968,0.3872,297.95,-0.64014,-0.1706,-0.74907,284.77,#28,-0.075647,0.99169,-0.10404,220.05,0.61003,0.12856,0.78188,247.07,0.78876,-0.0043199,-0.61469,278.47,#29,0.21722,0.2102,0.95322,181.56,-0.47442,-0.8307,0.29129,361.57,0.85308,-0.51551,-0.080719,251.47,#30,0.75016,0.64444,-0.14819,185.7,-0.40026,0.26415,-0.8775,326.47,-0.52635,0.71758,0.4561,300.37,#31,0.2808,0.11116,-0.95331,87.378,0.67964,0.6783,0.27928,173.5,0.67767,-0.72633,0.11492,625.89,#32,0.085863,0.88714,-0.45344,97.292,0.019196,-0.45651,-0.88951,319.25,-0.99612,0.067671,-0.056227,231.35,#33,-0.42317,-0.25444,0.86959,153.88,0.54564,-0.83777,0.020399,331.3,0.72333,0.48312,0.49335,227.97,#34,0.1826,0.98281,0.027205,182.16,0.93913,-0.18254,0.29104,299.21,0.29101,-0.027596,-0.95632,232,#35,-0.49471,-0.35996,0.79101,154.27,-0.78597,-0.20308,-0.58397,330.01,0.37084,-0.9106,-0.18245,227.45
> view matrix models
> #24,-0.091059,-0.67112,-0.73573,499.84,0.87121,-0.41156,0.2676,169.35,-0.48239,-0.61661,0.62217,356.4,#26,0.30058,-0.93312,-0.19732,135.52,0.86157,0.17692,0.47581,265.74,-0.40908,-0.31302,0.85713,265.57,#27,0.73782,-0.40823,-0.53756,171.79,-0.21409,-0.8968,0.3872,295.83,-0.64014,-0.1706,-0.74907,288.9,#28,-0.075647,0.99169,-0.10404,222.44,0.61003,0.12856,0.78188,244.95,0.78876,-0.0043199,-0.61469,282.59,#29,0.21722,0.2102,0.95322,183.94,-0.47442,-0.8307,0.29129,359.45,0.85308,-0.51551,-0.080719,255.59,#30,0.75016,0.64444,-0.14819,188.08,-0.40026,0.26415,-0.8775,324.34,-0.52635,0.71758,0.4561,304.49,#31,0.2808,0.11116,-0.95331,89.759,0.67964,0.6783,0.27928,171.37,0.67767,-0.72633,0.11492,630.02,#32,0.085863,0.88714,-0.45344,99.673,0.019196,-0.45651,-0.88951,317.12,-0.99612,0.067671,-0.056227,235.47,#33,-0.42317,-0.25444,0.86959,156.27,0.54564,-0.83777,0.020399,329.17,0.72333,0.48312,0.49335,232.09,#34,0.1826,0.98281,0.027205,184.54,0.93913,-0.18254,0.29104,297.08,0.29101,-0.027596,-0.95632,236.13,#35,-0.49471,-0.35996,0.79101,156.65,-0.78597,-0.20308,-0.58397,327.88,0.37084,-0.9106,-0.18245,231.58
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 76, shift = 11.3, angle = 4.11 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53642473 -0.84386935 -0.01153372 402.24113850
0.84356452 -0.53654284 0.02281861 56.37220675
-0.02544426 0.00251103 0.99967309 -108.72124741
Axis -0.01203331 0.00824273 0.99989362
Axis point 184.73115305 138.71203519 0.00000000
Rotation angle (degrees) 122.45569249
Shift along axis -113.08531389
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 76, shift = 11.3, angle = 4.11 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53642473 -0.84386935 -0.01153372 402.24113850
0.84356452 -0.53654284 0.02281861 56.37220675
-0.02544426 0.00251103 0.99967309 -108.72124741
Axis -0.01203331 0.00824273 0.99989362
Axis point 184.73115305 138.71203519 0.00000000
Rotation angle (degrees) 122.45569249
Shift along axis -113.08531389
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 40, shift = 0.011, angle = 0.00596 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53649562 -0.84382413 -0.01154465 402.25064108
0.84351775 -0.53661382 0.02287794 56.37426930
-0.02549998 0.00253580 0.99967160 -108.70923302
Axis -0.01205444 0.00826972 0.99989315
Axis point 184.73501117 138.70542498 0.00000000
Rotation angle (degrees) 122.46055944
Shift along axis -113.08032579
> view matrix models
> #24,-0.091059,-0.67112,-0.73573,498.55,0.87121,-0.41156,0.2676,170.34,-0.48239,-0.61661,0.62217,354.34,#26,0.30058,-0.93312,-0.19732,134.23,0.86157,0.17692,0.47581,266.73,-0.40908,-0.31302,0.85713,263.51,#27,0.73782,-0.40823,-0.53756,170.51,-0.21409,-0.8968,0.3872,296.82,-0.64014,-0.1706,-0.74907,286.83,#28,-0.075647,0.99169,-0.10404,221.15,0.61003,0.12856,0.78188,245.94,0.78876,-0.0043199,-0.61469,280.53,#29,0.21722,0.2102,0.95322,182.65,-0.47442,-0.8307,0.29129,360.44,0.85308,-0.51551,-0.080719,253.52,#30,0.75016,0.64444,-0.14819,186.79,-0.40026,0.26415,-0.8775,325.33,-0.52635,0.71758,0.4561,302.43,#31,0.2808,0.11116,-0.95331,88.471,0.67964,0.6783,0.27928,172.36,0.67767,-0.72633,0.11492,627.95,#32,0.085863,0.88714,-0.45344,98.385,0.019196,-0.45651,-0.88951,318.11,-0.99612,0.067671,-0.056227,233.41,#33,-0.42317,-0.25444,0.86959,154.98,0.54564,-0.83777,0.020399,330.16,0.72333,0.48312,0.49335,230.02,#34,0.1826,0.98281,0.027205,183.25,0.93913,-0.18254,0.29104,298.07,0.29101,-0.027596,-0.95632,234.06,#35,-0.49471,-0.35996,0.79101,155.36,-0.78597,-0.20308,-0.58397,328.87,0.37084,-0.9106,-0.18245,229.51
> view matrix models
> #24,-0.091059,-0.67112,-0.73573,496.48,0.87121,-0.41156,0.2676,170.21,-0.48239,-0.61661,0.62217,352.81,#26,0.30058,-0.93312,-0.19732,132.16,0.86157,0.17692,0.47581,266.6,-0.40908,-0.31302,0.85713,261.98,#27,0.73782,-0.40823,-0.53756,168.43,-0.21409,-0.8968,0.3872,296.69,-0.64014,-0.1706,-0.74907,285.3,#28,-0.075647,0.99169,-0.10404,219.08,0.61003,0.12856,0.78188,245.81,0.78876,-0.0043199,-0.61469,279,#29,0.21722,0.2102,0.95322,180.58,-0.47442,-0.8307,0.29129,360.31,0.85308,-0.51551,-0.080719,251.99,#30,0.75016,0.64444,-0.14819,184.72,-0.40026,0.26415,-0.8775,325.2,-0.52635,0.71758,0.4561,300.89,#31,0.2808,0.11116,-0.95331,86.398,0.67964,0.6783,0.27928,172.23,0.67767,-0.72633,0.11492,626.42,#32,0.085863,0.88714,-0.45344,96.313,0.019196,-0.45651,-0.88951,317.98,-0.99612,0.067671,-0.056227,231.88,#33,-0.42317,-0.25444,0.86959,152.9,0.54564,-0.83777,0.020399,330.03,0.72333,0.48312,0.49335,228.49,#34,0.1826,0.98281,0.027205,181.18,0.93913,-0.18254,0.29104,297.94,0.29101,-0.027596,-0.95632,232.53,#35,-0.49471,-0.35996,0.79101,153.29,-0.78597,-0.20308,-0.58397,328.75,0.37084,-0.9106,-0.18245,227.98
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.096153,-0.71647,-0.69095,496.71,0.87125,-0.39627,0.28966,162.28,-0.48134,-0.57414,0.66233,335.25,#26,0.2987,-0.94482,-0.13449,130.36,0.85155,0.20024,0.48453,267.91,-0.43086,-0.25926,0.86437,265.2,#27,0.6934,-0.44084,-0.56996,168.71,-0.2363,-0.88638,0.3981,297.12,-0.68071,-0.14136,-0.71879,286.2,#28,-0.013536,0.99278,-0.11916,217.55,0.61519,0.10221,0.78172,244.89,0.78826,-0.062724,-0.61214,277.26,#29,0.25406,0.15796,0.9542,180.55,-0.47636,-0.83818,0.26558,360.25,0.84175,-0.52202,-0.1377,251.87,#30,0.70746,0.69186,-0.1443,186.62,-0.42225,0.25005,-0.87131,325.26,-0.56674,0.67735,0.46904,300.65,#31,0.33753,0.086382,-0.93734,103.46,0.67485,0.672,0.30494,176.34,0.65624,-0.73549,0.16853,632.23,#32,0.028137,0.87731,-0.4791,94.182,0.012652,-0.47957,-0.87741,320.09,-0.99952,0.018626,-0.024593,236.94,#33,-0.36585,-0.24772,0.8971,150.78,0.55976,-0.82866,-0.0005438,330.62,0.74352,0.50196,0.44183,230.2,#34,0.2238,0.97441,-0.020957,178.39,0.9352,-0.20864,0.28613,297.81,0.27443,-0.083635,-0.95796,232.77,#35,-0.49268,-0.41762,0.76345,151.1,-0.77098,-0.19736,-0.6055,329.32,0.40354,-0.88693,-0.22474,229.67
> view matrix models
> #24,-0.070397,-0.68065,-0.72922,492.25,0.83661,-0.43842,0.32845,169.89,-0.54326,-0.58695,0.6003,365.56,#26,0.3209,-0.92866,-0.18604,130.31,0.82297,0.17618,0.54007,268.15,-0.46877,-0.32642,0.8208,267.47,#27,0.73258,-0.42933,-0.52821,167.29,-0.27642,-0.89677,0.34553,298.95,-0.62203,-0.10712,-0.77563,288.66,#28,-0.061227,0.99446,-0.08548,216.71,0.66619,0.10449,0.73843,246.57,0.74326,-0.011735,-0.6689,286.08,#29,0.20589,0.19051,0.95985,180.93,-0.41756,-0.86999,0.26224,359.74,0.88502,-0.45478,-0.099575,250.94,#30,0.7405,0.65047,-0.16893,184.25,-0.45427,0.29923,-0.83911,328.11,-0.49527,0.6981,0.51707,302.22,#31,0.29677,0.12721,-0.94644,82.315,0.71929,0.62212,0.30917,201.04,0.62813,-0.77252,0.093124,637.62,#32,0.086338,0.87609,-0.47436,95.694,-0.053717,-0.47135,-0.88031,318.09,-0.99482,0.10149,0.0063652,233.74,#33,-0.41017,-0.27421,0.86981,152.56,0.60553,-0.79506,0.034902,328.53,0.68197,0.54101,0.49216,229.6,#34,0.20476,0.97822,0.034127,180.06,0.95288,-0.20719,0.22158,296.15,0.22382,-0.012852,-0.97454,235.96,#35,-0.51318,-0.36462,0.77698,152.91,-0.74571,-0.25877,-0.61397,327.2,0.42492,-0.89448,-0.13911,229.18
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 96, shift = 8.58, angle = 6.65 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648617 -0.84383021 -0.01153978 402.25143206
0.84352386 -0.53660426 0.02287710 56.36820755
-0.02549668 0.00253916 0.99967168 -108.70823429
Axis -0.01205186 0.00827059 0.99989317
Axis point 184.73698445 138.70421395 0.00000000
Rotation angle (degrees) 122.45991149
Shift along axis -113.07830171
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 96, shift = 8.58, angle = 6.65 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648617 -0.84383021 -0.01153978 402.25143206
0.84352386 -0.53660426 0.02287710 56.36820755
-0.02549668 0.00253916 0.99967168 -108.70823429
Axis -0.01205186 0.00827059 0.99989317
Axis point 184.73698445 138.70421395 0.00000000
Rotation angle (degrees) 122.45991149
Shift along axis -113.07830171
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 96, shift = 8.58, angle = 6.65 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648617 -0.84383021 -0.01153978 402.25143206
0.84352386 -0.53660426 0.02287710 56.36820755
-0.02549668 0.00253916 0.99967168 -108.70823429
Axis -0.01205186 0.00827059 0.99989317
Axis point 184.73698445 138.70421395 0.00000000
Rotation angle (degrees) 122.45991149
Shift along axis -113.07830171
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.070397,-0.68065,-0.72922,494.95,0.83661,-0.43842,0.32845,171.78,-0.54326,-0.58695,0.6003,363.73,#26,0.3209,-0.92866,-0.18604,133.01,0.82297,0.17618,0.54007,270.03,-0.46877,-0.32642,0.8208,265.65,#27,0.73258,-0.42933,-0.52821,169.99,-0.27642,-0.89677,0.34553,300.84,-0.62203,-0.10712,-0.77563,286.84,#28,-0.061227,0.99446,-0.08548,219.41,0.66619,0.10449,0.73843,248.46,0.74326,-0.011735,-0.6689,284.25,#29,0.20589,0.19051,0.95985,183.63,-0.41756,-0.86999,0.26224,361.62,0.88502,-0.45478,-0.099575,249.12,#30,0.7405,0.65047,-0.16893,186.95,-0.45427,0.29923,-0.83911,330,-0.49527,0.6981,0.51707,300.4,#31,0.29677,0.12721,-0.94644,85.014,0.71929,0.62212,0.30917,202.92,0.62813,-0.77252,0.093124,635.8,#32,0.086338,0.87609,-0.47436,98.392,-0.053717,-0.47135,-0.88031,319.97,-0.99482,0.10149,0.0063652,231.91,#33,-0.41017,-0.27421,0.86981,155.25,0.60553,-0.79506,0.034902,330.41,0.68197,0.54101,0.49216,227.78,#34,0.20476,0.97822,0.034127,182.76,0.95288,-0.20719,0.22158,298.03,0.22382,-0.012852,-0.97454,234.13,#35,-0.51318,-0.36462,0.77698,155.61,-0.74571,-0.25877,-0.61397,329.09,0.42492,-0.89448,-0.13911,227.36
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 76, shift = 6.22, angle = 6.65 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648729 -0.84382948 -0.01154084 402.25291912
0.84352337 -0.53660543 0.02286769 56.36357459
-0.02548931 0.00253326 0.99967188 -108.70723034
Axis -0.01204980 0.00826560 0.99989324
Axis point 184.73930075 138.70193089 0.00000000
Rotation angle (degrees) 122.45998234
Shift along axis -113.07681168
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 76, shift = 6.22, angle = 6.65 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648729 -0.84382948 -0.01154084 402.25291912
0.84352337 -0.53660543 0.02286769 56.36357459
-0.02548931 0.00253326 0.99967188 -108.70723034
Axis -0.01204980 0.00826560 0.99989324
Axis point 184.73930075 138.70193089 0.00000000
Rotation angle (degrees) 122.45998234
Shift along axis -113.07681168
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 76, shift = 6.22, angle = 6.65 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53648729 -0.84382948 -0.01154084 402.25291912
0.84352337 -0.53660543 0.02286769 56.36357459
-0.02548931 0.00253326 0.99967188 -108.70723034
Axis -0.01204980 0.00826560 0.99989324
Axis point 184.73930075 138.70193089 0.00000000
Rotation angle (degrees) 122.45998234
Shift along axis -113.07681168
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.091446,-0.64225,-0.76102,499.15,0.83912,-0.4612,0.28839,184.6,-0.5362,-0.61222,0.5811,371.4,#26,0.29764,-0.92536,-0.23479,136.29,0.84203,0.13856,0.52133,267.81,-0.44988,-0.35287,0.82042,263.3,#27,0.76269,-0.38521,-0.51953,171.19,-0.236,-0.91365,0.33098,299.97,-0.60217,-0.12982,-0.78774,285.95,#28,-0.11348,0.98866,-0.098307,222.97,0.6538,0.14881,0.74189,249.88,0.74811,0.019914,-0.66328,284.32,#29,0.19762,0.24301,0.94968,183.23,-0.4186,-0.8551,0.30591,361.76,0.88641,-0.45799,-0.067257,249.31,#30,0.77476,0.61502,-0.14663,186.4,-0.41484,0.31947,-0.85197,329.69,-0.47713,0.7209,0.50265,300.33,#31,0.24509,0.12242,-0.96174,80.201,0.72418,0.63643,0.26556,194.17,0.64459,-0.76156,0.067324,631.07,#32,0.11865,0.8929,-0.43434,100.5,-0.037833,-0.43305,-0.90058,316.56,-0.99221,0.12329,-0.017602,229.06,#33,-0.45734,-0.25446,0.85211,156.93,0.5784,-0.81294,0.067679,329.57,0.67549,0.52382,0.51897,226.78,#34,0.15493,0.98647,0.053551,185.66,0.95829,-0.16324,0.2346,298.38,0.24017,0.01497,-0.97062,233.63,#35,-0.49178,-0.32547,0.8076,157.36,-0.77289,-0.26396,-0.57703,328.27,0.40098,-0.90796,-0.12174,226.36
> view matrix models
> #24,-0.09818,-0.66023,-0.74461,500.6,0.82524,-0.47218,0.30986,185.16,-0.55618,-0.58407,0.59121,368.1,#26,0.29289,-0.93256,-0.21106,135.87,0.82733,0.13652,0.54487,268.37,-0.47931,-0.3342,0.81152,266.53,#27,0.74617,-0.39496,-0.53595,171.54,-0.25807,-0.91367,0.31402,300.84,-0.61371,-0.096,-0.78368,287.46,#28,-0.090553,0.98993,-0.10883,222.89,0.67439,0.14136,0.72471,250.31,0.7328,-0.0077665,-0.6804,285.94,#29,0.21588,0.22557,0.95001,183.14,-0.3964,-0.86892,0.29639,361.53,0.89234,-0.44057,-0.098163,248.9,#30,0.75993,0.63459,-0.14072,187.31,-0.4336,0.33363,-0.83707,330.81,-0.48424,0.69713,0.52869,300.67,#31,0.26592,0.10868,-0.95785,88.133,0.73911,0.61491,0.27496,205.01,0.61887,-0.78107,0.083185,637.38,#32,0.094374,0.8924,-0.44127,99.617,-0.065209,-0.43675,-0.89722,316.48,-0.9934,0.11345,0.016975,231.86,#33,-0.43662,-0.24772,0.86487,156.07,0.59985,-0.79663,0.074651,328.97,0.67049,0.55138,0.49641,227.88,#34,0.16775,0.98532,0.031821,184.73,0.96307,-0.17069,0.20822,297.74,0.21059,-0.0042819,-0.97756,234.88,#35,-0.48764,-0.34924,0.80015,156.48,-0.75797,-0.28544,-0.58652,327.65,0.43324,-0.8925,-0.12552,227.48
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 6.48, angle = 5.9 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53645385 -0.84385081 -0.01153598 402.23915451
0.84354606 -0.53657201 0.02281500 56.39401907
-0.02544234 0.00250807 0.99967314 -108.72739308
Axis -0.01203319 0.00824044 0.99989364
Axis point 184.72484270 138.71777738 0.00000000
Rotation angle (degrees) 122.45766945
Shift along axis -113.09133960
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 84, shift = 6.48, angle = 5.9 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53645385 -0.84385081 -0.01153598 402.23915451
0.84354606 -0.53657201 0.02281500 56.39401907
-0.02544234 0.00250807 0.99967314 -108.72739308
Axis -0.01203319 0.00824044 0.99989364
Axis point 184.72484270 138.71777738 0.00000000
Rotation angle (degrees) 122.45766945
Shift along axis -113.09133960
> view matrix models
> #24,-0.11173,-0.63008,-0.76845,502.97,0.82758,-0.48708,0.27904,194.41,-0.55011,-0.60478,0.57586,374.23,#26,0.27709,-0.92819,-0.24837,138.26,0.84157,0.1097,0.52889,266.8,-0.46367,-0.35557,0.81153,264.6,#27,0.76885,-0.36234,-0.52687,172.33,-0.22698,-0.92495,0.30487,300.19,-0.59779,-0.11481,-0.79339,286.72,#28,-0.13032,0.98466,-0.11607,225.34,0.66312,0.17359,0.72811,251.38,0.73708,0.01792,-0.67556,285.95,#29,0.20713,0.26454,0.94187,182.87,-0.3988,-0.85629,0.32821,361.63,0.89334,-0.4436,-0.071869,249.07,#30,0.78523,0.60626,-0.12592,186.8,-0.40337,0.34654,-0.84688,330.51,-0.46979,0.71579,0.51666,300.61,#31,0.22649,0.1073,-0.96809,83.686,0.74063,0.62654,0.24272,197.91,0.63259,-0.77197,0.062434,633.51,#32,0.12045,0.90325,-0.41187,101.3,-0.051345,-0.40867,-0.91124,314.07,-0.99139,0.1309,-0.0028462,229.53,#33,-0.47214,-0.2347,0.8497,157.4,0.57802,-0.81019,0.09739,328.44,0.66556,0.53713,0.51819,227.06,#34,0.13092,0.9902,0.048593,186.89,0.96569,-0.13846,0.21971,298.08,0.22429,0.018161,-0.97435,234.44,#35,-0.47284,-0.31802,0.82176,157.86,-0.77808,-0.28698,-0.55877,327.14,0.41353,-0.90361,-0.11175,226.66
> view matrix models
> #24,-0.10334,-0.67936,-0.7265,501.55,0.82094,-0.47065,0.32334,182.85,-0.56159,-0.56299,0.60635,361.79,#26,0.28951,-0.93908,-0.18524,135.29,0.8196,0.14325,0.55474,268.96,-0.49441,-0.31242,0.81114,268.44,#27,0.72803,-0.40668,-0.55189,171.81,-0.27178,-0.91029,0.31226,301.25,-0.62937,-0.077342,-0.77324,288.17,#28,-0.065378,0.99085,-0.1181,222.58,0.68223,0.13076,0.71935,250.17,0.72821,-0.03354,-0.68453,285.88,#29,0.23377,0.20556,0.95032,183.08,-0.3902,-0.8754,0.28534,361.44,0.89056,-0.43752,-0.12443,248.75,#30,0.74317,0.65508,-0.13628,188.22,-0.44622,0.33345,-0.83048,331.18,-0.49859,0.678,0.54012,300.7,#31,0.28881,0.095699,-0.95259,96.099,0.74207,0.6063,0.2859,209.63,0.60491,-0.78946,0.10409,640.95,#32,0.069075,0.89035,-0.45001,98.699,-0.075612,-0.44511,-0.89228,317.12,-0.99474,0.09566,0.036575,234.21,#33,-0.41363,-0.24226,0.87762,155.17,0.61077,-0.78869,0.070156,328.98,0.67518,0.56505,0.47419,228.72,#34,0.1829,0.98308,0.0097771,183.66,0.96319,-0.18118,0.1986,297.51,0.19701,-0.026908,-0.98003,235.31,#35,-0.48462,-0.37417,0.79066,155.55,-0.74861,-0.29015,-0.59615,327.65,0.45248,-0.8808,-0.13949,228.33
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.10334,-0.67936,-0.7265,500.14,0.82094,-0.47065,0.32334,184.27,-0.56159,-0.56299,0.60635,360.94,#26,0.28951,-0.93908,-0.18524,133.88,0.8196,0.14325,0.55474,270.39,-0.49441,-0.31242,0.81114,267.59,#27,0.72803,-0.40668,-0.55189,170.4,-0.27178,-0.91029,0.31226,302.68,-0.62937,-0.077342,-0.77324,287.32,#28,-0.065378,0.99085,-0.1181,221.17,0.68223,0.13076,0.71935,251.59,0.72821,-0.03354,-0.68453,285.02,#29,0.23377,0.20556,0.95032,181.67,-0.3902,-0.8754,0.28534,362.87,0.89056,-0.43752,-0.12443,247.9,#30,0.74317,0.65508,-0.13628,186.81,-0.44622,0.33345,-0.83048,332.6,-0.49859,0.678,0.54012,299.84,#31,0.28881,0.095699,-0.95259,94.688,0.74207,0.6063,0.2859,211.06,0.60491,-0.78946,0.10409,640.1,#32,0.069075,0.89035,-0.45001,97.288,-0.075612,-0.44511,-0.89228,318.55,-0.99474,0.09566,0.036575,233.35,#33,-0.41363,-0.24226,0.87762,153.76,0.61077,-0.78869,0.070156,330.4,0.67518,0.56505,0.47419,227.87,#34,0.1829,0.98308,0.0097771,182.25,0.96319,-0.18118,0.1986,298.93,0.19701,-0.026908,-0.98003,234.46,#35,-0.48462,-0.37417,0.79066,154.14,-0.74861,-0.29015,-0.59615,329.07,0.45248,-0.8808,-0.13949,227.47
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 92, shift = 4.58, angle = 6.41 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650463 -0.84381837 -0.01154683 402.25242935
0.84351198 -0.53662289 0.02287816 56.37440069
-0.02550131 0.00253435 0.99967157 -108.70723273
Axis -0.01205551 0.00826927 0.99989314
Axis point 184.73604051 138.70452221 0.00000000
Rotation angle (degrees) 122.46117420
Shift along axis -113.07880045
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 92, shift = 4.58, angle = 6.41 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650463 -0.84381837 -0.01154683 402.25242935
0.84351198 -0.53662289 0.02287816 56.37440069
-0.02550131 0.00253435 0.99967157 -108.70723273
Axis -0.01205551 0.00826927 0.99989314
Axis point 184.73604051 138.70452221 0.00000000
Rotation angle (degrees) 122.46117420
Shift along axis -113.07880045
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 28339
points
correlation = 0.6996, correlation about mean = 0.3479, overlap = 18.84
steps = 92, shift = 4.58, angle = 6.41 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53650463 -0.84381837 -0.01154683 402.25242935
0.84351198 -0.53662289 0.02287816 56.37440069
-0.02550131 0.00253435 0.99967157 -108.70723273
Axis -0.01205551 0.00826927 0.99989314
Axis point 184.73604051 138.70452221 0.00000000
Rotation angle (degrees) 122.46117420
Shift along axis -113.07880045
> select subtract #35
39361 atoms, 40096 bonds, 1 pseudobond, 4960 residues, 12 models selected
> select subtract #34
36994 atoms, 37698 bonds, 1 pseudobond, 4662 residues, 11 models selected
> select subtract #33
35574 atoms, 36257 bonds, 1 pseudobond, 4485 residues, 10 models selected
> select subtract #32
28901 atoms, 29471 bonds, 3632 residues, 8 models selected
> select subtract #31
27439 atoms, 27990 bonds, 3453 residues, 7 models selected
> select subtract #30
20225 atoms, 20617 bonds, 2548 residues, 6 models selected
> select subtract #29
18768 atoms, 19134 bonds, 2367 residues, 5 models selected
> select subtract #28
17311 atoms, 17651 bonds, 2186 residues, 4 models selected
> select subtract #27
9810 atoms, 10032 bonds, 1233 residues, 3 models selected
> select subtract #26
2 models selected
> hide #!25 models
> select subtract #24
Nothing selected
> show #26 models
> fitmap #26 inMap #24
Fit molecule copy of CopA_F8WHL2.pdb (#26) to map postprocess_20231221.mrc
(#24) using 9810 atoms
average map value = 0.001845, steps = 116
shifted from previous position = 16.4
rotated from previous position = 4.06 degrees
atoms outside contour = 7851, contour level = 0.0032978
Position of copy of CopA_F8WHL2.pdb (#26) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.89996653 0.40445765 0.16270906 162.22736905
-0.20995376 0.72918744 -0.65131028 244.63095239
-0.38207283 0.55199608 0.74116170 239.12828538
Axis 0.82599894 0.37396068 -0.42175724
Axis point 0.00000000 -322.90335119 438.30306870
Rotation angle (degrees) 46.75197840
Shift along axis 124.62790578
> hide #26 models
> show #27 models
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002923, steps = 132
shifted from previous position = 5.04
rotated from previous position = 5.54 degrees
atoms outside contour = 5216, contour level = 0.0032978
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.04204995 -0.73306615 0.67885625 172.36139873
-0.03865825 0.68014219 0.73206020 204.57555030
-0.99836734 0.00453970 -0.05693900 236.22075458
Axis -0.37200954 0.85762968 0.35507778
Axis point 209.22295306 0.00000000 -39.71296119
Rotation angle (degrees) 102.08856313
Shift along axis 195.20672158
> select add #27
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> view matrix models
> #27,0.77002,-0.33054,-0.54573,169.9,-0.2377,-0.94238,0.23541,304.33,-0.59209,-0.051551,-0.80422,284.85
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002923, steps = 76
shifted from previous position = 4.69
rotated from previous position = 0.0487 degrees
atoms outside contour = 5211, contour level = 0.0032978
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.04153062 -0.73285289 0.67911843 172.37785500
-0.03806305 0.68037194 0.73187788 204.57714323
-0.99841194 0.00454602 -0.05615089 236.24348469
Axis -0.37185060 0.85764245 0.35521340
Axis point 209.26127593 0.00000000 -39.81318725
Rotation angle (degrees) 102.04353100
Shift along axis 195.27208462
> view matrix models
> #27,0.76958,-0.33073,-0.54623,170.89,-0.23753,-0.9423,0.23589,303.26,-0.59273,-0.051788,-0.80373,284.04
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.7306,-0.42488,-0.53451,171.25,-0.27862,-0.90018,0.33472,302.78,-0.62337,-0.095623,-0.77606,284.13
> view matrix models
> #27,0.76175,-0.3737,-0.52923,170.94,-0.17385,-0.90482,0.38868,301.97,-0.62411,-0.20407,-0.75422,284.28
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002633, steps = 44
shifted from previous position = 3.61
rotated from previous position = 3.9 degrees
atoms outside contour = 5376, contour level = 0.0032978
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.05431385 -0.66256715 0.74703064 172.62333642
-0.01180746 0.74765647 0.66398071 209.75331516
-0.99845410 -0.04488388 0.03278487 233.19327392
Axis -0.35564828 0.87573658 0.32649616
Axis point 217.41288898 0.00000000 -50.32061187
Rotation angle (degrees) 94.73931746
Shift along axis 198.43216601
> view matrix models
> #27,0.79432,-0.34789,-0.49803,172.17,-0.172,-0.91504,0.36487,302.85,-0.58265,-0.20416,-0.78666,281.24
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.79432,-0.34789,-0.49803,175.55,-0.172,-0.91504,0.36487,308.21,-0.58265,-0.20416,-0.78666,283.6
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002923, steps = 112
shifted from previous position = 4.6
rotated from previous position = 8.94 degrees
atoms outside contour = 5214, contour level = 0.0032978
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.04165939 -0.73303937 0.67890925 172.36144600
-0.03865688 0.68017292 0.73203172 204.56515197
-0.99838376 0.00425148 -0.05667260 236.23504293
Axis -0.37211436 0.85760065 0.35503807
Axis point 209.28231383 0.00000000 -39.74893852
Rotation angle (degrees) 102.06841613
Shift along axis 195.16947240
> select subtract #27
Nothing selected
> hide #27 models
> show #28 models
> fitmap #28 inMap #24
Fit molecule copy of hArf1_P84078 (#28) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.002588, steps = 88
shifted from previous position = 12.8
rotated from previous position = 6.38 degrees
atoms outside contour = 1281, contour level = 0.0032978
Position of copy of hArf1_P84078 (#28) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.15847948 0.02339073 0.98708516 126.69876215
-0.68653702 -0.71588385 0.12718971 200.56846102
0.70961339 -0.69782747 -0.09739430 178.43391214
Axis -0.73450547 0.24703066 -0.63204237
Axis point 0.00000000 138.25364345 -15.33318730
Rotation angle (degrees) 145.83250639
Shift along axis -156.29216940
> hide #28 models
> show #29 models
> fitmap #29 inMap #24
Fit molecule copy of hArf1_P84078 (#29) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.003766, steps = 60
shifted from previous position = 5.01
rotated from previous position = 6.4 degrees
atoms outside contour = 617, contour level = 0.0032978
Position of copy of hArf1_P84078 (#29) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.84456626 -0.49420934 0.20607023 243.01078108
-0.47688761 0.51925293 -0.70919291 195.93798301
0.24348719 -0.69723275 -0.67422582 220.56872240
Axis 0.27858679 -0.87154962 0.40347325
Axis point 151.42747314 0.00000000 157.15853491
Rotation angle (degrees) 178.77000789
Shift along axis -14.07649955
> hide #29 models
> show #30 models
> fitmap #30 inMap #24
Fit molecule copy of CopBprime_O55029.pdb (#30) to map
postprocess_20231221.mrc (#24) using 7214 atoms
average map value = 0.00312, steps = 80
shifted from previous position = 4.34
rotated from previous position = 6.44 degrees
atoms outside contour = 3972, contour level = 0.0032978
Position of copy of CopBprime_O55029.pdb (#30) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.16261321 -0.17515584 -0.97101873 188.51477883
-0.01403262 -0.98360736 0.17977662 177.40448822
-0.98659010 0.04285999 0.15748965 238.56224194
Axis -0.64579491 0.07344552 0.75997019
Axis point 189.60066445 85.40633709 0.00000000
Rotation angle (degrees) 173.91485430
Shift along axis 72.58787161
> hide #30 models
> show #31 models
> fitmap #31 inMap #24
Fit molecule copy of CopD_Q5XJY5 (#31) to map postprocess_20231221.mrc (#24)
using 1462 atoms
average map value = 0.003203, steps = 324
shifted from previous position = 5.13
rotated from previous position = 24.8 degrees
atoms outside contour = 880, contour level = 0.0032978
Position of copy of CopD_Q5XJY5 (#31) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.03835878 0.89491137 0.44459224 -96.27105677
-0.99475022 -0.07643914 0.06803729 102.74398933
0.09487159 -0.43964840 0.89314538 477.54730683
Axis -0.25541626 0.17594418 -0.95068722
Axis point -29.88566959 190.29797301 0.00000000
Rotation angle (degrees) 96.36294863
Shift along axis -411.33171958
> hide #31 models
> show #!32 models
> fitmap #32 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#32) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.003524, steps = 72
shifted from previous position = 3.77
rotated from previous position = 6.37 degrees
atoms outside contour = 4307, contour level = 0.0032978
Position of copy of CopG_Q9QZE5 (#32) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.48899567 -0.51150146 -0.70657589 223.56207168
0.54905607 -0.44893907 0.70497599 282.28594871
-0.67780577 -0.73267999 0.06131372 258.73118766
Axis -0.80462203 -0.01610195 0.59356896
Axis point 0.00000000 245.02634740 103.88878785
Rotation angle (degrees) 116.69973303
Shift along axis -30.85352207
> hide #!32 models
> show #33 models
> fitmap #33 inMap #24
Fit molecule copy of CopZ1_P61924.pdb (#33) to map postprocess_20231221.mrc
(#24) using 1420 atoms
average map value = 0.003933, steps = 76
shifted from previous position = 5.94
rotated from previous position = 6.42 degrees
atoms outside contour = 669, contour level = 0.0032978
Position of copy of CopZ1_P61924.pdb (#33) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.16475049 -0.94009197 -0.29847006 230.52229673
-0.38691226 0.21675387 -0.89627935 241.47790202
0.90727955 0.26314418 -0.32802281 218.17037219
Axis 0.65807298 -0.68436703 0.31397725
Axis point 143.58778508 -0.00000000 249.38897644
Rotation angle (degrees) 118.24606873
Shift along axis 54.94151398
> hide #33 models
> show #34 models
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.0031, steps = 88
shifted from previous position = 9.02
rotated from previous position = 6.41 degrees
atoms outside contour = 1383, contour level = 0.0032978
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.66108762 -0.23544106 0.71241186 198.02227460
-0.68860963 -0.56744408 0.45146871 233.20913977
0.29795962 -0.78903404 -0.53725724 191.32293326
Axis -0.89619456 0.29941880 -0.32738920
Axis point 0.00000000 180.08833448 -4.24101466
Rotation angle (degrees) 136.20385961
Shift along axis -170.27634703
> hide #34 models
> show #35 models
> fitmap #35 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#35) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.003943, steps = 76
shifted from previous position = 6.08
rotated from previous position = 6.44 degrees
atoms outside contour = 720, contour level = 0.0032978
Position of copy of CopZ2_Q9CTG7.pdb (#35) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.81885698 0.29532139 -0.49219768 229.57861768
0.42661204 0.88681622 -0.17764905 242.04930135
0.38402532 -0.35544661 -0.85216330 217.25627407
Axis -0.19675097 -0.96962927 0.14528637
Axis point 59.03656762 0.00000000 149.01652041
Rotation angle (degrees) 153.13858612
Shift along axis -248.30352928
> hide #35 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_2_fitting.cxs"
> hide #!24 models
> show #!24 models
> show #!16 models
> show #!17 models
> hide #!17 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!24 models
> show #!37 models
> show #!2 models
> hide #!2 models
> hide #!16 models
> hide #!25 models
> show #!36 models
> select add #36
2 models selected
> select add #38
9810 atoms, 10032 bonds, 1233 residues, 3 models selected
> select add #39
17311 atoms, 17651 bonds, 2186 residues, 4 models selected
> select add #40
18768 atoms, 19134 bonds, 2367 residues, 5 models selected
> select add #41
20225 atoms, 20617 bonds, 2548 residues, 6 models selected
> select add #42
27439 atoms, 27990 bonds, 3453 residues, 7 models selected
> select add #43
28901 atoms, 29471 bonds, 3632 residues, 8 models selected
> select add #44
35574 atoms, 36257 bonds, 1 pseudobond, 4485 residues, 10 models selected
> select add #45
36994 atoms, 37698 bonds, 1 pseudobond, 4662 residues, 11 models selected
> select add #46
39361 atoms, 40096 bonds, 1 pseudobond, 4960 residues, 12 models selected
> select add #47
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 13 models selected
> view matrix models
> #36,-0.30646,-0.94615,-0.10436,428.92,0.54097,-0.26333,0.79875,152.1,-0.78322,0.18832,0.59254,362.01,#38,-0.037217,-0.87154,0.48891,122.81,0.23648,0.46767,0.85168,366.41,-0.97092,0.14732,0.1887,422.69,#39,0.26132,-0.57917,-0.77219,164.06,-0.69745,-0.66634,0.26375,372.92,-0.66729,0.46964,-0.57807,404.78,#40,0.52778,0.74255,-0.41239,181.69,0.83267,-0.3565,0.42374,310.33,0.16763,-0.56703,-0.80646,406.23,#41,0.68427,-0.26654,0.67877,146.04,-0.13657,-0.96118,-0.23976,408.14,0.71632,0.071359,-0.69411,339.27,#42,0.16647,0.97979,0.11088,178.42,-0.87213,0.19877,-0.44709,397.9,-0.46009,-0.022274,0.88759,389.11,#43,0.72317,-0.33836,-0.60212,308.31,0.68009,0.19682,0.70621,451.73,-0.12045,-0.9202,0.37245,734.45,#44,-0.59861,0.65798,-0.45687,66.328,-0.4217,-0.74376,-0.51864,405.38,-0.68106,-0.1178,0.72269,393.38,#45,0.54534,0.56794,-0.61648,107.45,-0.56926,0.79078,0.22495,385.74,0.61526,0.22826,0.75456,356.26,#46,0.41891,0.69144,-0.58858,127.57,0.77647,-0.60882,-0.16258,350.66,-0.47075,-0.38891,-0.79192,364.19,#47,-0.19261,-0.89222,0.40847,106.89,-0.2483,-0.35841,-0.89994,386.1,0.94934,-0.27476,-0.15251,356.52
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.68445,0.68576,-0.2475,239.5,-0.35539,-0.61024,-0.70803,758.89,-0.63658,-0.39665,0.66139,423.44,#38,-0.66512,0.086485,-0.74171,237.05,0.079164,-0.97951,-0.1852,382.68,-0.74252,-0.1819,0.64465,381.28,#39,0.068042,0.98166,-0.17808,205.84,0.786,-0.16268,-0.59644,414.74,-0.61447,-0.09939,-0.78265,389.23,#40,-0.75447,-0.33405,-0.56497,246.16,-0.13891,0.92256,-0.35997,465.14,0.64147,-0.19311,-0.74245,381.2,#41,0.19091,0.86663,-0.46098,152.95,0.41826,0.35303,0.83691,396.79,0.88804,-0.35259,-0.29508,336.91,#42,0.34544,-0.56524,0.74912,173.08,0.76513,0.63184,0.12393,414.75,-0.54337,0.53036,0.65074,390.84,#43,-0.87038,-0.48469,-0.086666,258.19,0.1745,-0.13907,-0.97479,392.9,0.46041,-0.86356,0.20562,753.21,#44,0.20986,0.22373,0.95179,216.02,-0.02883,0.97446,-0.22271,323.98,-0.97731,0.019296,0.21095,340.28,#45,0.5198,-0.70827,0.47766,194.48,0.5969,-0.098898,-0.7962,376.47,0.61116,0.69898,0.37135,324.95,#46,-0.99845,-0.031687,-0.045733,216.53,-0.024622,0.98875,-0.14753,410.68,0.049893,-0.14618,-0.988,331.4,#47,0.75776,0.49451,0.42575,194.58,-0.24129,-0.39387,0.88693,375.76,0.60629,-0.77481,-0.17914,324.99
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.68445,0.68576,-0.2475,264.07,-0.35539,-0.61024,-0.70803,585.08,-0.63658,-0.39665,0.66139,317.76,#38,-0.66512,0.086485,-0.74171,261.62,0.079164,-0.97951,-0.1852,208.87,-0.74252,-0.1819,0.64465,275.59,#39,0.068042,0.98166,-0.17808,230.41,0.786,-0.16268,-0.59644,240.93,-0.61447,-0.09939,-0.78265,283.54,#40,-0.75447,-0.33405,-0.56497,270.73,-0.13891,0.92256,-0.35997,291.33,0.64147,-0.19311,-0.74245,275.51,#41,0.19091,0.86663,-0.46098,177.52,0.41826,0.35303,0.83691,222.98,0.88804,-0.35259,-0.29508,231.22,#42,0.34544,-0.56524,0.74912,197.65,0.76513,0.63184,0.12393,240.94,-0.54337,0.53036,0.65074,285.15,#43,-0.87038,-0.48469,-0.086666,282.76,0.1745,-0.13907,-0.97479,219.09,0.46041,-0.86356,0.20562,647.52,#44,0.20986,0.22373,0.95179,240.58,-0.02883,0.97446,-0.22271,150.17,-0.97731,0.019296,0.21095,234.6,#45,0.5198,-0.70827,0.47766,219.04,0.5969,-0.098898,-0.7962,202.67,0.61116,0.69898,0.37135,219.27,#46,-0.99845,-0.031687,-0.045733,241.1,-0.024622,0.98875,-0.14753,236.88,0.049893,-0.14618,-0.988,225.72,#47,0.75776,0.49451,0.42575,219.15,-0.24129,-0.39387,0.88693,201.96,0.60629,-0.77481,-0.17914,219.31
> view matrix models
> #36,-0.68445,0.68576,-0.2475,307.56,-0.35539,-0.61024,-0.70803,573.88,-0.63658,-0.39665,0.66139,321.66,#38,-0.66512,0.086485,-0.74171,305.11,0.079164,-0.97951,-0.1852,197.67,-0.74252,-0.1819,0.64465,279.5,#39,0.068042,0.98166,-0.17808,273.9,0.786,-0.16268,-0.59644,229.73,-0.61447,-0.09939,-0.78265,287.45,#40,-0.75447,-0.33405,-0.56497,314.22,-0.13891,0.92256,-0.35997,280.13,0.64147,-0.19311,-0.74245,279.42,#41,0.19091,0.86663,-0.46098,221.01,0.41826,0.35303,0.83691,211.78,0.88804,-0.35259,-0.29508,235.13,#42,0.34544,-0.56524,0.74912,241.14,0.76513,0.63184,0.12393,229.74,-0.54337,0.53036,0.65074,289.06,#43,-0.87038,-0.48469,-0.086666,326.25,0.1745,-0.13907,-0.97479,207.9,0.46041,-0.86356,0.20562,651.43,#44,0.20986,0.22373,0.95179,284.08,-0.02883,0.97446,-0.22271,138.97,-0.97731,0.019296,0.21095,238.51,#45,0.5198,-0.70827,0.47766,262.54,0.5969,-0.098898,-0.7962,191.47,0.61116,0.69898,0.37135,223.18,#46,-0.99845,-0.031687,-0.045733,284.59,-0.024622,0.98875,-0.14753,225.68,0.049893,-0.14618,-0.988,229.62,#47,0.75776,0.49451,0.42575,262.64,-0.24129,-0.39387,0.88693,190.76,0.60629,-0.77481,-0.17914,223.21
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.33209,0.77442,-0.53851,271.48,-0.57183,-0.61933,-0.53799,589.35,-0.75015,0.12928,0.64851,251.4,#38,-0.25536,0.13315,-0.95763,278.3,-0.17872,-0.9799,-0.088585,216.46,-0.95018,0.14853,0.27403,316.39,#39,0.35938,0.91587,0.17899,247.73,0.607,-0.08374,-0.79027,246.2,-0.7088,0.39265,-0.58603,300.7,#40,-0.96634,-0.18593,-0.17783,288.66,-0.046133,0.80521,-0.59119,296.68,0.25311,-0.56309,-0.78668,297.95,#41,-0.21994,0.94151,-0.25531,223.74,0.64689,0.33666,0.68425,210.37,0.73018,-0.014662,-0.68309,237.47,#42,0.57403,-0.7268,0.37716,217.79,0.63267,0.68608,0.3592,243.35,-0.51983,0.032429,0.85365,287.61,#43,-0.97949,-0.045608,-0.19625,129.33,0.19787,-0.40139,-0.89428,322.82,-0.037987,-0.91477,0.40218,641.01,#44,0.62803,0.21681,0.74737,276.5,-0.25487,0.96474,-0.065694,147.48,-0.73527,-0.14923,0.66115,287.97,#45,0.20322,-0.95007,0.2368,265.62,0.78129,0.011578,-0.62405,191.94,0.59015,0.31183,0.74463,251.1,#46,-0.91347,0.064231,0.4018,283.29,-0.1107,0.91099,-0.3973,228.69,-0.39155,-0.40741,-0.82505,257.07,#47,0.3952,0.78057,0.48428,265.68,-0.002587,-0.52625,0.85033,191.28,0.91859,-0.3373,-0.20595,251.37
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.33209,0.77442,-0.53851,273.75,-0.57183,-0.61933,-0.53799,571.61,-0.75015,0.12928,0.64851,247.18,#38,-0.25536,0.13315,-0.95763,280.57,-0.17872,-0.9799,-0.088585,198.72,-0.95018,0.14853,0.27403,312.17,#39,0.35938,0.91587,0.17899,250.01,0.607,-0.08374,-0.79027,228.47,-0.7088,0.39265,-0.58603,296.48,#40,-0.96634,-0.18593,-0.17783,290.93,-0.046133,0.80521,-0.59119,278.94,0.25311,-0.56309,-0.78668,293.74,#41,-0.21994,0.94151,-0.25531,226.02,0.64689,0.33666,0.68425,192.64,0.73018,-0.014662,-0.68309,233.26,#42,0.57403,-0.7268,0.37716,220.07,0.63267,0.68608,0.3592,225.61,-0.51983,0.032429,0.85365,283.39,#43,-0.97949,-0.045608,-0.19625,131.61,0.19787,-0.40139,-0.89428,305.08,-0.037987,-0.91477,0.40218,636.79,#44,0.62803,0.21681,0.74737,278.78,-0.25487,0.96474,-0.065694,129.74,-0.73527,-0.14923,0.66115,283.76,#45,0.20322,-0.95007,0.2368,267.9,0.78129,0.011578,-0.62405,174.2,0.59015,0.31183,0.74463,246.89,#46,-0.91347,0.064231,0.4018,285.57,-0.1107,0.91099,-0.3973,210.96,-0.39155,-0.40741,-0.82505,252.86,#47,0.3952,0.78057,0.48428,267.96,-0.002587,-0.52625,0.85033,173.54,0.91859,-0.3373,-0.20595,247.16
> view matrix models
> #36,-0.33209,0.77442,-0.53851,267.88,-0.57183,-0.61933,-0.53799,565.81,-0.75015,0.12928,0.64851,258.39,#38,-0.25536,0.13315,-0.95763,274.7,-0.17872,-0.9799,-0.088585,192.92,-0.95018,0.14853,0.27403,323.38,#39,0.35938,0.91587,0.17899,244.13,0.607,-0.08374,-0.79027,222.66,-0.7088,0.39265,-0.58603,307.69,#40,-0.96634,-0.18593,-0.17783,285.06,-0.046133,0.80521,-0.59119,273.14,0.25311,-0.56309,-0.78668,304.94,#41,-0.21994,0.94151,-0.25531,220.14,0.64689,0.33666,0.68425,186.83,0.73018,-0.014662,-0.68309,244.46,#42,0.57403,-0.7268,0.37716,214.19,0.63267,0.68608,0.3592,219.81,-0.51983,0.032429,0.85365,294.6,#43,-0.97949,-0.045608,-0.19625,125.73,0.19787,-0.40139,-0.89428,299.28,-0.037987,-0.91477,0.40218,648,#44,0.62803,0.21681,0.74737,272.9,-0.25487,0.96474,-0.065694,123.94,-0.73527,-0.14923,0.66115,294.96,#45,0.20322,-0.95007,0.2368,262.02,0.78129,0.011578,-0.62405,168.4,0.59015,0.31183,0.74463,258.09,#46,-0.91347,0.064231,0.4018,279.69,-0.1107,0.91099,-0.3973,205.15,-0.39155,-0.40741,-0.82505,264.06,#47,0.3952,0.78057,0.48428,262.08,-0.002587,-0.52625,0.85033,167.74,0.91859,-0.3373,-0.20595,258.36
> view matrix models
> #36,-0.33209,0.77442,-0.53851,273.57,-0.57183,-0.61933,-0.53799,569.61,-0.75015,0.12928,0.64851,261.33,#38,-0.25536,0.13315,-0.95763,280.39,-0.17872,-0.9799,-0.088585,196.72,-0.95018,0.14853,0.27403,326.32,#39,0.35938,0.91587,0.17899,249.82,0.607,-0.08374,-0.79027,226.46,-0.7088,0.39265,-0.58603,310.63,#40,-0.96634,-0.18593,-0.17783,290.75,-0.046133,0.80521,-0.59119,276.93,0.25311,-0.56309,-0.78668,307.88,#41,-0.21994,0.94151,-0.25531,225.83,0.64689,0.33666,0.68425,190.63,0.73018,-0.014662,-0.68309,247.41,#42,0.57403,-0.7268,0.37716,219.88,0.63267,0.68608,0.3592,223.61,-0.51983,0.032429,0.85365,297.54,#43,-0.97949,-0.045608,-0.19625,131.42,0.19787,-0.40139,-0.89428,303.07,-0.037987,-0.91477,0.40218,650.94,#44,0.62803,0.21681,0.74737,278.59,-0.25487,0.96474,-0.065694,127.74,-0.73527,-0.14923,0.66115,297.91,#45,0.20322,-0.95007,0.2368,267.71,0.78129,0.011578,-0.62405,172.2,0.59015,0.31183,0.74463,261.03,#46,-0.91347,0.064231,0.4018,285.38,-0.1107,0.91099,-0.3973,208.95,-0.39155,-0.40741,-0.82505,267,#47,0.3952,0.78057,0.48428,267.77,-0.002587,-0.52625,0.85033,171.53,0.91859,-0.3373,-0.20595,261.3
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.093312,0.86488,-0.49323,146.31,-0.21567,-0.46607,-0.85806,526.72,-0.972,0.18644,0.14304,413.38,#38,0.091092,0.39627,-0.91361,255.1,0.23201,-0.90062,-0.3675,172.58,-0.96844,-0.17849,-0.17398,335.51,#39,0.32564,0.74623,0.58059,222.19,0.91482,-0.093551,-0.39287,200.42,-0.23886,0.65908,-0.71314,321.12,#40,-0.9294,-0.27219,0.24925,243.63,-0.3224,0.92748,-0.18931,252.83,-0.17964,-0.25631,-0.94976,353.11,#41,-0.6113,0.74662,-0.26242,229.67,0.19495,0.46344,0.86442,193.73,0.76701,0.47726,-0.42885,245.26,#42,0.45892,-0.88839,-0.012509,199.68,0.88836,0.45904,-0.0093881,198.71,0.014082,-0.0068042,0.99988,297.33,#43,-0.93933,0.34302,0.00011685,-4.311,0.020915,0.057615,-0.99812,92.075,-0.34238,-0.93756,-0.061294,590.68,#44,0.85492,-0.074664,0.51335,283.7,0.22034,0.94815,-0.22904,124.93,-0.46964,0.30893,0.82705,285.71,#45,-0.23316,-0.94969,0.20909,269.72,0.44918,-0.29589,-0.84302,178.67,0.86248,-0.10264,0.49557,266.43,#46,-0.68145,-0.12347,0.72138,272.15,-0.076401,0.99228,0.097667,211.11,-0.72787,0.011441,-0.68562,291.72,#47,0.10284,0.97005,0.22004,269.91,-0.35187,-0.17143,0.92021,177.97,0.93038,-0.17206,0.32371,266.43
> view matrix models
> #36,-0.013617,0.67237,-0.74009,262.08,-0.46659,-0.65891,-0.59003,563.73,-0.88437,0.33728,0.32269,324.78,#38,0.12972,0.076397,-0.9886,247.4,-0.055809,-0.99488,-0.084205,185.79,-0.98998,0.066096,-0.12479,340.98,#39,0.59696,0.69661,0.39796,224.86,0.67235,-0.16377,-0.72189,218.3,-0.4377,0.69851,-0.56613,318.62,#40,-0.98908,0.035376,0.14307,263.19,-0.039286,0.87236,-0.48729,267.17,-0.14205,-0.48759,-0.86144,337.92,#41,-0.48947,0.87182,0.018493,227.28,0.56416,0.30042,0.76907,191.1,0.66494,0.38687,-0.63889,247.13,#42,0.72264,-0.69099,0.017855,202.25,0.66749,0.7043,0.24169,218.14,-0.17958,-0.16274,0.97019,294.87,#43,-0.89235,0.31226,-0.32589,-15.591,0.23763,-0.28882,-0.92742,258.68,-0.38372,-0.90503,0.18353,594.76,#44,0.8643,0.24731,0.43799,257.34,-0.18989,0.96677,-0.17117,120.75,-0.46576,0.064773,0.88254,305.76,#45,-0.046371,-0.99713,-0.059776,260.94,0.69813,0.010451,-0.71589,169.62,0.71447,-0.074928,0.69565,273.31,#46,-0.69278,0.20576,0.69117,274.6,-0.029393,0.94958,-0.31215,204.73,-0.72055,-0.23657,-0.65181,290.04,#47,0.013445,0.8557,0.5173,260.9,-0.12564,-0.5118,0.84987,168.93,0.99198,-0.076423,0.10063,273.5
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.013617,0.67237,-0.74009,272.84,-0.46659,-0.65891,-0.59003,545.17,-0.88437,0.33728,0.32269,323.96,#38,0.12972,0.076397,-0.9886,258.17,-0.055809,-0.99488,-0.084205,167.23,-0.98998,0.066096,-0.12479,340.16,#39,0.59696,0.69661,0.39796,235.63,0.67235,-0.16377,-0.72189,199.75,-0.4377,0.69851,-0.56613,317.8,#40,-0.98908,0.035376,0.14307,273.96,-0.039286,0.87236,-0.48729,248.62,-0.14205,-0.48759,-0.86144,337.1,#41,-0.48947,0.87182,0.018493,238.04,0.56416,0.30042,0.76907,172.54,0.66494,0.38687,-0.63889,246.31,#42,0.72264,-0.69099,0.017855,213.01,0.66749,0.7043,0.24169,199.58,-0.17958,-0.16274,0.97019,294.05,#43,-0.89235,0.31226,-0.32589,-4.8246,0.23763,-0.28882,-0.92742,240.13,-0.38372,-0.90503,0.18353,593.94,#44,0.8643,0.24731,0.43799,268.11,-0.18989,0.96677,-0.17117,102.2,-0.46576,0.064773,0.88254,304.94,#45,-0.046371,-0.99713,-0.059776,271.71,0.69813,0.010451,-0.71589,151.07,0.71447,-0.074928,0.69565,272.49,#46,-0.69278,0.20576,0.69117,285.36,-0.029393,0.94958,-0.31215,186.17,-0.72055,-0.23657,-0.65181,289.22,#47,0.013445,0.8557,0.5173,271.67,-0.12564,-0.5118,0.84987,150.38,0.99198,-0.076423,0.10063,272.68
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.31277,0.41013,-0.85672,418.59,-0.65173,-0.74881,-0.12055,503.05,-0.69096,0.52064,0.5015,204.47,#38,-0.039786,-0.30025,-0.95303,263.36,-0.38312,-0.87631,0.29208,185.33,-0.92284,0.37674,-0.080167,339.65,#39,0.74135,0.67104,0.010192,252.05,0.2173,-0.22564,-0.94967,216.34,-0.63497,0.70625,-0.3131,308.41,#40,-0.93873,0.29735,-0.17426,308.39,0.32637,0.60448,-0.7267,248.75,-0.11075,-0.73904,-0.66449,310.8,#41,-0.14028,0.965,0.2216,233.99,0.87791,0.017741,0.4785,171.36,0.45782,0.26167,-0.84966,249.19,#42,0.89011,-0.38568,0.2428,228.03,0.23567,0.84552,0.47911,218.6,-0.39007,-0.36925,0.8435,286.2,#43,-0.77822,0.050011,-0.62599,85.89,0.45883,-0.63531,-0.62117,427.56,-0.42877,-0.77064,0.47147,560.35,#44,0.65315,0.60355,0.45731,242.77,-0.64802,0.75794,-0.074794,114.78,-0.39176,-0.24749,0.88616,326.72,#45,0.32267,-0.91784,-0.2312,260.2,0.82876,0.39196,-0.39941,146.52,0.45721,-0.062734,0.88714,280.42,#46,-0.74423,0.51729,0.42253,288.38,0.050028,0.674,-0.73703,176.24,-0.66604,-0.52739,-0.52749,285.02,#47,0.10176,0.57649,0.81074,259.92,0.16804,-0.81322,0.55716,145.99,0.98051,0.079539,-0.17963,280.82
> view matrix models
> #36,-0.16023,0.74534,-0.64714,273.17,-0.59399,-0.59643,-0.53986,552.33,-0.78835,0.29789,0.53829,261.63,#38,-0.053073,0.12156,-0.99116,274.78,-0.20275,-0.9732,-0.1085,181,-0.97779,0.1952,0.076298,335.32,#39,0.48252,0.81862,0.3115,247.4,0.60306,-0.052581,-0.79596,209.64,-0.63522,0.57192,-0.51905,313.07,#40,-0.99636,-0.085208,-0.0013797,286.92,-0.066682,0.7896,-0.60998,261.11,0.053065,-0.60767,-0.79241,317.5,#41,-0.37774,0.91729,-0.12611,237.53,0.65423,0.36079,0.66469,172.04,0.65521,0.16858,-0.7364,247.15,#42,0.6537,-0.73304,0.18797,220.81,0.63778,0.66736,0.38454,205.77,-0.40733,-0.13149,0.90377,294.26,#43,-0.95544,0.14993,-0.25428,60.697,0.1715,-0.41918,-0.89156,289.38,-0.24026,-0.89544,0.37479,620.45,#44,0.7697,0.22149,0.59875,280.3,-0.25186,0.96717,-0.03401,111.49,-0.58663,-0.12462,0.80021,308.74,#45,0.062007,-0.99362,0.094178,276.17,0.79704,-0.0074975,-0.60388,154.96,0.60073,0.11251,0.79149,269.41,#46,-0.81226,0.12574,0.56958,291.45,-0.14168,0.90471,-0.40177,192.27,-0.56583,-0.40704,-0.71705,277.97,#47,0.20033,0.84411,0.49734,276.18,0.024602,-0.51181,0.85875,154.31,0.97942,-0.1598,-0.1233,269.7
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.16023,0.74534,-0.64714,267.12,-0.59399,-0.59643,-0.53986,565.33,-0.78835,0.29789,0.53829,260.86,#38,-0.053073,0.12156,-0.99116,268.74,-0.20275,-0.9732,-0.1085,194,-0.97779,0.1952,0.076298,334.55,#39,0.48252,0.81862,0.3115,241.35,0.60306,-0.052581,-0.79596,222.65,-0.63522,0.57192,-0.51905,312.31,#40,-0.99636,-0.085208,-0.0013797,280.87,-0.066682,0.7896,-0.60998,274.11,0.053065,-0.60767,-0.79241,316.73,#41,-0.37774,0.91729,-0.12611,231.49,0.65423,0.36079,0.66469,185.05,0.65521,0.16858,-0.7364,246.38,#42,0.6537,-0.73304,0.18797,214.77,0.63778,0.66736,0.38454,218.77,-0.40733,-0.13149,0.90377,293.49,#43,-0.95544,0.14993,-0.25428,54.652,0.1715,-0.41918,-0.89156,302.38,-0.24026,-0.89544,0.37479,619.69,#44,0.7697,0.22149,0.59875,274.25,-0.25186,0.96717,-0.03401,124.49,-0.58663,-0.12462,0.80021,307.98,#45,0.062007,-0.99362,0.094178,270.13,0.79704,-0.0074975,-0.60388,167.96,0.60073,0.11251,0.79149,268.64,#46,-0.81226,0.12574,0.56958,285.41,-0.14168,0.90471,-0.40177,205.27,-0.56583,-0.40704,-0.71705,277.21,#47,0.20033,0.84411,0.49734,270.14,0.024602,-0.51181,0.85875,167.31,0.97942,-0.1598,-0.1233,268.93
> view matrix models
> #36,-0.16023,0.74534,-0.64714,282.03,-0.59399,-0.59643,-0.53986,563.36,-0.78835,0.29789,0.53829,263.36,#38,-0.053073,0.12156,-0.99116,283.64,-0.20275,-0.9732,-0.1085,192.03,-0.97779,0.1952,0.076298,337.05,#39,0.48252,0.81862,0.3115,256.26,0.60306,-0.052581,-0.79596,220.68,-0.63522,0.57192,-0.51905,314.81,#40,-0.99636,-0.085208,-0.0013797,295.78,-0.066682,0.7896,-0.60998,272.14,0.053065,-0.60767,-0.79241,319.23,#41,-0.37774,0.91729,-0.12611,246.4,0.65423,0.36079,0.66469,183.08,0.65521,0.16858,-0.7364,248.88,#42,0.6537,-0.73304,0.18797,229.68,0.63778,0.66736,0.38454,216.81,-0.40733,-0.13149,0.90377,295.99,#43,-0.95544,0.14993,-0.25428,69.559,0.1715,-0.41918,-0.89156,300.41,-0.24026,-0.89544,0.37479,622.19,#44,0.7697,0.22149,0.59875,289.16,-0.25186,0.96717,-0.03401,122.52,-0.58663,-0.12462,0.80021,310.48,#45,0.062007,-0.99362,0.094178,285.03,0.79704,-0.0074975,-0.60388,166,0.60073,0.11251,0.79149,271.14,#46,-0.81226,0.12574,0.56958,300.31,-0.14168,0.90471,-0.40177,203.3,-0.56583,-0.40704,-0.71705,279.71,#47,0.20033,0.84411,0.49734,285.05,0.024602,-0.51181,0.85875,165.34,0.97942,-0.1598,-0.1233,271.43
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.19859,0.6822,-0.70368,315.42,-0.49522,-0.68943,-0.52863,555.3,-0.84576,0.2435,0.47475,301.12,#38,-0.052704,0.028797,-0.99819,281.85,-0.098661,-0.99484,-0.023492,179.93,-0.99372,0.097244,0.055273,336.99,#39,0.54736,0.79943,0.24761,257.62,0.61609,-0.18466,-0.76572,213.05,-0.56641,0.57168,-0.5936,317.48,#40,-0.99912,-0.0014639,-0.041801,301.56,0.020733,0.85064,-0.52534,259.95,0.036327,-0.52575,-0.84986,327.47,#41,-0.32904,0.94293,-0.051101,245.63,0.61787,0.2559,0.74347,183.27,0.71412,0.21306,-0.66681,248.01,#42,0.71663,-0.66666,0.20496,231.15,0.612,0.742,0.27367,213.54,-0.33452,-0.070681,0.93973,298.12,#43,-0.93114,0.12817,-0.34141,73.134,0.28212,-0.34004,-0.8971,278.71,-0.23107,-0.93164,0.28046,629.5,#44,0.75461,0.31088,0.57786,281.53,-0.26227,0.95014,-0.16866,113.19,-0.60148,-0.024281,0.79852,303.6,#45,0.12282,-0.99214,0.023796,282.12,0.72414,0.0732,-0.68576,160.56,0.67863,0.10146,0.72744,268.81,#46,-0.81088,0.21523,0.5442,300.57,-0.0089905,0.92522,-0.37932,195.26,-0.58515,-0.31248,-0.74831,281.25,#47,0.18309,0.79694,0.57565,282.07,-0.09161,-0.56917,0.8171,159.89,0.97882,-0.20234,-0.031202,269.03
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.19859,0.6822,-0.70368,306.31,-0.49522,-0.68943,-0.52863,542.7,-0.84576,0.2435,0.47475,307.53,#38,-0.052704,0.028797,-0.99819,272.74,-0.098661,-0.99484,-0.023492,167.33,-0.99372,0.097244,0.055273,343.41,#39,0.54736,0.79943,0.24761,248.5,0.61609,-0.18466,-0.76572,200.46,-0.56641,0.57168,-0.5936,323.9,#40,-0.99912,-0.0014639,-0.041801,292.45,0.020733,0.85064,-0.52534,247.35,0.036327,-0.52575,-0.84986,333.88,#41,-0.32904,0.94293,-0.051101,236.51,0.61787,0.2559,0.74347,170.68,0.71412,0.21306,-0.66681,254.43,#42,0.71663,-0.66666,0.20496,222.04,0.612,0.742,0.27367,200.95,-0.33452,-0.070681,0.93973,304.53,#43,-0.93114,0.12817,-0.34141,64.019,0.28212,-0.34004,-0.8971,266.11,-0.23107,-0.93164,0.28046,635.92,#44,0.75461,0.31088,0.57786,272.41,-0.26227,0.95014,-0.16866,100.6,-0.60148,-0.024281,0.79852,310.01,#45,0.12282,-0.99214,0.023796,273.01,0.72414,0.0732,-0.68576,147.97,0.67863,0.10146,0.72744,275.23,#46,-0.81088,0.21523,0.5442,291.45,-0.0089905,0.92522,-0.37932,182.66,-0.58515,-0.31248,-0.74831,287.66,#47,0.18309,0.79694,0.57565,272.95,-0.09161,-0.56917,0.8171,147.29,0.97882,-0.20234,-0.031202,275.45
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.16756,0.78462,-0.59691,256.18,-0.69887,-0.52158,-0.48942,550.21,-0.69534,0.33515,0.63574,219.47,#38,-0.087126,0.17496,-0.98071,278.23,-0.33213,-0.93323,-0.13698,192.24,-0.9392,0.31379,0.13942,340.66,#39,0.42539,0.84483,0.32452,248.59,0.53263,0.056197,-0.84448,216.57,-0.73168,0.53208,-0.42607,316.28,#40,-0.98887,-0.14856,-0.0084755,285.85,-0.098837,0.69835,-0.7089,269.71,0.11123,-0.70017,-0.70526,311.99,#41,-0.37801,0.90623,-0.18933,237.55,0.71945,0.41626,0.55599,170.23,0.58267,0.073955,-0.80934,256.39,#42,0.60476,-0.76821,0.21005,221.4,0.60397,0.61431,0.50779,209.19,-0.51912,-0.18022,0.83548,299.49,#43,-0.97209,0.12912,-0.19589,72.273,0.099945,-0.52749,-0.84366,328.7,-0.21226,-0.83969,0.49987,619.66,#44,0.75363,0.17081,0.63471,285.76,-0.29621,0.95029,0.09597,120.1,-0.58677,-0.26033,0.76677,323.11,#45,0.051804,-0.98622,0.15711,277.89,0.87126,-0.032256,-0.48975,157.8,0.48807,0.16226,0.85759,278.71,#46,-0.82923,0.065573,0.55505,291.79,-0.24754,0.84729,-0.46991,196.49,-0.5011,-0.52706,-0.68637,281.57,#47,0.24238,0.8589,0.45116,277.94,0.16178,-0.4943,0.85411,157.19,0.9566,-0.13403,-0.25877,279.08
> view matrix models
> #36,-0.081555,0.83063,-0.55082,217.11,-0.56608,-0.49347,-0.66033,551.03,-0.82031,0.25796,0.51045,290.98,#38,-0.037028,0.26874,-0.9625,275.38,-0.15317,-0.95331,-0.26028,180.61,-0.98751,0.13779,0.076461,343.05,#39,0.37715,0.82589,0.41913,243.68,0.70342,0.038945,-0.7097,206.02,-0.60246,0.56249,-0.56626,322.69,#40,-0.97425,-0.21162,0.077821,275.12,-0.21848,0.80072,-0.55778,262.5,0.055721,-0.56041,-0.82634,329.82,#41,-0.46133,0.85545,-0.23532,238.55,0.5522,0.48445,0.67852,171.13,0.69444,0.18308,-0.69587,254.77,#42,0.54465,-0.82654,0.14207,217.7,0.75061,0.55598,0.35703,199.26,-0.37408,-0.087817,0.92323,303.86,#43,-0.97389,0.19729,-0.11231,51.859,0.039252,-0.34092,-0.93927,239.4,-0.2236,-0.91915,0.32428,635.4,#44,0.78969,0.072388,0.60922,290.83,-0.10001,0.99492,0.01142,114.32,-0.6053,-0.069946,0.79292,312.47,#45,-0.048785,-0.97949,0.1955,279.65,0.76229,-0.16299,-0.62638,158.82,0.6454,0.11847,0.7546,275.74,#46,-0.79045,-0.017227,0.61229,289.3,-0.23007,0.93476,-0.27072,197.46,-0.56768,-0.35486,-0.74284,286.35,#47,0.20929,0.90864,0.36134,279.76,-0.00064692,-0.3694,0.92927,158.16,0.97785,-0.19472,-0.076723,275.99
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.081555,0.83063,-0.55082,214.5,-0.56608,-0.49347,-0.66033,546.37,-0.82031,0.25796,0.51045,283.6,#38,-0.037028,0.26874,-0.9625,272.77,-0.15317,-0.95331,-0.26028,175.95,-0.98751,0.13779,0.076461,335.67,#39,0.37715,0.82589,0.41913,241.07,0.70342,0.038945,-0.7097,201.36,-0.60246,0.56249,-0.56626,315.3,#40,-0.97425,-0.21162,0.077821,272.51,-0.21848,0.80072,-0.55778,257.85,0.055721,-0.56041,-0.82634,322.44,#41,-0.46133,0.85545,-0.23532,235.95,0.5522,0.48445,0.67852,166.47,0.69444,0.18308,-0.69587,247.39,#42,0.54465,-0.82654,0.14207,215.09,0.75061,0.55598,0.35703,194.6,-0.37408,-0.087817,0.92323,296.47,#43,-0.97389,0.19729,-0.11231,49.25,0.039252,-0.34092,-0.93927,234.75,-0.2236,-0.91915,0.32428,628.02,#44,0.78969,0.072388,0.60922,288.22,-0.10001,0.99492,0.01142,109.66,-0.6053,-0.069946,0.79292,305.09,#45,-0.048785,-0.97949,0.1955,277.04,0.76229,-0.16299,-0.62638,154.17,0.6454,0.11847,0.7546,268.36,#46,-0.79045,-0.017227,0.61229,286.69,-0.23007,0.93476,-0.27072,192.8,-0.56768,-0.35486,-0.74284,278.97,#47,0.20929,0.90864,0.36134,277.15,-0.00064692,-0.3694,0.92927,153.51,0.97785,-0.19472,-0.076723,268.61
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3989, overlap = 19.86
steps = 120, shift = 7.95, angle = 9.21 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53609396 -0.84407508 -0.01185528 402.27426069
0.84374881 -0.53621844 0.02361709 56.07946034
-0.02629162 0.00265811 0.99965079 -108.53618381
Axis -0.01241634 0.00855226 0.99988634
Axis point 184.79184089 138.62878392 0.00000000
Rotation angle (degrees) 122.43420777
Shift along axis -113.03901729
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3989, overlap = 19.86
steps = 120, shift = 7.95, angle = 9.21 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53609396 -0.84407508 -0.01185528 402.27426069
0.84374881 -0.53621844 0.02361709 56.07946034
-0.02629162 0.00265811 0.99965079 -108.53618381
Axis -0.01241634 0.00855226 0.99988634
Axis point 184.79184089 138.62878392 0.00000000
Rotation angle (degrees) 122.43420777
Shift along axis -113.03901729
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3989, overlap = 19.86
steps = 120, shift = 7.95, angle = 9.21 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53609396 -0.84407508 -0.01185528 402.27426069
0.84374881 -0.53621844 0.02361709 56.07946034
-0.02629162 0.00265811 0.99965079 -108.53618381
Axis -0.01241634 0.00855226 0.99988634
Axis point 184.79184089 138.62878392 0.00000000
Rotation angle (degrees) 122.43420777
Shift along axis -113.03901729
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.065537,0.95596,-0.28609,128.98,-0.68929,-0.25068,-0.67973,533.55,-0.72151,0.15265,0.67536,244.22,#38,-0.15019,0.51269,-0.84533,283.8,-0.30757,-0.83683,-0.45289,197.9,-0.9396,0.19198,0.28338,325.99,#39,0.095098,0.86759,0.4881,244.08,0.66844,0.30769,-0.67714,212.18,-0.73766,0.39066,-0.55067,309.15,#40,-0.87005,-0.48575,0.08401,261.39,-0.41845,0.63764,-0.64678,274.65,0.26061,-0.59788,-0.75804,303.88,#41,-0.47001,0.72786,-0.49931,237.27,0.53583,0.68481,0.49388,167,0.70141,-0.035423,-0.71188,247.76,#42,0.27905,-0.94115,0.1907,217.97,0.78625,0.33794,0.51731,196.99,-0.55132,0.0055821,0.83428,296.38,#43,-0.97614,0.13073,0.17337,100.57,-0.2132,-0.42571,-0.87938,249.75,-0.041162,-0.89537,0.44343,646.33,#44,0.68688,-0.186,0.70257,310.16,-0.013747,0.9632,0.26844,132.8,-0.72664,-0.19404,0.65905,300.74,#45,-0.1344,-0.87902,0.45746,282.85,0.8223,-0.35654,-0.44351,167.52,0.55295,0.31656,0.77074,261.96,#46,-0.78751,-0.30094,0.53783,284.24,-0.48461,0.84153,-0.23871,208.49,-0.38077,-0.44862,-0.80855,266.15,#47,0.35135,0.93027,0.10561,283.16,0.19632,-0.1835,0.96322,166.94,0.91543,-0.31769,-0.2471,262.26
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 156, shift = 4.54, angle = 14.5 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53620908 -0.84400250 -0.01181641 402.28711030
0.84367320 -0.53633217 0.02373510 56.06758820
-0.02637001 0.00275779 0.99964846 -108.51146781
Axis -0.01242828 0.00862247 0.99988559
Axis point 184.80143895 138.61200459 0.00000000
Rotation angle (degrees) 122.44205518
Shift along axis -113.01535017
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 156, shift = 4.54, angle = 14.5 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53620908 -0.84400250 -0.01181641 402.28711030
0.84367320 -0.53633217 0.02373510 56.06758820
-0.02637001 0.00275779 0.99964846 -108.51146781
Axis -0.01242828 0.00862247 0.99988559
Axis point 184.80143895 138.61200459 0.00000000
Rotation angle (degrees) 122.44205518
Shift along axis -113.01535017
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.065537,0.95596,-0.28609,132.48,-0.68929,-0.25068,-0.67973,535.05,-0.72151,0.15265,0.67536,246.35,#38,-0.15019,0.51269,-0.84533,287.3,-0.30757,-0.83683,-0.45289,199.4,-0.9396,0.19198,0.28338,328.12,#39,0.095098,0.86759,0.4881,247.58,0.66844,0.30769,-0.67714,213.68,-0.73766,0.39066,-0.55067,311.28,#40,-0.87005,-0.48575,0.08401,264.89,-0.41845,0.63764,-0.64678,276.15,0.26061,-0.59788,-0.75804,306.01,#41,-0.47001,0.72786,-0.49931,240.76,0.53583,0.68481,0.49388,168.5,0.70141,-0.035423,-0.71188,249.89,#42,0.27905,-0.94115,0.1907,221.47,0.78625,0.33794,0.51731,198.5,-0.55132,0.0055821,0.83428,298.51,#43,-0.97614,0.13073,0.17337,104.06,-0.2132,-0.42571,-0.87938,251.25,-0.041162,-0.89537,0.44343,648.46,#44,0.68688,-0.186,0.70257,313.65,-0.013747,0.9632,0.26844,134.31,-0.72664,-0.19404,0.65905,302.88,#45,-0.1344,-0.87902,0.45746,286.35,0.8223,-0.35654,-0.44351,169.02,0.55295,0.31656,0.77074,264.09,#46,-0.78751,-0.30094,0.53783,287.73,-0.48461,0.84153,-0.23871,210,-0.38077,-0.44862,-0.80855,268.29,#47,0.35135,0.93027,0.10561,286.66,0.19632,-0.1835,0.96322,168.45,0.91543,-0.31769,-0.2471,264.39
> ui mousemode right "rotate selected models"
> view matrix models
> #36,-0.050417,0.98638,-0.15654,94.782,-0.69213,-0.1475,-0.70654,522,-0.72001,0.072722,0.69014,257.94,#38,-0.19253,0.61249,-0.76668,290.47,-0.32152,-0.77754,-0.54042,204.72,-0.92712,0.14246,0.34663,323.93,#39,-0.036605,0.85889,0.51084,248.23,0.675,0.3982,-0.62114,214.69,-0.73691,0.32208,-0.59433,310.48,#40,-0.79668,-0.59762,0.090311,258.32,-0.5088,0.58247,-0.63392,278.66,0.32624,-0.55098,-0.76811,304.39,#41,-0.46567,0.64579,-0.60507,241.28,0.48251,0.75844,0.43812,169.07,0.74184,-0.087932,-0.66479,249.44,#42,0.14833,-0.96812,0.20187,222.92,0.81166,0.23579,0.53442,196.82,-0.56498,0.084577,0.82076,299.72,#43,-0.94811,0.102,0.30114,129.4,-0.31592,-0.40909,-0.85606,236.67,0.035873,-0.90678,0.42008,658.47,#44,0.62315,-0.3023,0.72131,321.45,0.059705,0.93798,0.34152,142.81,-0.77982,-0.16975,0.60255,296.06,#45,-0.17553,-0.80759,0.56302,287.55,0.80314,-0.44822,-0.39251,174.43,0.56934,0.38329,0.72728,259.92,#46,-0.75995,-0.42398,0.49266,284.92,-0.5656,0.80484,-0.17982,215.32,-0.32027,-0.4153,-0.85144,264.35,#47,0.40173,0.91559,-0.017617,287.94,0.23233,-0.083291,0.96906,173.9,0.8858,-0.39339,-0.24618,260.18
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 220, shift = 7.58, angle = 21.8 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53607361 -0.84408781 -0.01186894 402.29604491
0.84376073 -0.53619838 0.02364655 56.04641062
-0.02632388 0.00266175 0.99964993 -108.50518664
Axis -0.01243145 0.00856314 0.99988606
Axis point 184.81046621 138.62140563 0.00000000
Rotation angle (degrees) 122.43286561
Shift along axis -113.01401480
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 220, shift = 7.58, angle = 21.8 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53607361 -0.84408781 -0.01186894 402.29604491
0.84376073 -0.53619838 0.02364655 56.04641062
-0.02632388 0.00266175 0.99964993 -108.50518664
Axis -0.01243145 0.00856314 0.99988606
Axis point 184.81046621 138.62140563 0.00000000
Rotation angle (degrees) 122.43286561
Shift along axis -113.01401480
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 220, shift = 7.58, angle = 21.8 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53607361 -0.84408781 -0.01186894 402.29604491
0.84376073 -0.53619838 0.02364655 56.04641062
-0.02632388 0.00266175 0.99964993 -108.50518664
Axis -0.01243145 0.00856314 0.99988606
Axis point 184.81046621 138.62140563 0.00000000
Rotation angle (degrees) 122.43286561
Shift along axis -113.01401480
> view matrix models
> #36,-0.11403,0.90821,-0.40267,178.49,-0.69628,-0.36218,-0.6197,544.72,-0.70866,0.20971,0.67367,232.87,#38,-0.13921,0.39392,-0.90854,285.89,-0.31342,-0.88784,-0.33692,195.01,-0.93936,0.23785,0.24706,330.28,#39,0.21519,0.8781,0.42735,249.17,0.63027,0.20939,-0.74761,213.59,-0.74596,0.43023,-0.50838,311,#40,-0.92758,-0.37134,0.041313,274.37,-0.30035,0.67533,-0.67359,273.28,0.22223,-0.63721,-0.73795,305.3,#41,-0.43473,0.80839,-0.39688,239.92,0.60951,0.58854,0.53114,167.86,0.66295,-0.010997,-0.74858,250.33,#42,0.40264,-0.89074,0.21087,222.05,0.72977,0.45143,0.51347,201.39,-0.55256,-0.052859,0.8318,297.17,#43,-0.99172,0.12217,0.039548,94.434,-0.092294,-0.46398,-0.88102,278.19,-0.089289,-0.87738,0.47141,639,#44,0.71599,-0.054344,0.69599,305.18,-0.11909,0.97284,0.19847,126.47,-0.68788,-0.22499,0.69008,307.93,#45,-0.0589,-0.9316,0.35867,284.42,0.84805,-0.23624,-0.47433,163.16,0.52663,0.27624,0.80396,266.97,#46,-0.8213,-0.17042,0.54444,290.69,-0.39449,0.85906,-0.3262,203.76,-0.41212,-0.48268,-0.77277,270.33,#47,0.3259,0.91513,0.23732,284.65,0.17756,-0.3058,0.93539,162.56,0.92858,-0.2627,-0.26215,267.3
> view matrix models
> #36,0.013272,0.97765,-0.20983,93.112,-0.69251,-0.14239,-0.70721,521.27,-0.72128,0.1547,0.67515,245.96,#38,-0.11301,0.60248,-0.79009,284.25,-0.32269,-0.77434,-0.54431,205.02,-0.93973,0.19345,0.28192,328.21,#39,0.02142,0.82703,0.56174,243.22,0.67466,0.4027,-0.6186,214.77,-0.73782,0.39224,-0.54934,311.29,#40,-0.81845,-0.55265,0.15722,253.46,-0.51285,0.57927,-0.63359,278.78,0.25908,-0.59919,-0.75753,306.02,#41,-0.52831,0.64696,-0.54985,241.62,0.48024,0.76175,0.43486,169.1,0.70019,-0.034323,-0.71313,249.9,#42,0.19069,-0.97299,0.13007,218.99,0.81231,0.2308,0.53561,196.76,-0.55117,0.0035211,0.83439,298.47,#43,-0.94617,0.17926,0.26951,95.719,-0.32081,-0.40873,-0.85441,236.19,-0.043005,-0.89488,0.44423,648.16,#44,0.68561,-0.29193,0.66687,317.76,0.062778,0.93637,0.34536,143.27,-0.72525,-0.19492,0.66031,303.06,#45,-0.22646,-0.83438,0.50251,286.83,0.80233,-0.45231,-0.38946,174.7,0.55225,0.31499,0.77188,264.2,#46,-0.72773,-0.39205,0.56277,283.62,-0.56958,0.80256,-0.17743,215.58,-0.38209,-0.44966,-0.80735,268.37,#47,0.32537,0.94558,-0.0020339,287.2,0.23457,-0.07863,0.96891,174.17,0.91603,-0.31573,-0.24739,264.5
> view matrix models
> #36,-0.14951,0.80671,-0.57173,243.12,-0.64566,-0.51758,-0.56146,549.54,-0.74885,0.28519,0.59824,244.51,#38,-0.085158,0.21226,-0.9735,279.51,-0.25753,-0.94853,-0.18429,183.96,-0.96251,0.23501,0.13544,335.84,#39,0.39772,0.84795,0.35044,248.74,0.60592,0.044072,-0.7943,209.08,-0.68897,0.52825,-0.49626,313.76,#40,-0.98334,-0.18151,0.0097117,283.99,-0.14431,0.74705,-0.64892,263.74,0.11053,-0.63951,-0.76079,313.54,#41,-0.39763,0.89121,-0.21826,238.75,0.65502,0.44229,0.61264,167.39,0.64252,0.10064,-0.75963,250.37,#42,0.57666,-0.79201,0.20047,221.66,0.66634,0.59793,0.44551,202.08,-0.47271,-0.12333,0.87255,296.64,#43,-0.97733,0.13913,-0.15956,71.763,0.080654,-0.45217,-0.88828,289.48,-0.19574,-0.88101,0.4307,626.67,#44,0.75751,0.13321,0.63908,289.48,-0.21917,0.97404,0.056749,113.82,-0.61493,-0.18306,0.76704,312.39,#45,0.025308,-0.98257,0.18417,279.75,0.82993,-0.08205,-0.55179,154.69,0.55729,0.16681,0.81339,271.28,#46,-0.82505,0.028912,0.56432,292.27,-0.23659,0.88926,-0.39146,193.51,-0.51315,-0.45648,-0.72685,277.19,#47,0.2467,0.87484,0.41689,279.84,0.092232,-0.44943,0.88854,154.05,0.96469,-0.18076,-0.19156,271.6
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 116, shift = 10.7, angle = 6.02 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53604611 -0.84410513 -0.01187962 402.29755272
0.84377740 -0.53617111 0.02366990 56.02829232
-0.02634940 0.00266441 0.99964925 -108.49711526
Axis -0.01244346 0.00857176 0.99988584
Axis point 184.81473908 138.61703908 0.00000000
Rotation angle (degrees) 122.43102963
Shift along axis -113.01044181
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 116, shift = 10.7, angle = 6.02 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53604611 -0.84410513 -0.01187962 402.29755272
0.84377740 -0.53617111 0.02366990 56.02829232
-0.02634940 0.00266441 0.99964925 -108.49711526
Axis -0.01244346 0.00857176 0.99988584
Axis point 184.81473908 138.61703908 0.00000000
Rotation angle (degrees) 122.43102963
Shift along axis -113.01044181
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 116, shift = 10.7, angle = 6.02 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53604611 -0.84410513 -0.01187962 402.29755272
0.84377740 -0.53617111 0.02366990 56.02829232
-0.02634940 0.00266441 0.99964925 -108.49711526
Axis -0.01244346 0.00857176 0.99988584
Axis point 184.81473908 138.61703908 0.00000000
Rotation angle (degrees) 122.43102963
Shift along axis -113.01044181
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 116, shift = 10.7, angle = 6.02 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53604611 -0.84410513 -0.01187962 402.29755272
0.84377740 -0.53617111 0.02366990 56.02829232
-0.02634940 0.00266441 0.99964925 -108.49711526
Axis -0.01244346 0.00857176 0.99988584
Axis point 184.81473908 138.61703908 0.00000000
Rotation angle (degrees) 122.43102963
Shift along axis -113.01044181
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 116, shift = 10.7, angle = 6.02 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53604611 -0.84410513 -0.01187962 402.29755272
0.84377740 -0.53617111 0.02366990 56.02829232
-0.02634940 0.00266441 0.99964925 -108.49711526
Axis -0.01244346 0.00857176 0.99988584
Axis point 184.81473908 138.61703908 0.00000000
Rotation angle (degrees) 122.43102963
Shift along axis -113.01044181
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 116, shift = 10.7, angle = 6.02 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53604611 -0.84410513 -0.01187962 402.29755272
0.84377740 -0.53617111 0.02366990 56.02829232
-0.02634940 0.00266441 0.99964925 -108.49711526
Axis -0.01244346 0.00857176 0.99988584
Axis point 184.81473908 138.61703908 0.00000000
Rotation angle (degrees) 122.43102963
Shift along axis -113.01044181
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3988, overlap = 19.85
steps = 116, shift = 10.7, angle = 6.02 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53604611 -0.84410513 -0.01187962 402.29755272
0.84377740 -0.53617111 0.02366990 56.02829232
-0.02634940 0.00266441 0.99964925 -108.49711526
Axis -0.01244346 0.00857176 0.99988584
Axis point 184.81473908 138.61703908 0.00000000
Rotation angle (degrees) 122.43102963
Shift along axis -113.01044181
> ui mousemode right "translate selected models"
> view matrix models
> #36,-0.14951,0.80671,-0.57173,238.38,-0.64566,-0.51758,-0.56146,549.39,-0.74885,0.28519,0.59824,244.73,#38,-0.085158,0.21226,-0.9735,274.78,-0.25753,-0.94853,-0.18429,183.8,-0.96251,0.23501,0.13544,336.05,#39,0.39772,0.84795,0.35044,244,0.60592,0.044072,-0.7943,208.93,-0.68897,0.52825,-0.49626,313.98,#40,-0.98334,-0.18151,0.0097117,279.25,-0.14431,0.74705,-0.64892,263.59,0.11053,-0.63951,-0.76079,313.75,#41,-0.39763,0.89121,-0.21826,234.01,0.65502,0.44229,0.61264,167.24,0.64252,0.10064,-0.75963,250.58,#42,0.57666,-0.79201,0.20047,216.92,0.66634,0.59793,0.44551,201.93,-0.47271,-0.12333,0.87255,296.85,#43,-0.97733,0.13913,-0.15956,67.025,0.080654,-0.45217,-0.88828,289.33,-0.19574,-0.88101,0.4307,626.89,#44,0.75751,0.13321,0.63908,284.74,-0.21917,0.97404,0.056749,113.67,-0.61493,-0.18306,0.76704,312.6,#45,0.025308,-0.98257,0.18417,275.02,0.82993,-0.08205,-0.55179,154.54,0.55729,0.16681,0.81339,271.5,#46,-0.82505,0.028912,0.56432,287.53,-0.23659,0.88926,-0.39146,193.36,-0.51315,-0.45648,-0.72685,277.4,#47,0.2467,0.87484,0.41689,275.1,0.092232,-0.44943,0.88854,153.9,0.96469,-0.18076,-0.19156,271.82
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3989, overlap = 19.86
steps = 100, shift = 9.01, angle = 6.01 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53613146 -0.84405165 -0.01182794 402.27530857
0.84372460 -0.53625512 0.02364888 56.08871721
-0.02630367 0.00269939 0.99965036 -108.53812129
Axis -0.01241107 0.00857583 0.99988620
Axis point 184.79018629 138.62940526 0.00000000
Rotation angle (degrees) 122.43674034
Shift along axis -113.03742918
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3989, overlap = 19.86
steps = 100, shift = 9.01, angle = 6.01 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53613146 -0.84405165 -0.01182794 402.27530857
0.84372460 -0.53625512 0.02364888 56.08871721
-0.02630367 0.00269939 0.99965036 -108.53812129
Axis -0.01241107 0.00857583 0.99988620
Axis point 184.79018629 138.62940526 0.00000000
Rotation angle (degrees) 122.43674034
Shift along axis -113.03742918
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.3989, overlap = 19.86
steps = 100, shift = 9.01, angle = 6.01 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53613146 -0.84405165 -0.01182794 402.27530857
0.84372460 -0.53625512 0.02364888 56.08871721
-0.02630367 0.00269939 0.99965036 -108.53812129
Axis -0.01241107 0.00857583 0.99988620
Axis point 184.79018629 138.62940526 0.00000000
Rotation angle (degrees) 122.43674034
Shift along axis -113.03742918
> fitmap #36 inMap #37
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 41936
points
correlation = 0.6638, correlation about mean = 0.399, overlap = 19.86
steps = 44, shift = 0.00723, angle = 0.00449 degrees
Position of postprocess_20231221.mrc (#36) relative to emd_3720_2017_leaf.map
(#37) coordinates:
Matrix rotation and translation
-0.53615244 -0.84403825 -0.01183341 402.28427282
0.84371314 -0.53627643 0.02357444 56.11035694
-0.02624370 0.00265549 0.99965206 -108.53922466
Axis -0.01239316 0.00853720 0.99988676
Axis point 184.79135404 138.63796538 0.00000000
Rotation angle (degrees) 122.43811842
Shift along axis -113.03348140
> select subtract #36
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 11 models selected
> select subtract #38
31014 atoms, 31550 bonds, 1 pseudobond, 3912 residues, 10 models selected
> select subtract #39
23513 atoms, 23931 bonds, 1 pseudobond, 2959 residues, 9 models selected
> select subtract #40
22056 atoms, 22448 bonds, 1 pseudobond, 2778 residues, 8 models selected
> hide #!37 models
> select subtract #41
20599 atoms, 20965 bonds, 1 pseudobond, 2597 residues, 7 models selected
> select subtract #42
13385 atoms, 13592 bonds, 1 pseudobond, 1692 residues, 6 models selected
> select subtract #43
11923 atoms, 12111 bonds, 1 pseudobond, 1513 residues, 5 models selected
> select subtract #44
5250 atoms, 5325 bonds, 660 residues, 3 models selected
> select subtract #45
3830 atoms, 3884 bonds, 483 residues, 2 models selected
> select subtract #46
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> select subtract #47
Nothing selected
> show #38 models
> fitmap #38 inMap #36
Fit molecule copy of CopA_F8WHL2.pdb (#38) to map postprocess_20231221.mrc
(#36) using 9810 atoms
average map value = 0.001845, steps = 100
shifted from previous position = 13.2
rotated from previous position = 6.01 degrees
atoms outside contour = 7364, contour level = 0.0030265
Position of copy of CopA_F8WHL2.pdb (#38) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.89962787 0.40507870 0.16303658 162.22050948
-0.21016116 0.72895774 -0.65150049 244.61856024
-0.38275575 0.55184404 0.74092251 239.08858201
Axis 0.82559489 0.37445914 -0.42210595
Axis point 0.00000000 -322.85722656 438.16719469
Rotation angle (degrees) 46.78373091
Shift along axis 124.60736685
> hide #38 models
> show #39 models
> fitmap #39 inMap #36
Fit molecule copy of CopB_Q9JIF7.pdb (#39) to map postprocess_20231221.mrc
(#36) using 7501 atoms
average map value = 0.002525, steps = 152
shifted from previous position = 8.96
rotated from previous position = 5.97 degrees
atoms outside contour = 5351, contour level = 0.0030265
Position of copy of CopB_Q9JIF7.pdb (#39) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.06472481 -0.55243097 0.83104194 167.09562729
-0.18885300 0.81095780 0.55378875 200.49830852
-0.97987001 -0.19278864 -0.05183916 229.32932065
Axis -0.37474512 0.90898871 0.18249826
Axis point 225.52004092 0.00000000 -20.08070126
Rotation angle (degrees) 95.05306122
Shift along axis 161.48462904
> hide #39 models
> show #40 models
> fitmap #40 inMap #36
Fit molecule copy of hArf1_P84078 (#40) to map postprocess_20231221.mrc (#36)
using 1457 atoms
average map value = 0.002588, steps = 92
shifted from previous position = 11.4
rotated from previous position = 6.03 degrees
atoms outside contour = 1109, contour level = 0.0030265
Position of copy of hArf1_P84078 (#40) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.15801986 0.02346451 0.98715709 126.68399998
-0.68662820 -0.71584286 0.12692792 200.56114650
0.70962767 -0.69786703 -0.09700599 178.42871677
Axis -0.73433684 0.24709181 -0.63221439
Axis point 0.00000000 138.25600143 -15.36555268
Rotation angle (degrees) 145.83405390
Shift along axis -156.27691420
> hide #40 models
> show #41 models
> fitmap #41 inMap #36
Fit molecule copy of hArf1_P84078 (#41) to map postprocess_20231221.mrc (#36)
using 1457 atoms
average map value = 0.003766, steps = 68
shifted from previous position = 8.18
rotated from previous position = 5.97 degrees
atoms outside contour = 534, contour level = 0.0030265
Position of copy of hArf1_P84078 (#41) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
-0.84428374 -0.49456571 0.20637270 242.99409799
-0.47730328 0.51888718 -0.70918098 195.95467590
0.24365245 -0.69725235 -0.67414585 220.55144469
Axis 0.27884153 -0.87144483 0.40352361
Axis point 151.45924998 0.00000000 157.15946705
Rotation angle (degrees) 178.77437128
Shift along axis -14.00912865
> hide #41 models
> show #42 models
> fitmap #42 inMap #36
Fit molecule copy of CopBprime_O55029.pdb (#42) to map
postprocess_20231221.mrc (#36) using 7214 atoms
average map value = 0.00312, steps = 56
shifted from previous position = 5.95
rotated from previous position = 5.98 degrees
atoms outside contour = 3628, contour level = 0.0030265
Position of copy of CopBprime_O55029.pdb (#42) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.16268022 -0.17529317 -0.97098272 188.48242636
-0.01387082 -0.98358841 0.17989284 177.42102522
-0.98658134 0.04273334 0.15757892 238.54302847
Axis -0.64576423 0.07344028 0.75999677
Axis point 189.55660736 85.43076212 0.00000000
Rotation angle (degrees) 173.90372847
Shift along axis 72.60657227
> hide #42 models
> show #43 models
> fitmap #43 inMap #36
Fit molecule copy of CopD_Q5XJY5 (#43) to map postprocess_20231221.mrc (#36)
using 1462 atoms
average map value = 0.003142, steps = 164
shifted from previous position = 6.52
rotated from previous position = 35 degrees
atoms outside contour = 865, contour level = 0.0030265
Position of copy of CopD_Q5XJY5 (#43) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
-0.32491016 0.89810858 0.29636864 -149.93069389
-0.91987837 -0.37289481 0.12154526 221.26426157
0.21967517 -0.23313181 0.94730797 434.62351627
Axis -0.19131934 0.04136987 -0.98065562
Axis point -35.80244399 196.85797289 0.00000000
Rotation angle (degrees) 112.03967239
Shift along axis -388.37767818
> select add #43
1462 atoms, 1481 bonds, 179 residues, 1 model selected
> view matrix models
> #43,-0.97733,0.13913,-0.15956,67.371,0.080654,-0.45217,-0.88828,293.04,-0.19574,-0.88101,0.4307,624.54
> fitmap #43 inMap #36
Fit molecule copy of CopD_Q5XJY5 (#43) to map postprocess_20231221.mrc (#36)
using 1462 atoms
average map value = 0.003729, steps = 88
shifted from previous position = 5.98
rotated from previous position = 6.06 degrees
atoms outside contour = 772, contour level = 0.0030265
Position of copy of CopD_Q5XJY5 (#43) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.23754336 0.93136597 0.27591773 -93.05673218
-0.88686680 0.09206350 0.45275999 106.11011123
0.39628329 -0.35225240 0.84786662 472.43405137
Axis -0.40410032 -0.06042114 -0.91271694
Axis point -102.04661937 189.92856592 0.00000000
Rotation angle (degrees) 84.90906303
Shift along axis -400.00560060
> view matrix models
> #43,-0.99401,0.079827,-0.074614,95.992,0.032531,-0.43569,-0.89951,279.06,-0.10431,-0.89655,0.43049,631.69
> fitmap #43 inMap #36
Fit molecule copy of CopD_Q5XJY5 (#43) to map postprocess_20231221.mrc (#36)
using 1462 atoms
average map value = 0.003729, steps = 68
shifted from previous position = 4.11
rotated from previous position = 0.109 degrees
atoms outside contour = 773, contour level = 0.0030265
Position of copy of CopD_Q5XJY5 (#43) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.23900079 0.93130387 0.27486677 -92.97642963
-0.88620586 0.09350435 0.45375778 105.80878398
0.39688514 -0.35203701 0.84767455 472.41541880
Axis -0.40454241 -0.06125829 -0.91246527
Axis point -102.44395100 189.84768420 0.00000000
Rotation angle (degrees) 84.83122436
Shift along axis -399.93141732
> select subtract #43
Nothing selected
> hide #43 models
> show #!44 models
> fitmap #44 inMap #36
Fit molecule copy of CopG_Q9QZE5 (#44) to map postprocess_20231221.mrc (#36)
using 6673 atoms
average map value = 0.003524, steps = 84
shifted from previous position = 12.9
rotated from previous position = 6.04 degrees
atoms outside contour = 4070, contour level = 0.0030265
Position of copy of CopG_Q9QZE5 (#44) relative to postprocess_20231221.mrc
(#36) coordinates:
Matrix rotation and translation
0.48946347 -0.51115936 -0.70649955 223.51199949
0.54898811 -0.44884913 0.70508617 282.29297018
-0.67752311 -0.73297378 0.06092515 258.74098150
Axis -0.80480981 -0.01621666 0.59331121
Axis point 0.00000000 245.02374166 103.83319278
Rotation angle (degrees) 116.69430856
Shift along axis -30.94857405
> hide #!44 models
> show #45 models
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.003341, steps = 140
shifted from previous position = 7.55
rotated from previous position = 28.6 degrees
atoms outside contour = 848, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.79241779 -0.25904378 -0.55224123 225.83639020
-0.24122239 -0.69846324 0.67376618 252.43001963
-0.56025513 0.66711726 0.49098754 221.81404820
Axis -0.32212885 0.38825989 0.86341604
Axis point 153.79328451 77.22601021 0.00000000
Rotation angle (degrees) 179.40868121
Shift along axis 216.77784350
> hide #45 models
> show #46 models
> fitmap #46 inMap #36
Fit molecule copy of Golph3_ Q9CRA5.pdb (#46) to map postprocess_20231221.mrc
(#36) using 2367 atoms
average map value = 0.002844, steps = 96
shifted from previous position = 15.2
rotated from previous position = 22.1 degrees
atoms outside contour = 1512, contour level = 0.0030265
Position of copy of Golph3_ Q9CRA5.pdb (#46) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.88215741 -0.29722968 0.36531195 188.44731661
-0.47090905 -0.56749136 0.67542448 245.58008344
0.00655517 -0.76785941 -0.64058485 188.06587507
Axis -0.96391743 0.23960076 -0.11599421
Axis point 0.00000000 186.21158181 17.25382099
Rotation angle (degrees) 131.52596597
Shift along axis -144.62103243
> select add #46
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> view matrix models
> #46,-0.82505,0.028912,0.56432,291.15,-0.23659,0.88926,-0.39146,195.77,-0.51315,-0.45648,-0.72685,263.31
> fitmap #46 inMap #36
Fit molecule copy of Golph3_ Q9CRA5.pdb (#46) to map postprocess_20231221.mrc
(#36) using 2367 atoms
average map value = 0.0031, steps = 56
shifted from previous position = 6.03
rotated from previous position = 6.01 degrees
atoms outside contour = 1160, contour level = 0.0030265
Position of copy of Golph3_ Q9CRA5.pdb (#46) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.66096817 -0.23564404 0.71245559 198.02898892
-0.68872881 -0.56745747 0.45127003 233.22010661
0.29794916 -0.78896381 -0.53736617 191.32937752
Axis -0.89616357 0.29951252 -0.32738832
Axis point 0.00000000 180.10300621 -4.23076087
Rotation angle (degrees) 136.21386820
Shift along axis -170.25302671
> show #45 models
> select subtract #46
Nothing selected
> select add #45
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> view matrix models
> #45,0.21012,-0.87378,0.43859,277.7,0.96106,0.10223,-0.25675,165.54,0.1795,0.47545,0.86123,257.13
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.003252, steps = 76
shifted from previous position = 3.55
rotated from previous position = 5.44 degrees
atoms outside contour = 813, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.74307979 -0.25499030 -0.61871834 231.17592815
-0.25871991 -0.74320531 0.61701692 238.13464030
-0.61716809 0.61856756 0.48628977 211.26405643
Axis 0.35841371 -0.35832445 -0.86205754
Axis point 159.61400354 74.97358294 0.00000000
Rotation angle (degrees) 179.87605755
Shift along axis -184.59461497
> select subtract #45
Nothing selected
> show #47 models
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003943, steps = 84
shifted from previous position = 12.6
rotated from previous position = 6.02 degrees
atoms outside contour = 660, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.81856850 0.29541049 -0.49262388 229.56463346
0.42692248 0.88665736 -0.17769625 242.04056520
0.38429525 -0.35576876 -0.85190715 217.27719994
Axis -0.19688936 -0.96958283 0.14540881
Axis point 58.97509138 0.00000000 149.05910006
Rotation angle (degrees) 153.11413728
Shift along axis -248.28319028
> hide #!36 models
> show #!36 models
> select add #47
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> view matrix models
> #47,0.32785,0.87698,0.35131,275.82,0.096539,-0.40101,0.91097,160.42,0.93978,-0.26475,-0.21614,255.31
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003943, steps = 72
shifted from previous position = 5.7
rotated from previous position = 0.0285 degrees
atoms outside contour = 662, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.81884961 0.29515291 -0.49231100 229.57867805
0.42656715 0.88679941 -0.17784067 242.04679876
0.38409091 -0.35562846 -0.85205787 217.26175350
Axis -0.19669890 -0.96962391 0.14539264
Axis point 59.03249218 0.00000000 149.04035077
Rotation angle (degrees) 153.13250017
Shift along axis -248.26397584
> view matrix models
> #47,0.3277,0.87708,0.3512,275.64,0.097012,-0.401,0.91093,162.99,0.93979,-0.26444,-0.21649,257.75
> view matrix models
> #47,0.3277,0.87708,0.3512,275.87,0.097012,-0.401,0.91093,160.24,0.93979,-0.26444,-0.21649,257.67
> ui mousemode right "rotate selected models"
> view matrix models
> #47,0.099911,0.92585,0.36445,276.02,0.092207,-0.37333,0.92311,159.99,0.99071,-0.058624,-0.12267,255.51
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003943, steps = 72
shifted from previous position = 4.67
rotated from previous position = 13.4 degrees
atoms outside contour = 662, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.81870415 0.29453144 -0.49292472 229.57598062
0.42644716 0.88673453 -0.17845091 242.04233282
0.38453397 -0.35630484 -0.85157532 217.27081545
Axis -0.19653058 -0.96960163 0.14576834
Axis point 58.99807446 0.00000000 149.13106012
Rotation angle (degrees) 153.09682552
Shift along axis -248.13213561
> hide #!36 models
> view matrix models
> #47,0.22168,0.97072,0.092523,273.06,0.86044,-0.15008,-0.48696,143.03,-0.45881,0.18756,-0.86851,254.23
> view matrix models
> #47,0.3029,0.90974,0.28394,275.09,0.61891,-0.41434,0.66729,156.13,0.72471,-0.026388,-0.68855,254.8
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003336, steps = 64
shifted from previous position = 5.95
rotated from previous position = 10.5 degrees
atoms outside contour = 802, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.95758064 0.24644955 0.14933843 234.39384468
0.20215165 0.94383530 -0.26136118 238.42578689
-0.20536323 -0.22008539 -0.95361858 220.01146182
Axis 0.11470840 0.98574167 -0.12310707
Axis point 114.77598687 0.00000000 115.34990095
Rotation angle (degrees) 169.63512521
Shift along axis 234.82821042
> view matrix models
> #47,-0.70547,-0.10535,-0.70087,280.07,-0.705,0.0028904,0.7092,155.05,-0.072687,0.99443,-0.076309,250.98
> view matrix models
> #47,-0.80485,-0.090919,-0.58647,281.06,-0.57553,-0.12162,0.80869,157.07,-0.14485,0.9884,0.045562,252.21
> ui mousemode right "translate selected models"
> view matrix models
> #47,-0.80485,-0.090919,-0.58647,273.14,-0.57553,-0.12162,0.80869,155.64,-0.14485,0.9884,0.045562,258.19
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003447, steps = 132
shifted from previous position = 4.97
rotated from previous position = 22.8 degrees
atoms outside contour = 763, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.30588544 -0.72116594 -0.62157365 234.08714943
-0.47200092 0.45211849 -0.75683817 239.69779730
0.82683085 0.52488911 -0.20209452 215.51541985
Axis 0.65727153 -0.74274384 0.12777217
Axis point 107.57558101 0.00000000 252.91913519
Rotation angle (degrees) 102.82919125
Shift along axis 3.36162952
> view matrix models
> #47,-0.86066,0.2634,-0.43576,315.58,-0.46594,-0.062242,0.88263,179.49,0.20536,0.96268,0.1763,210.55
> view matrix models
> #47,-0.86066,0.2634,-0.43576,318.6,-0.46594,-0.062242,0.88263,152.04,0.20536,0.96268,0.1763,201.33
> ui mousemode right "rotate selected models"
> view matrix models
> #47,-0.70672,0.10683,-0.69938,318.18,-0.6883,-0.3325,0.64473,154.47,-0.16367,0.93703,0.30851,203.82
> view matrix models
> #47,-0.65261,-0.74609,0.13214,335.68,0.74868,-0.66178,-0.039003,149.16,0.11655,0.073477,0.99046,219.62
> view matrix models
> #47,-0.97051,-0.18493,-0.15461,327.03,0.2146,-0.37077,-0.90359,140.31,0.10978,-0.91013,0.39952,228.12
> view matrix models
> #47,-0.94215,-0.083255,-0.32468,324.29,0.33323,-0.3371,-0.88052,139.67,-0.036144,-0.93778,0.34535,228.51
> ui mousemode right "translate selected models"
> view matrix models
> #47,-0.94215,-0.083255,-0.32468,291.69,0.33323,-0.3371,-0.88052,148.12,-0.036144,-0.93778,0.34535,275.46
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003524, steps = 296
shifted from previous position = 6.93
rotated from previous position = 36.8 degrees
atoms outside contour = 843, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.23600017 0.84960641 0.47167032 222.05629774
-0.91651317 -0.03328767 -0.39861707 257.82571853
-0.32296680 -0.52636575 0.78653135 224.18820747
Axis -0.06582058 0.40942479 -0.90996648
Axis point 233.55009631 87.16188170 0.00000000
Rotation angle (degrees) 103.96789961
Shift along axis -113.05938715
> ui mousemode right "rotate selected models"
> view matrix models
> #47,-0.69303,-0.58037,0.42765,305.93,-0.11104,-0.5002,-0.85876,156.99,0.71231,-0.64263,0.28221,268.54
> view matrix models
> #47,-0.74623,-0.37782,0.54808,304.34,-0.19131,-0.66689,-0.72018,160.51,0.63761,-0.64227,0.42537,269.86
> view matrix models
> #47,-0.79925,-0.30357,0.5187,303.3,-0.20727,-0.67088,-0.71201,160.67,0.56413,-0.67658,0.47328,270.91
> ui mousemode right "translate selected models"
> view matrix models
> #47,-0.79925,-0.30357,0.5187,302.6,-0.20727,-0.67088,-0.71201,165.43,0.56413,-0.67658,0.47328,255.98
> view matrix models
> #47,-0.79925,-0.30357,0.5187,280.85,-0.20727,-0.67088,-0.71201,177.97,0.56413,-0.67658,0.47328,238.93
> view matrix models
> #47,-0.79925,-0.30357,0.5187,268.48,-0.20727,-0.67088,-0.71201,168.94,0.56413,-0.67658,0.47328,253.68
> ui mousemode right "rotate selected models"
> view matrix models
> #47,-0.95716,0.042458,-0.28642,258.2,0.2287,-0.49584,-0.83776,164.32,-0.17759,-0.86738,0.46488,258.42
> ui mousemode right "translate selected models"
> view matrix models
> #47,-0.95716,0.042458,-0.28642,269.87,0.2287,-0.49584,-0.83776,164.07,-0.17759,-0.86738,0.46488,266.05
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003418, steps = 200
shifted from previous position = 5.22
rotated from previous position = 24.6 degrees
atoms outside contour = 772, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.26044120 0.94244973 0.20966382 226.85831724
-0.94833218 0.29046575 -0.12765478 239.40983299
-0.18120836 -0.16558438 0.96940465 217.26827378
Axis -0.01964111 0.20240559 -0.97910480
Axis point 293.57103397 -6.82403053 0.00000000
Rotation angle (degrees) 74.92069348
Shift along axis -168.72627056
> ui mousemode right "rotate selected models"
> view matrix models
> #47,-0.77651,-0.35256,-0.52223,281.7,0.59896,-0.15569,-0.7855,154.26,0.19563,-0.92275,0.33206,261.79
> view matrix models
> #47,-0.87705,-0.38104,-0.29257,284.15,0.40177,-0.24788,-0.88155,155.34,0.26338,-0.89071,0.37049,261.45
> ui mousemode right "translate selected models"
> view matrix models
> #47,-0.87705,-0.38104,-0.29257,274.89,0.40177,-0.24788,-0.88155,163.35,0.26338,-0.89071,0.37049,254.91
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003586, steps = 132
shifted from previous position = 4.79
rotated from previous position = 8.83 degrees
atoms outside contour = 722, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.33536384 0.83016103 0.44538049 228.49116961
-0.82065670 -0.48959996 0.29464296 240.71463678
0.46265938 -0.26669189 0.84547133 214.80312053
Axis -0.32191614 -0.00990915 -0.94671633
Axis point 151.27276822 76.39905039 0.00000000
Rotation angle (degrees) 119.32390386
Shift along axis -279.29789433
> ui mousemode right "rotate selected models"
> view matrix models
> #47,-0.91252,0.0016876,-0.40902,269.21,0.35726,-0.48365,-0.79903,167.66,-0.19917,-0.87526,0.44074,262.81
> view matrix models
> #47,-0.94788,-0.16031,-0.27537,272.49,0.31847,-0.44938,-0.83465,167.06,0.010056,-0.87884,0.47701,262.49
> ui mousemode right "translate selected models"
> view matrix models
> #47,-0.94788,-0.16031,-0.27537,271.44,0.31847,-0.44938,-0.83465,161.58,0.010056,-0.87884,0.47701,260.2
> view matrix models
> #47,-0.94788,-0.16031,-0.27537,275.35,0.31847,-0.44938,-0.83465,161.71,0.010056,-0.87884,0.47701,257.04
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003554, steps = 144
shifted from previous position = 2.44
rotated from previous position = 8.11 degrees
atoms outside contour = 759, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.02967744 0.93785449 0.34575747 230.60267565
-0.97181536 -0.05386033 0.22950813 237.60977330
0.23386785 -0.34282363 0.90982296 212.71121886
Axis -0.28663485 0.05603649 -0.95639969
Axis point 207.82482217 47.44475019 0.00000000
Rotation angle (degrees) 93.27795871
Shift along axis -256.22088917
> fitmap #47 inMap #36
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#36) using 1463 atoms
average map value = 0.003554, steps = 64
shifted from previous position = 0.0428
rotated from previous position = 0.0858 degrees
atoms outside contour = 757, contour level = 0.0030265
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
0.02972147 0.93767602 0.34623739 230.58929566
-0.97214566 -0.05344952 0.22820164 237.64468398
0.23248543 -0.34337567 0.90996906 212.69033249
Axis -0.28625208 0.05696821 -0.95645929
Axis point 208.02160818 47.45879110 0.00000000
Rotation angle (degrees) 93.26071473
Shift along axis -255.89811636
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.003251, steps = 48
shifted from previous position = 0.0293
rotated from previous position = 0.012 degrees
atoms outside contour = 814, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.74308490 -0.25515086 -0.61864601 231.19634471
-0.25852657 -0.74323382 0.61706361 238.12726488
-0.61724295 0.61846709 0.48632255 211.28277057
Axis 0.35841059 -0.35830483 -0.86206699
Axis point 159.61699509 74.98658362 0.00000000
Rotation angle (degrees) 179.88781970
Shift along axis -184.59883245
> fitmap #45 inMap #36
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#36) using 1420 atoms
average map value = 0.00325, steps = 44
shifted from previous position = 0.0394
rotated from previous position = 0.073 degrees
atoms outside contour = 812, contour level = 0.0030265
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#36) coordinates:
Matrix rotation and translation
-0.74235412 -0.25550993 -0.61937472 231.20075895
-0.25920664 -0.74292440 0.61715092 238.15986692
-0.61783677 0.61869058 0.48528312 211.26007469
Axis 0.35891956 -0.35852041 -0.86176555
Axis point 159.70161943 74.94960414 0.00000000
Rotation angle (degrees) 179.87710908
Shift along axis -184.45935437
> select subtract #47
Nothing selected
> hide #47 models
> hide #46 models
> hide #45 models
> show #!1 models
> show #!16 models
> show #!24 models
> show #!36 models
> show #38 models
> show #39 models
> show #40 models
> show #41 models
> show #42 models
> show #43 models
> show #!44 models
> show #45 models
> show #46 models
> show #47 models
> show #35 models
> show #34 models
> show #33 models
> show #!32 models
> show #31 models
> show #30 models
> show #29 models
> show #28 models
> show #27 models
> show #26 models
> show #12 models
> show #11 models
> show #10 models
> show #!9 models
> show #8 models
> show #7 models
> show #6 models
> show #5 models
> show #4 models
> show #3 models
> hide #!1 models
> hide #!16 models
> show #!16 models
> hide #!24 models
> hide #!36 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_2_fitting_final.cxs"
> hide #40 models
> hide #39 models
> hide #38 models
> hide #41 models
> hide #42 models
> hide #43 models
> hide #!44 models
> hide #45 models
> hide #46 models
> hide #47 models
> hide #35 models
> hide #34 models
> hide #33 models
> hide #!32 models
> hide #31 models
> hide #30 models
> hide #29 models
> hide #28 models
> hide #27 models
> hide #26 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #!16 models
> show #!19 models
> show #!1 models
> volume #19 level 0.5397
> show #4 models
> hide #4 models
> show #7 models
> hide #7 models
> show #7 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> select add #20
2 models selected
> volume #20 level 1.011
> view matrix models #20,1,0,0,312.34,0,1,0,273.87,0,0,1,241.7
> view matrix models #20,1,0,0,332.44,0,1,0,260.55,0,0,1,299.91
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.95666,0.21298,-0.19859,329.18,-0.24071,0.96215,-0.12773,257.74,0.16387,0.17,0.97172,300.02
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.95666,0.21298,-0.19859,361.78,-0.24071,0.96215,-0.12773,267.27,0.16387,0.17,0.97172,311.62
> view matrix models
> #20,0.95666,0.21298,-0.19859,333.5,-0.24071,0.96215,-0.12773,213.9,0.16387,0.17,0.97172,295.17
> view matrix models
> #20,0.95666,0.21298,-0.19859,357.76,-0.24071,0.96215,-0.12773,227.65,0.16387,0.17,0.97172,300.14
> select subtract #20
Nothing selected
> select add #20
2 models selected
> select subtract #20
Nothing selected
> hide #7 models
> select add #20
2 models selected
> view matrix models
> #20,0.95666,0.21298,-0.19859,311.96,-0.24071,0.96215,-0.12773,227.73,0.16387,0.17,0.97172,284.57
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.89857,0.42787,-0.097447,314.09,-0.41305,0.74969,-0.51706,219.97,-0.14818,0.50487,0.85038,282.45
> view matrix models
> #20,0.88872,0.4396,-0.13009,313.51,-0.43969,0.73699,-0.51335,219.97,-0.12979,0.51342,0.84826,282.46
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.88872,0.4396,-0.13009,347.36,-0.43969,0.73699,-0.51335,231.34,-0.12979,0.51342,0.84826,299.01
> fitmap #20 inMap #19
Fit map emd_2988_2015_linkage3.map in map COPI_golph_linkage3_postprocess.mrc
using 652612 points
correlation = 0.9026, correlation about mean = 0.3729, overlap = 8.04e+05
steps = 112, shift = 18.2, angle = 12.3 degrees
Position of emd_2988_2015_linkage3.map (#20) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.99933497 0.03646392 0.00008145 272.09854390
-0.03646391 0.99933497 -0.00004234 272.11937185
-0.00008294 0.00003934 1.00000000 360.59420077
Axis 0.00112008 0.00225413 -0.99999683
Axis point 7618.69992125 -7334.22915568 0.00000000
Rotation angle (degrees) 2.08969831
Shift along axis -359.67489280
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> select subtract #20
Nothing selected
> hide #!1 models
> show #!2 models
> show #!25 models
> select add #25
2 models selected
> view matrix models
> #25,0.6466,0.19867,-0.73651,11.706,-0.076592,0.97752,0.19644,4.369,0.75898,-0.070608,0.64728,-32.071
> view matrix models
> #25,0.6466,0.19867,-0.73651,-19.879,-0.076592,0.97752,0.19644,83.472,0.75898,-0.070608,0.64728,-52.205
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.12133,0.26002,-0.95795,59.291,-0.88041,-0.41751,-0.22484,392.3,-0.45842,0.87067,0.17827,30.565
> view matrix models
> #25,0.16005,0.3047,-0.9389,47.254,-0.93859,-0.24756,-0.24034,380.5,-0.30567,0.91971,0.24637,-0.8887
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.16005,0.3047,-0.9389,108.88,-0.93859,-0.24756,-0.24034,444.07,-0.30567,0.91971,0.24637,158.42
> view matrix models
> #25,0.16005,0.3047,-0.9389,245.61,-0.93859,-0.24756,-0.24034,440.82,-0.30567,0.91971,0.24637,152.37
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.68844,0.71936,-0.092628,187.99,-0.58828,-0.62851,-0.50883,479.68,-0.42425,-0.29581,0.85587,235.84
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.68844,0.71936,-0.092628,228.29,-0.58828,-0.62851,-0.50883,426.64,-0.42425,-0.29581,0.85587,244.71
> view matrix models
> #25,-0.68844,0.71936,-0.092628,228.62,-0.58828,-0.62851,-0.50883,425.78,-0.42425,-0.29581,0.85587,227.31
> view matrix models
> #25,-0.68844,0.71936,-0.092628,235.42,-0.58828,-0.62851,-0.50883,425.2,-0.42425,-0.29581,0.85587,231.72
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8183, correlation about mean = 0.05053, overlap = 5958
steps = 148, shift = 49.8, angle = 31.3 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.46489818 0.75248179 -0.46651995 215.17123274
-0.88308305 -0.43190505 0.18336412 384.52257675
-0.06351416 0.49722150 0.86529577 161.30552428
Axis 0.18317022 -0.23519810 -0.95453157
Axis point 222.63405314 97.56461346 0.00000000
Rotation angle (degrees) 121.04784811
Shift along axis -204.99723344
> view matrix models
> #25,-0.63568,0.58961,-0.49826,178.72,-0.60337,-0.78211,-0.15572,220.21,-0.48151,0.20165,0.85293,33.15
> view matrix models
> #25,-0.63568,0.58961,-0.49826,204.73,-0.60337,-0.78211,-0.15572,153.55,-0.48151,0.20165,0.85293,68.534
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.10316,0.6244,-0.77426,174.37,-0.78422,0.42777,0.44946,-44.644,0.61184,0.65356,0.44554,-58.732
> view matrix models
> #25,-0.018668,0.44332,-0.89617,201.4,-0.41766,0.81092,0.40985,-126.85,0.90841,0.38194,0.17002,-25.977
> view matrix models
> #25,-0.021163,0.4584,-0.8885,198.94,-0.44909,0.78963,0.41809,-121.77,0.89324,0.40786,0.18915,-29.705
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.021163,0.4584,-0.8885,349.6,-0.44909,0.78963,0.41809,84.38,0.89324,0.40786,0.18915,41.841
> view matrix models
> #25,-0.021163,0.4584,-0.8885,274.98,-0.44909,0.78963,0.41809,192.78,0.89324,0.40786,0.18915,61.831
> view matrix models
> #25,-0.021163,0.4584,-0.8885,42.531,-0.44909,0.78963,0.41809,110.28,0.89324,0.40786,0.18915,-60.794
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.13919,0.30541,-0.94199,49.246,-0.1004,0.9507,0.2934,67.03,0.98516,0.053742,0.163,-25.73
> view matrix models
> #25,0.23609,0.03095,-0.97124,74.628,0.3876,0.91354,0.12333,37.266,0.89108,-0.40557,0.20368,34.664
> view matrix models
> #25,0.43747,0.69352,-0.57241,-76.094,-0.71054,0.65674,0.25265,175.96,0.55114,0.2962,0.78007,-81.442
> view matrix models
> #25,0.74812,0.65918,0.076091,-186.71,-0.64557,0.69653,0.31318,156.45,0.15345,-0.28342,0.94664,12.108
> view matrix models
> #25,0.77221,0.46411,0.43393,-210.12,-0.62128,0.6946,0.36269,147.85,-0.13308,-0.54967,0.82472,91.173
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.77221,0.46411,0.43393,-219.73,-0.62128,0.6946,0.36269,143.24,-0.13308,-0.54967,0.82472,138
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.93919,-0.2422,0.24345,81.058,0.084195,-0.84969,-0.52052,356.24,0.33292,-0.46837,0.81841,76.482
> view matrix models
> #25,-0.031081,0.99339,-0.11047,-125.32,-0.36442,-0.11417,-0.92421,368.75,-0.93072,0.011531,0.36556,217.5
> view matrix models
> #25,0.59583,0.57327,0.56244,-228.63,-0.68436,0.72893,-0.017973,193.02,-0.42028,-0.3742,0.82664,149.26
> view matrix models
> #25,0.75972,-0.62162,-0.19084,-12.12,0.53019,0.76208,-0.37167,95.419,0.37647,0.18118,0.90854,-16.961
> view matrix models
> #25,0.89727,-0.3718,0.23805,-110.11,0.43717,0.67312,-0.59648,144.14,0.061533,0.63927,0.76651,-18.596
> view matrix models
> #25,0.76784,-0.5143,-0.38199,-2.3573,0.18231,0.74702,-0.63931,169.35,0.61415,0.42125,0.66736,-42.795
> view matrix models
> #25,0.89678,-0.033832,-0.44118,-66.936,0.13282,0.97167,0.19547,45.621,0.42207,-0.23389,0.87587,31.4
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.89678,-0.033832,-0.44118,171.25,0.13282,0.97167,0.19547,53.745,0.42207,-0.23389,0.87587,88.916
> view matrix models
> #25,0.89678,-0.033832,-0.44118,195.74,0.13282,0.97167,0.19547,86.943,0.42207,-0.23389,0.87587,93.725
> view matrix models
> #25,0.89678,-0.033832,-0.44118,195.82,0.13282,0.97167,0.19547,119.59,0.42207,-0.23389,0.87587,139.26
> view matrix models
> #25,0.89678,-0.033832,-0.44118,184.36,0.13282,0.97167,0.19547,100.48,0.42207,-0.23389,0.87587,129.53
> view matrix models
> #25,0.89678,-0.033832,-0.44118,145.7,0.13282,0.97167,0.19547,57.277,0.42207,-0.23389,0.87587,113.63
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.78116,0.27107,-0.56241,137.28,-0.5906,0.61291,-0.52491,270.19,0.20242,0.7422,0.63887,51.138
> view matrix models
> #25,0.77342,0.1674,-0.6114,156.54,-0.58448,0.56168,-0.58558,283.06,0.24538,0.81024,0.53225,51.27
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.77342,0.1674,-0.6114,169.97,-0.58448,0.56168,-0.58558,306.64,0.24538,0.81024,0.53225,81.849
> view matrix models
> #25,0.77342,0.1674,-0.6114,167.16,-0.58448,0.56168,-0.58558,296.96,0.24538,0.81024,0.53225,59.331
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.6409,-0.51173,-0.57217,258.28,0.14465,0.81254,-0.56468,182.18,0.75387,0.27914,0.59477,57.59
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8146, correlation about mean = 0.05, overlap = 5646
steps = 180, shift = 38.8, angle = 14.9 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.70479046 -0.52630711 -0.47567979 198.09278448
0.41600529 0.84975311 -0.32381983 129.68092723
0.57463905 0.03033982 0.81784442 144.26284646
Axis 0.24343593 -0.72194938 0.64770985
Axis point -60.73686098 0.00000000 429.54979468
Rotation angle (degrees) 46.67042076
Shift along axis 48.04030265
> view matrix models
> #25,0.078449,-0.39198,-0.91662,387.45,0.82643,0.5398,-0.16011,98.418,0.55755,-0.74496,0.36629,225.6
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.808, correlation about mean = 0.04063, overlap = 5479
steps = 100, shift = 14.7, angle = 17.9 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.12186889 -0.39353508 -0.91119600 296.34979061
0.96823416 0.24908247 0.02192166 111.44966518
0.21833601 -0.88492265 0.41138951 343.50685782
Axis -0.45613137 -0.56814051 0.68495294
Axis point 175.93624035 403.10747204 0.00000000
Rotation angle (degrees) 96.24784959
Shift along axis 36.79252640
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> view matrix models
> #25,-0.75203,0.6566,0.057618,234.67,-0.22465,-0.17315,-0.95893,414,-0.61966,-0.73409,0.27772,375.53
> view matrix models
> #25,-0.7827,0.55937,-0.27292,290.32,-0.46771,-0.81792,-0.33505,441.7,-0.41064,-0.1346,0.90181,203.8
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8588, correlation about mean = 0.04115, overlap = 5859
steps = 260, shift = 39.3, angle = 35.6 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.08947556 0.98600460 -0.14067366 91.46359821
-0.99282867 -0.09954020 -0.06620422 408.30779591
-0.07928035 0.13374118 0.98784004 172.71556867
Axis 0.10048233 -0.03085313 -0.99446035
Axis point 237.58375679 151.90296586 0.00000000
Rotation angle (degrees) 95.77302294
Shift along axis -175.16588479
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.29299,0.92356,-0.24736,80.419,-0.77649,-0.3808,-0.50204,253.08,-0.55786,0.044977,0.82871,111.22
> view matrix models
> #25,-0.29299,0.92356,-0.24736,173.28,-0.77649,-0.3808,-0.50204,215.96,-0.55786,0.044977,0.82871,123.87
> view matrix models
> #25,-0.29299,0.92356,-0.24736,215.9,-0.77649,-0.3808,-0.50204,302.83,-0.55786,0.044977,0.82871,206.96
> view matrix models
> #25,-0.29299,0.92356,-0.24736,240.89,-0.77649,-0.3808,-0.50204,293.39,-0.55786,0.044977,0.82871,202.8
> view matrix models
> #25,-0.29299,0.92356,-0.24736,232.09,-0.77649,-0.3808,-0.50204,294.57,-0.55786,0.044977,0.82871,196.09
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.7571, correlation about mean = 0.009396, overlap = 5333
steps = 188, shift = 58.4, angle = 34.9 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.15382053 0.91961510 -0.36145171 179.19271353
-0.77488219 -0.33924589 -0.53335714 349.30800026
-0.61310428 0.19804121 0.76477634 274.04621748
Axis 0.39265820 0.13510209 -0.90970708
Axis point 286.49579405 108.34974591 0.00000000
Rotation angle (degrees) 111.35497625
Shift along axis -131.74805496
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.030336,-0.86677,-0.49779,448.07,0.71714,0.36579,-0.59322,94.296,0.69627,-0.33899,0.63269,94.527
> view matrix models
> #25,0.43392,-0.79587,-0.42226,384.79,0.61903,0.6039,-0.50209,65.782,0.65461,-0.043527,0.75472,49.009
> view matrix models
> #25,0.34359,-0.81546,-0.46579,402.67,0.69512,0.55434,-0.45773,57.656,0.63147,-0.16651,0.75731,65.967
> view matrix models
> #25,0.13981,-0.8098,-0.56981,437.77,0.83787,0.40342,-0.36774,48.488,0.52767,-0.42601,0.7349,111.38
> view matrix models
> #25,0.2084,-0.92602,-0.31473,412.56,0.54467,0.37716,-0.74906,131.55,0.81235,-0.015318,0.58297,48.934
> view matrix models
> #25,0.23733,-0.93595,-0.26013,403.77,0.46879,0.34488,-0.8132,151.84,0.85083,0.07105,0.52061,41.95
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8149, correlation about mean = 0.08031, overlap = 5858
steps = 84, shift = 20.3, angle = 10.7 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.00934477 -0.99698756 0.07699679 343.92842577
0.87412989 -0.04553773 -0.48355277 133.66638721
0.48560235 0.06278651 0.87192215 138.36935964
Axis 0.27431989 -0.20516304 0.93949812
Axis point 67.24504758 222.70660197 0.00000000
Rotation angle (degrees) 95.24876618
Shift along axis 196.92075807
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.13176,-0.98466,-0.11442,383.56,0.50261,0.16584,-0.84846,154.19,0.85441,0.054283,0.51675,20.013
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8157, correlation about mean = 0.1387, overlap = 5885
steps = 280, shift = 60.4, angle = 7.32 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.11704114 -0.98261050 0.14414582 335.90492708
0.86614263 -0.17200813 -0.46926558 162.73902599
0.48589952 0.06992746 0.87121285 140.55907935
Axis 0.27567991 -0.17473266 0.94523494
Axis point 63.08781834 214.85282853 0.00000000
Rotation angle (degrees) 102.05896395
Shift along axis 197.02777020
> view matrix models
> #25,0.025365,-0.99862,-0.046025,403.88,0.52109,0.052498,-0.85189,187.7,0.85312,-0.002375,0.5217,-8.0185
> view matrix models
> #25,0.025365,-0.99862,-0.046025,371.17,0.52109,0.052498,-0.85189,164.03,0.85312,-0.002375,0.5217,9.0216
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.17214,-0.82699,-0.53522,394.22,0.58883,0.52196,-0.61712,71.567,0.78971,-0.20892,0.57681,34.042
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.17214,-0.82699,-0.53522,412.87,0.58883,0.52196,-0.61712,72.241,0.78971,-0.20892,0.57681,28.677
> view matrix models
> #25,0.17214,-0.82699,-0.53522,416.21,0.58883,0.52196,-0.61712,77.092,0.78971,-0.20892,0.57681,47.65
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8115, correlation about mean = 0.105, overlap = 5819
steps = 136, shift = 51.6, angle = 33.7 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.17587965 -0.98196640 0.06934235 312.28291010
0.77224676 0.09394623 -0.62833835 155.26941272
0.61049268 0.16406133 0.77484359 121.80457015
Axis 0.39629869 -0.27064267 0.87732542
Axis point 8.39504876 234.85898165 0.00000000
Rotation angle (degrees) 88.72020735
Shift along axis 188.59702491
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.87079,-0.16509,-0.4631,267.92,-0.20788,0.72996,-0.65111,188.78,0.44554,0.66325,0.60133,2.6993
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.87079,-0.16509,-0.4631,267.89,-0.20788,0.72996,-0.65111,158.85,0.44554,0.66325,0.60133,-23.238
> view matrix models
> #25,0.87079,-0.16509,-0.4631,264.02,-0.20788,0.72996,-0.65111,170.51,0.44554,0.66325,0.60133,-11.694
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8574, correlation about mean = 0.06226, overlap = 5939
steps = 152, shift = 42.9, angle = 19.7 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.83576487 -0.54749831 -0.04174577 239.45517769
0.47363075 0.75728994 -0.44965086 78.95568397
0.27779673 0.35603031 0.89222835 115.34252799
Axis 0.60153371 -0.23857524 0.76239035
Axis point -147.29949365 247.37304955 0.00000000
Rotation angle (degrees) 42.04307465
Shift along axis 213.13952084
> view matrix models
> #25,0.88695,-0.40365,-0.22447,318.07,0.067299,0.59377,-0.80181,-9.1712,0.45694,0.69606,0.55381,-229.71
> view matrix models
> #25,0.88695,-0.40365,-0.22447,485.47,0.067299,0.59377,-0.80181,-54.795,0.45694,0.69606,0.55381,-140.66
> view matrix models
> #25,0.88695,-0.40365,-0.22447,346.68,0.067299,0.59377,-0.80181,195.8,0.45694,0.69606,0.55381,-33.674
> view matrix models
> #25,0.88695,-0.40365,-0.22447,363.31,0.067299,0.59377,-0.80181,198.15,0.45694,0.69606,0.55381,43.09
> view matrix models
> #25,0.88695,-0.40365,-0.22447,393.26,0.067299,0.59377,-0.80181,186.33,0.45694,0.69606,0.55381,35.013
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.95786,-0.28603,0.026445,340.41,0.28488,0.93414,-0.21501,49.115,0.036797,0.21348,0.97625,88.098
> view matrix models
> #25,0.83502,0.46023,0.30154,231.5,-0.21229,0.77509,-0.59512,170.88,-0.50762,0.43293,0.74492,151.79
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.83502,0.46023,0.30154,208.26,-0.21229,0.77509,-0.59512,140.36,-0.50762,0.43293,0.74492,122.33
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8403, correlation about mean = 0.01596, overlap = 5988
steps = 140, shift = 35.1, angle = 15.4 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.93891298 0.25657600 0.22937132 170.43893478
-0.28672401 0.95179196 0.10900194 109.83885758
-0.19034650 -0.16810960 0.96721632 235.14602314
Axis -0.37429438 0.56691261 -0.73383500
Axis point 765.62360610 -228.04437911 0.00000000
Rotation angle (degrees) 21.72663142
Shift along axis -174.08368442
> view matrix models
> #25,0.86913,0.47067,0.15194,-21.085,-0.37006,0.82267,-0.4316,225.62,-0.32813,0.31889,0.88918,397.35
> view matrix models
> #25,0.86913,0.47067,0.15194,-74.083,-0.37006,0.82267,-0.4316,290.45,-0.32813,0.31889,0.88918,350.98
> view matrix models
> #25,0.86913,0.47067,0.15194,10.83,-0.37006,0.82267,-0.4316,180.97,-0.32813,0.31889,0.88918,234.15
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.98465,0.17164,-0.031778,278.29,-0.093892,-0.67424,-0.73252,365.26,-0.14716,-0.71829,0.68,363.09
> view matrix models
> #25,-0.87015,-0.44791,-0.20547,360.58,0.34679,-0.85281,0.39044,198.9,-0.35011,0.26849,0.89741,241.63
> view matrix models
> #25,-0.76484,0.28034,-0.58003,307.86,0.016261,-0.89166,-0.45241,344.36,-0.64402,-0.35545,0.67742,376.22
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.76484,0.28034,-0.58003,379.57,0.016261,-0.89166,-0.45241,350.25,-0.64402,-0.35545,0.67742,283.8
> view matrix models
> #25,-0.76484,0.28034,-0.58003,369.76,0.016261,-0.89166,-0.45241,367.24,-0.64402,-0.35545,0.67742,282.59
> view matrix models
> #25,-0.76484,0.28034,-0.58003,383.29,0.016261,-0.89166,-0.45241,385.34,-0.64402,-0.35545,0.67742,302.6
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.69538,-0.27921,-0.66219,452.27,0.67736,-0.56247,-0.47414,274.14,-0.24008,-0.77825,0.58025,319.35
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.7729, correlation about mean = 0.06428, overlap = 5559
steps = 124, shift = 14, angle = 12.6 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.79496812 -0.33189805 -0.50780843 371.67559918
0.44723250 -0.88620585 -0.12092275 302.28317545
-0.40988877 -0.32323816 0.85294098 317.05588803
Axis -0.24949388 -0.12075380 0.96081805
Axis point 191.34710771 216.85866741 0.00000000
Rotation angle (degrees) 156.08056652
Shift along axis 175.40039127
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.63612,-0.48177,-0.6027,436.89,0.76263,-0.51126,-0.39624,246.44,-0.11724,-0.71169,0.69264,289.97
> view matrix models
> #25,-0.63612,-0.48177,-0.6027,457.81,0.76263,-0.51126,-0.39624,201.89,-0.11724,-0.71169,0.69264,293.57
> view matrix models
> #25,-0.63612,-0.48177,-0.6027,451.62,0.76263,-0.51126,-0.39624,205.28,-0.11724,-0.71169,0.69264,288.28
> view matrix models
> #25,-0.63612,-0.48177,-0.6027,468.69,0.76263,-0.51126,-0.39624,160.3,-0.11724,-0.71169,0.69264,287.48
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.71382,-0.18447,-0.6756,289.81,-0.19431,0.87464,-0.44413,108.93,0.67284,0.44831,0.58848,72.766
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.71382,-0.18447,-0.6756,261.34,-0.19431,0.87464,-0.44413,165.52,0.67284,0.44831,0.58848,66.122
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8211, correlation about mean = 0.05696, overlap = 5865
steps = 140, shift = 37.1, angle = 19.5 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.63558453 -0.13882733 -0.75944671 215.48549026
0.10214723 0.99017298 -0.09551674 109.20996656
0.76524393 -0.01686642 0.64351944 156.79176190
Axis 0.05088599 -0.98645996 0.15590819
Axis point -69.62726704 0.00000000 321.99608968
Rotation angle (degrees) 50.60682500
Shift along axis -72.32094683
> hide #!19 models
> show #!19 models
> view matrix models
> #25,0.56487,0.079977,-0.82129,357.25,-0.43496,0.87465,-0.21398,-91.971,0.70124,0.4781,0.52885,-166.95
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #!9 models
> hide #!9 models
> show #10 models
> hide #10 models
> show #12 models
> hide #12 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #!9 models
> hide #!9 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> show #3 models
> hide #3 models
> view matrix models
> #25,0.56487,0.079977,-0.82129,433.19,-0.43496,0.87465,-0.21398,-169.73,0.70124,0.4781,0.52885,-154.32
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.81689,-0.095976,-0.56876,394.71,-0.45716,0.49352,-0.73989,-57.178,0.3517,0.86442,0.35927,-140.11
> view matrix models
> #25,0.91216,-0.10231,-0.39687,363.6,-0.36624,0.23113,-0.90136,-16.321,0.18394,0.96753,0.17336,-110.64
> view matrix models
> #25,0.6864,-0.61028,-0.39548,449.48,-0.36183,0.18514,-0.91368,-9.821,0.63082,0.77025,-0.09374,-104.75
> view matrix models
> #25,0.5107,-0.54979,-0.66099,494.71,-0.22312,0.65772,-0.71946,-105.69,0.8303,0.51491,0.21323,-134.52
> view matrix models
> #25,0.46377,-0.49765,-0.73298,502.63,-0.15472,0.76913,-0.62009,-138.9,0.87234,0.40098,0.2797,-133.84
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.46377,-0.49765,-0.73298,397.52,-0.15472,0.76913,-0.62009,147.62,0.87234,0.40098,0.2797,-20.364
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.039249,-0.99891,-0.02545,418.32,0.50742,0.041866,-0.86068,189.15,0.8608,0.020867,0.50851,-1.8357
> view matrix models
> #25,0.51519,-0.7739,-0.36833,379.88,0.28033,0.55826,-0.78087,143.4,0.80994,0.29904,0.50456,-28.78
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.51519,-0.7739,-0.36833,398.73,0.28033,0.55826,-0.78087,133.35,0.80994,0.29904,0.50456,-15.749
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.22769,-0.95906,0.16839,387.34,0.81191,0.091523,-0.57657,103.92,0.53755,0.268,0.79951,-17.528
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.22769,-0.95906,0.16839,401.46,0.81191,0.091523,-0.57657,93.113,0.53755,0.268,0.79951,-9.3092
> view matrix models
> #25,0.22769,-0.95906,0.16839,398.34,0.81191,0.091523,-0.57657,95.384,0.53755,0.268,0.79951,-6.8133
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8531, correlation about mean = 0.008104, overlap = 6210
steps = 144, shift = 43.5, angle = 28.6 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.08298051 -0.99467949 -0.06104899 406.48563616
0.92333542 -0.05369233 -0.38022212 128.58648940
0.37492128 -0.08791972 0.92287821 157.15698151
Axis 0.14699346 -0.21924137 0.96453416
Axis point 112.69615180 258.89460178 0.00000000
Rotation angle (degrees) 96.13649005
Shift along axis 183.14253084
> view matrix models
> #25,0.081608,-0.96946,-0.23127,474.58,0.61509,0.23157,-0.75368,-67.784,0.78422,-0.080746,0.61521,-173.58
> hide #!19 models
> show #!19 models
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.37285,-0.71606,-0.59013,455.57,0.21025,0.68464,-0.6979,-82.967,0.90376,0.13614,0.40581,-187.22
> view matrix models
> #25,0.31841,-0.75997,-0.56662,464.06,0.28981,0.64715,-0.70513,-86.589,0.90256,0.060308,0.42631,-180.56
> view matrix models
> #25,0.53859,-0.56055,-0.62905,423.1,0.45902,0.82128,-0.33884,-171.44,0.70656,-0.10625,0.69963,-172.15
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.53859,-0.56055,-0.62905,330.34,0.45902,0.82128,-0.33884,-40.428,0.70656,-0.10625,0.69963,37.478
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.447,-0.74707,-0.49201,346.09,0.16849,0.61049,-0.77389,70.935,0.87852,0.26304,0.39877,10.984
> view matrix models
> #25,0.36882,-0.88185,-0.2938,346.64,0.3929,0.43436,-0.81053,71.107,0.84238,0.18351,0.50668,11.293
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.36882,-0.88185,-0.2938,363.04,0.3929,0.43436,-0.81053,69.66,0.84238,0.18351,0.50668,37.521
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.44893,-0.71625,-0.53427,363.79,0.056221,0.61936,-0.78309,82.231,0.8918,0.32152,0.31832,38.62
> view matrix models
> #25,0.47199,-0.68515,-0.55479,360,0.039622,0.64515,-0.76303,78.566,0.88072,0.33816,0.33165,36.249
> view matrix models
> #25,0.55,-0.55755,-0.6218,344.2,-0.029642,0.73103,-0.6817,66.154,0.83464,0.39337,0.38554,28.247
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.55,-0.55755,-0.6218,369.97,-0.029642,0.73103,-0.6817,99.681,0.83464,0.39337,0.38554,50.008
> view matrix models
> #25,0.55,-0.55755,-0.6218,369.48,-0.029642,0.73103,-0.6817,110.8,0.83464,0.39337,0.38554,69.87
> view matrix models
> #25,0.55,-0.55755,-0.6218,371.53,-0.029642,0.73103,-0.6817,110.15,0.83464,0.39337,0.38554,70.187
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.7637, correlation about mean = 0.0666, overlap = 5308
steps = 228, shift = 76.4, angle = 26.6 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.40288608 -0.61084859 -0.68157673 313.87552292
0.12259994 0.77399628 -0.62120773 155.05660514
0.90700170 0.16671467 0.38672232 152.41943803
Axis 0.41060187 -0.82783948 0.38221446
Axis point 90.53176517 0.00000000 345.79455804
Rotation angle (degrees) 73.63219680
Shift along axis 58.77281021
> view matrix models
> #25,0.32934,-0.44313,-0.83377,392.76,-0.43176,0.71463,-0.55036,210.98,0.83971,0.54124,0.044026,87.459
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.90115,0.0090876,-0.43341,225.11,-0.31011,0.71212,-0.62985,207.31,0.30292,0.70199,0.64455,55.123
> view matrix models
> #25,0.27623,-0.83406,-0.47755,401.62,0.68728,0.51875,-0.50848,102.88,0.67183,-0.18775,0.71652,110.74
> view matrix models
> #25,0.065076,-0.90953,-0.41052,426.22,0.65902,0.34809,-0.66673,145.86,0.74931,-0.22715,0.62205,118.3
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.065076,-0.90953,-0.41052,462.84,0.65902,0.34809,-0.66673,115.41,0.74931,-0.22715,0.62205,146.28
> view matrix models
> #25,0.065076,-0.90953,-0.41052,520.5,0.65902,0.34809,-0.66673,-171.62,0.74931,-0.22715,0.62205,-2.5936
> view matrix models
> #25,0.065076,-0.90953,-0.41052,557.28,0.65902,0.34809,-0.66673,156.86,0.74931,-0.22715,0.62205,164.1
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.0033305,-0.98972,-0.14295,540.95,0.98705,0.02618,-0.15826,95.772,0.16037,-0.14058,0.97699,176.65
> view matrix models
> #25,-0.74418,-0.65339,-0.13885,584.71,0.66699,-0.71554,-0.20768,226.42,0.036341,-0.24716,0.96829,204.43
> view matrix models
> #25,-0.89731,-0.33527,-0.28709,582.27,0.41715,-0.85673,-0.3033,283.2,-0.14428,-0.39192,0.90862,249.41
> view matrix models
> #25,-0.56159,-0.77969,-0.27696,596.12,0.81486,-0.46306,-0.34869,196.94,0.14362,-0.4215,0.89538,222.07
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.8074, correlation about mean = 0.07623, overlap = 6716
steps = 112, shift = 33.7, angle = 18.4 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.73423213 -0.67026487 0.10792683 446.28940662
0.67742109 -0.73379952 0.05137081 273.55820272
0.04476460 0.11083001 0.99283073 225.18985831
Axis 0.04402836 0.04677038 0.99793488
Axis point 167.25613122 216.19175428 0.00000000
Rotation angle (degrees) 137.52741016
Shift along axis 257.16862959
> hide #!19 models
> show #!19 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_3_fitting.cxs"
——— End of log from Thu Jan 25 18:04:25 2024 ———
opened ChimeraX session
> select add #25
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.57191,-0.8201,0.019025,692.21,0.72153,-0.51394,-0.46397,-57.266,0.39028,-0.25162,0.88565,111.7
> select subtract #25
Nothing selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> show #12 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> hide #!25 models
> show #!25 models
> show #26 models
> hide #26 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!36 models
> hide #!36 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/postprocess_20231221.mrc"
Opened postprocess_20231221.mrc as #48, grid size 156,156,156, pixel 2.55,
shown at level 0.00309, step 1, values float32
> hide #12 models
> hide #11 models
> hide #10 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #!2 models
> show #!1 models
> hide #!25 models
> hide #!48 models
> show #!48 models
> volume #48 level 0.003869
> select add #48
2 models selected
> view matrix models #48,1,0,0,116.2,0,1,0,120.77,0,0,1,87.705
> view matrix models #48,1,0,0,112.94,0,1,0,103.77,0,0,1,99.528
> ui tool show "Fit in Map"
> fitmap #48 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 16754
points
correlation = 0.6069, correlation about mean = 0.153, overlap = 0.3715
steps = 68, shift = 4.98, angle = 1.44 degrees
Position of postprocess_20231221.mrc (#48) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99972992 -0.01626780 0.01659628 2.42719609
0.01643779 0.99981328 -0.01015862 -7.47507851
-0.01642792 0.01042868 0.99981067 -7.15635708
Axis 0.40499110 0.64964855 0.64338089
Axis point -99.52364532 0.00000000 -354.74004849
Rotation angle (degrees) 1.45644214
Shift along axis -8.47744448
> select subtract #48
Nothing selected
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/5a1x_COPI_coat_linkage3_2015.cif"
5a1x_COPI_coat_linkage3_2015.cif title:
The structure of the COPI coat linkage III [more info...]
Chain information for 5a1x_COPI_coat_linkage3_2015.cif #49
---
Chain | Description | UniProt
A B I J | ADP-RIBOSYLATION FACTOR 1 | ARF1_YEAST 1-181
C K | COATOMER SUBUNIT ALPHA | COPA_MOUSE 1-1224
D L | COATOMER SUBUNIT BETA' | COPB2_MOUSE 1-905
E M | COATOMER SUBUNIT GAMMA-1 | COPG1_MOUSE 1-874
F N | COATOMER SUBUNIT ZETA-1 | COPZ1_MOUSE 1-177
G O | COATOMER SUBUNIT BETA | COPB_MOUSE 1-968
H P Q | COATOMER SUBUNIT DELTA | COPD_MOUSE 1-511
> hide #!49 atoms
> show #!49 cartoons
> close #49
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Reference structures/emd_3720_2017_leaf.map"
Opened emd_3720_2017_leaf.map as #49, grid size 128,128,128, pixel 1.78, shown
at level 0.226, step 1, values float32
> hide #!48 models
> show #!48 models
> select add #49
2 models selected
> view matrix models #49,1,0,0,268.81,0,1,0,56.189,0,0,1,40.587
> view matrix models #49,1,0,0,210.92,0,1,0,75.8,0,0,1,212.42
> view matrix models #49,1,0,0,219.19,0,1,0,199.07,0,0,1,191.45
> fitmap #49 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 20947
points
correlation = 0.7115, correlation about mean = 0.145, overlap = 14.04
steps = 212, shift = 6.68, angle = 6.88 degrees
Position of emd_3720_2017_leaf.map (#49) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
0.99596942 0.02399632 0.08642391 97.42320621
-0.03099432 0.99626744 0.08056385 75.43929140
-0.08416809 -0.08291778 0.99299566 100.35660765
Axis -0.67388984 0.70319963 -0.22667767
Axis point 1163.48088171 0.00000000 -797.35103447
Rotation angle (degrees) 6.96696174
Shift along axis -35.35222896
> ui mousemode right "rotate selected models"
> view matrix models
> #49,-0.36361,-0.91597,0.1697,461.12,0.91486,-0.31678,0.25036,224.15,-0.17557,0.24628,0.95316,187.19
> fitmap #49 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 20947
points
correlation = 0.6286, correlation about mean = 0.03473, overlap = 13.91
steps = 120, shift = 9.27, angle = 5.25 degrees
Position of emd_3720_2017_leaf.map (#49) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.37712124 -0.91815484 0.12153704 361.34832305
0.88885124 -0.32192586 0.32604787 98.25850449
-0.26023651 0.23098793 0.93750815 87.71784471
Axis -0.05140209 0.20643773 0.97710864
Axis point 155.49421926 165.23084937 0.00000000
Rotation angle (degrees) 112.38135407
Shift along axis 87.42006807
> view matrix models
> #49,-0.96284,-0.25919,-0.075825,480.47,0.26981,-0.91128,-0.31107,423.66,0.011531,-0.31998,0.94736,236
> fitmap #49 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 20947
points
correlation = 0.6939, correlation about mean = 0.01582, overlap = 13.96
steps = 216, shift = 10, angle = 11.1 degrees
Position of emd_3720_2017_leaf.map (#49) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.96338804 -0.26456440 0.04346448 351.31286233
0.21696407 -0.86453226 -0.45333274 335.04411294
0.15751215 -0.42730511 0.89028100 118.52082392
Axis 0.05252441 -0.23015104 0.97173643
Axis point 149.91600402 204.11390906 0.00000000
Rotation angle (degrees) 165.65458511
Shift along axis 56.51275209
> view matrix models
> #49,0.3605,0.83622,0.41326,143.37,-0.92655,0.27001,0.26191,349.54,0.10743,-0.47732,0.87214,244.28
> fitmap #49 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 20947
points
correlation = 0.7336, correlation about mean = 0.04116, overlap = 14.08
steps = 192, shift = 3.76, angle = 4.39 degrees
Position of emd_3720_2017_leaf.map (#49) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
0.33574710 0.84776690 0.41056689 32.32305883
-0.94090697 0.28131321 0.18856552 244.31851482
0.04436172 -0.44961557 0.89211988 136.24823204
Axis -0.32996314 0.18934157 -0.92481030
Axis point 175.22937179 134.35930874 0.00000000
Rotation angle (degrees) 75.25070263
Shift along axis -90.40953594
> view matrix models
> #49,-0.73344,0.66639,-0.13415,346.45,-0.67575,-0.69338,0.25019,438.51,0.073705,0.27415,0.95886,149.68
> fitmap #49 inMap #1
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 20947
points
correlation = 0.7373, correlation about mean = 0.05131, overlap = 14.78
steps = 156, shift = 16.4, angle = 6.06 degrees
Position of emd_3720_2017_leaf.map (#49) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.75027238 0.63080879 -0.19791822 260.14816342
-0.65754750 -0.68086871 0.32256638 324.88423036
0.06872138 0.37215328 0.92562374 32.96806789
Axis 0.03766304 -0.20252240 -0.97855310
Axis point 189.62506423 108.46905602 0.00000000
Rotation angle (degrees) 138.82991172
Shift along axis -88.25936981
> hide #!1 models
> show #!2 models
> hide #!48 models
> color #49 #d783ffff models
> view matrix models
> #49,-0.74761,0.6602,-0.072235,353.83,-0.64586,-0.69736,0.31073,439.09,0.15477,0.27896,0.94775,144.49
> ui mousemode right "translate selected models"
> view matrix models
> #49,-0.74761,0.6602,-0.072235,339.45,-0.64586,-0.69736,0.31073,433.49,0.15477,0.27896,0.94775,142.67
> fitmap #49 inMap #2
Fit map emd_3720_2017_leaf.map in map emdb 3720 using 20947 points
correlation = 0.3418, correlation about mean = 0.04388, overlap = 252.2
steps = 164, shift = 24.8, angle = 2.9 degrees
Position of emd_3720_2017_leaf.map (#49) relative to emdb 3720 (#2)
coordinates:
Matrix rotation and translation
0.94294873 0.25000953 -0.21987024 3.72814650
-0.28736076 0.94466072 -0.15824008 75.52086766
0.16814125 0.21239436 0.96260955 -54.20533629
Axis 0.48806167 -0.51094425 -0.70762404
Axis point 256.63130008 46.75350863 0.00000000
Rotation angle (degrees) 22.31512695
Shift along axis 1.58961171
> ui mousemode right "rotate selected models"
> view matrix models
> #49,-0.97788,0.038289,-0.20562,459.88,-0.092506,-0.96089,0.26101,409.82,-0.18758,0.27426,0.94318,205.04
> ui mousemode right "translate selected models"
> view matrix models
> #49,-0.97788,0.038289,-0.20562,546.42,-0.092506,-0.96089,0.26101,229.35,-0.18758,0.27426,0.94318,246.35
> view matrix models
> #49,-0.97788,0.038289,-0.20562,539.54,-0.092506,-0.96089,0.26101,393.65,-0.18758,0.27426,0.94318,164.28
> ui mousemode right "rotate selected models"
> view matrix models
> #49,-0.68369,0.72944,0.022136,397.17,-0.6197,-0.59632,0.51026,377.32,0.3854,0.33514,0.85973,104.62
> ui mousemode right "translate selected models"
> view matrix models
> #49,-0.68369,0.72944,0.022136,405.64,-0.6197,-0.59632,0.51026,417.1,0.3854,0.33514,0.85973,113.88
> view matrix models
> #49,-0.68369,0.72944,0.022136,322.15,-0.6197,-0.59632,0.51026,402.73,0.3854,0.33514,0.85973,78.369
> view matrix models
> #49,-0.68369,0.72944,0.022136,320.93,-0.6197,-0.59632,0.51026,424.67,0.3854,0.33514,0.85973,142.55
> view matrix models
> #49,-0.68369,0.72944,0.022136,319.54,-0.6197,-0.59632,0.51026,407.37,0.3854,0.33514,0.85973,144.39
> fitmap #49 inMap #2
Fit map emd_3720_2017_leaf.map in map emdb 3720 using 20947 points
correlation = 0.2752, correlation about mean = 0.06505, overlap = 198.1
steps = 148, shift = 15, angle = 5.01 degrees
Position of emd_3720_2017_leaf.map (#49) relative to emdb 3720 (#2)
coordinates:
Matrix rotation and translation
0.89280795 0.18089064 -0.41251973 37.51137462
-0.28427541 0.93667495 -0.20451778 66.14953212
0.34940155 0.29986431 0.88769361 -71.87027738
Axis 0.49192097 -0.74309747 -0.45367379
Axis point 213.86140005 0.00000000 33.09207816
Rotation angle (degrees) 30.84155937
Shift along axis 1.90274273
> view matrix models
> #49,-0.73029,0.6828,0.021545,265.57,-0.59958,-0.65576,0.45879,202.65,0.32739,0.32213,0.88828,214.09
> ui mousemode right "rotate selected models"
> view matrix models
> #49,0.96208,0.052255,0.2677,129.67,-0.25796,0.49316,0.83081,-17.264,-0.088605,-0.86837,0.48794,450.43
> view matrix models
> #49,0.93713,0.17502,0.30193,113.48,-0.30166,0.84128,0.44862,-9.7978,-0.17549,-0.51149,0.84118,375.1
> view matrix models
> #49,-0.73136,0.58943,0.34305,239.22,-0.21182,-0.67446,0.70727,133.71,0.64827,0.4446,0.61813,196.23
> view matrix models
> #49,-0.7478,0.56297,0.35194,243.16,-0.26997,-0.74213,0.61349,159.22,0.60656,0.36375,0.70695,200.1
> view matrix models
> #49,-0.62127,0.75793,-0.19889,270.55,-0.78358,-0.59925,0.16404,250.37,0.0051501,0.25776,0.96619,247.65
> ui mousemode right "translate selected models"
> view matrix models
> #49,-0.62127,0.75793,-0.19889,287.72,-0.78358,-0.59925,0.16404,464.32,0.0051501,0.25776,0.96619,210.07
> view matrix models
> #49,-0.62127,0.75793,-0.19889,308.13,-0.78358,-0.59925,0.16404,463.05,0.0051501,0.25776,0.96619,216.95
> view matrix models
> #49,-0.62127,0.75793,-0.19889,315.35,-0.78358,-0.59925,0.16404,462.71,0.0051501,0.25776,0.96619,194.9
> fitmap #49 inMap #2
Fit map emd_3720_2017_leaf.map in map emdb 3720 using 20947 points
correlation = 1, correlation about mean = 0.9999, overlap = 1662
steps = 112, shift = 5.43, angle = 14.7 degrees
Position of emd_3720_2017_leaf.map (#49) relative to emdb 3720 (#2)
coordinates:
Matrix rotation and translation
0.99999999 -0.00012557 0.00002858 0.01420688
0.00012557 0.99999999 -0.00005443 0.00493431
-0.00002858 0.00005443 0.99999999 -0.00266256
Axis 0.38932690 0.20440202 0.89813383
Axis point -32.53401205 100.27720859 0.00000000
Rotation angle (degrees) 0.00801087
Shift along axis 0.00414837
> select subtract #49
Nothing selected
> hide #!49 models
> color #49 #eff0f0ff models
> color #49 #fffeb6ff models
> color #48 #eff0f0ff models
> color #48 #dbdbdbff models
> show #!48 models
> show #!49 models
> fitmap #49 inMap #48
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 20947
points
correlation = 0.5968, correlation about mean = 0.06947, overlap = 14.69
steps = 88, shift = 11.4, angle = 3.98 degrees
Position of emd_3720_2017_leaf.map (#49) relative to postprocess_20231221.mrc
(#48) coordinates:
Matrix rotation and translation
-0.50717000 0.85774429 -0.08398407 163.99807809
-0.85976131 -0.51030904 -0.01987900 384.21661524
-0.05990893 0.06212422 0.99626879 111.64334070
Axis 0.04768653 -0.01400018 -0.99876423
Axis point 193.70984459 143.11340542 0.00000000
Rotation angle (degrees) 120.70414533
Shift along axis -109.06397880
> hide #!49 models
> show #!49 models
> hide #!2 models
> fitmap #49 inMap #48
Fit map emd_3720_2017_leaf.map in map postprocess_20231221.mrc using 20947
points
correlation = 0.5968, correlation about mean = 0.06947, overlap = 14.69
steps = 88, shift = 11.4, angle = 3.98 degrees
Position of emd_3720_2017_leaf.map (#49) relative to postprocess_20231221.mrc
(#48) coordinates:
Matrix rotation and translation
-0.50717000 0.85774429 -0.08398407 163.99807809
-0.85976131 -0.51030904 -0.01987900 384.21661524
-0.05990893 0.06212422 0.99626879 111.64334070
Axis 0.04768653 -0.01400018 -0.99876423
Axis point 193.70984459 143.11340542 0.00000000
Rotation angle (degrees) 120.70414533
Shift along axis -109.06397880
> fitmap #48 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 16754
points
correlation = 0.6069, correlation about mean = 0.1529, overlap = 0.3715
steps = 48, shift = 0.00188, angle = 0.00348 degrees
Position of postprocess_20231221.mrc (#48) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99972875 -0.01630667 0.01662903 2.42798953
0.01647645 0.99981299 -0.01012473 -7.48955343
-0.01646082 0.01039597 0.99981046 -7.14110640
Axis 0.40316027 0.65010033 0.64407403
Axis point -97.58067328 -0.00000000 -353.42317789
Rotation angle (degrees) 1.45832380
Shift along axis -8.48949343
> fitmap #48 inMap #1
Fit map postprocess_20231221.mrc in map postprocess_20231221.mrc using 16754
points
correlation = 0.6073, correlation about mean = 0.1526, overlap = 0.3711
steps = 40, shift = 0.055, angle = 0.0241 degrees
Position of postprocess_20231221.mrc (#48) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99972533 -0.01619964 0.01693647 2.32919760
0.01636816 0.99981743 -0.00985898 -7.49097502
-0.01677367 0.01013349 0.99980796 -6.97819495
Axis 0.39233107 0.66152593 0.63910858
Axis point -88.25260490 0.00000000 -335.89244486
Rotation angle (degrees) 1.46000177
Shift along axis -8.50148186
> combine #38
> close #50
> combine #3
> combine #4
> combine #5
> combine #6
> combine #7
> combine #8
> combine #9
> combine #10
> combine #11
> combine #12
> fitmap #50 inMap #48
Fit molecule copy of CopA_F8WHL2.pdb (#50) to map postprocess_20231221.mrc
(#48) using 9810 atoms
average map value = 0.001845, steps = 100
shifted from previous position = 10.6
rotated from previous position = 1.5 degrees
atoms outside contour = 8562, contour level = 0.0038686
Position of copy of CopA_F8WHL2.pdb (#50) relative to postprocess_20231221.mrc
(#48) coordinates:
Matrix rotation and translation
0.89986795 0.40449377 0.16316389 162.21800882
-0.20982329 0.72942358 -0.65108787 244.64306871
-0.38237657 0.55165752 0.74125712 239.08371875
Axis 0.82573810 0.37453774 -0.42175593
Axis point 0.00000000 -323.18738252 438.29584637
Rotation angle (degrees) 46.74281473
Shift along axis 124.74267766
> fitmap #51 inMap #48
Fit molecule copy of CopB_Q9JIF7.pdb (#51) to map postprocess_20231221.mrc
(#48) using 7501 atoms
average map value = 0.002923, steps = 108
shifted from previous position = 11.7
rotated from previous position = 4.16 degrees
atoms outside contour = 5816, contour level = 0.0038686
Position of copy of CopB_Q9JIF7.pdb (#51) relative to postprocess_20231221.mrc
(#48) coordinates:
Matrix rotation and translation
-0.04198846 -0.73296225 0.67897224 172.35467443
-0.03842872 0.68025347 0.73196888 204.56990533
-0.99837879 0.00464221 -0.05672960 236.22992719
Axis -0.37189487 0.85765897 0.35512716
Axis point 209.20957536 0.00000000 -39.72378407
Rotation angle (degrees) 102.07736641
Shift along axis 195.24505821
> fitmap #52 inMap #48
Fit molecule copy of hArf1_P84078 (#52) to map postprocess_20231221.mrc (#48)
using 1457 atoms
average map value = 0.002588, steps = 80
shifted from previous position = 10.3
rotated from previous position = 1.47 degrees
atoms outside contour = 1414, contour level = 0.0038686
Position of copy of hArf1_P84078 (#52) relative to postprocess_20231221.mrc
(#48) coordinates:
Matrix rotation and translation
0.15747029 0.02364037 0.98724072 126.68344693
-0.68701149 -0.71551264 0.12671568 200.57043431
0.70937882 -0.69819967 -0.09643077 178.41026657
Axis -0.73410147 0.24727243 -0.63241710
Axis point 0.00000000 138.29307647 -15.45936629
Rotation angle (degrees) 145.81590428
Shift along axis -156.23266836
> fitmap #53 inMap #48
Fit molecule copy of hArf1_P84078 (#53) to map postprocess_20231221.mrc (#48)
using 1457 atoms
average map value = 0.003766, steps = 68
shifted from previous position = 11.1
rotated from previous position = 1.53 degrees
atoms outside contour = 827, contour level = 0.0038686
Position of copy of hArf1_P84078 (#53) relative to postprocess_20231221.mrc
(#48) coordinates:
Matrix rotation and translation
-0.84441476 -0.49440268 0.20622727 242.99938249
-0.47700141 0.51875180 -0.70948306 195.94811419
0.24378956 -0.69746867 -0.67387246 220.55731684
Axis 0.27872119 -0.87140571 0.40369120
Axis point 151.43808226 0.00000000 157.19336564
Rotation angle (degrees) 178.76502585
Shift along axis -13.98418102
> fitmap #54 inMap #48
Fit molecule copy of CopBprime_O55029.pdb (#54) to map
postprocess_20231221.mrc (#48) using 7214 atoms
average map value = 0.00312, steps = 92
shifted from previous position = 11.3
rotated from previous position = 1.45 degrees
atoms outside contour = 4652, contour level = 0.0038686
Position of copy of CopBprime_O55029.pdb (#54) relative to
postprocess_20231221.mrc (#48) coordinates:
Matrix rotation and translation
-0.16270160 -0.17511802 -0.97101074 188.50447383
-0.01416695 -0.98360781 0.17976365 177.39926418
-0.98657361 0.04300409 0.15755367 238.56491900
Axis -0.64576341 0.07348611 0.75999304
Axis point 189.59583986 85.38839714 0.00000000
Rotation angle (degrees) 173.92156405
Shift along axis 72.61476818
> fitmap #55 inMap #48
Fit molecule copy of CopD_Q5XJY5 (#55) to map postprocess_20231221.mrc (#48)
using 1462 atoms
average map value = 0.002999, steps = 96
shifted from previous position = 1.82
rotated from previous position = 26.1 degrees
atoms outside contour = 1071, contour level = 0.0038686
Position of copy of CopD_Q5XJY5 (#55) relative to postprocess_20231221.mrc
(#48) coordinates:
Matrix rotation and translation
-0.22365199 0.94640781 0.23300654 -165.73099604
-0.84733918 -0.30693575 0.43336679 248.84898866
0.48165975 -0.10051222 0.87057520 408.88830413
Axis -0.28278127 -0.13170488 -0.95009925
Axis point -69.18363529 197.53193420 0.00000000
Rotation angle (degrees) 109.26915596
Shift along axis -374.39347406
> fitmap #56 inMap #48
Fit molecule copy of CopG_Q9QZE5 (#56) to map postprocess_20231221.mrc (#48)
using 6673 atoms
average map value = 0.002616, steps = 72
shifted from previous position = 7.46
rotated from previous position = 12.1 degrees
atoms outside contour = 5242, contour level = 0.0038686
Position of copy of CopG_Q9QZE5 (#56) relative to postprocess_20231221.mrc
(#48) coordinates:
Matrix rotation and translation
0.38672365 -0.40023335 -0.83081771 216.26930998
0.63094855 -0.54221509 0.55489343 287.24095726
-0.67256876 -0.73879365 0.04283925 259.15606717
Axis -0.77842541 -0.09522009 0.62047322
Axis point 0.00000000 226.69812121 118.40040222
Rotation angle (degrees) 123.80210140
Shift along axis -34.90123560
> fitmap #57 inMap #48
Fit molecule copy of CopZ1_P61924.pdb (#57) to map postprocess_20231221.mrc
(#48) using 1420 atoms
average map value = 0.003311, steps = 80
shifted from previous position = 5.47
rotated from previous position = 13.7 degrees
atoms outside contour = 956, contour level = 0.0038686
Position of copy of CopZ1_P61924.pdb (#57) relative to
postprocess_20231221.mrc (#48) coordinates:
Matrix rotation and translation
0.12580671 -0.94891133 -0.28937861 228.54452918
-0.15144065 0.26990781 -0.95090247 253.54454699
0.98042767 0.16345359 -0.10974754 228.24940507
Axis 0.59648772 -0.67969644 0.42686667
Axis point 123.22437247 0.00000000 290.91541660
Rotation angle (degrees) 110.91708216
Shift along axis 61.42274304
> fitmap #58 inMap #48
Fit molecule copy of Golph3_ Q9CRA5.pdb (#58) to map postprocess_20231221.mrc
(#48) using 2367 atoms
average map value = 0.0031, steps = 64
shifted from previous position = 10.2
rotated from previous position = 1.46 degrees
atoms outside contour = 1837, contour level = 0.0038686
Position of copy of Golph3_ Q9CRA5.pdb (#58) relative to
postprocess_20231221.mrc (#48) coordinates:
Matrix rotation and translation
0.66051665 -0.23635093 0.71264016 198.05029470
-0.68930093 -0.56714636 0.45078735 233.23936530
0.29762726 -0.78897607 -0.53752653 191.34146193
Axis -0.89602686 0.29994650 -0.32736517
Axis point 0.00000000 180.17635975 -4.23439426
Rotation angle (degrees) 136.22632166
Shift along axis -170.13758312
> fitmap #59 inMap #48
Fit molecule copy of CopZ2_Q9CTG7.pdb (#59) to map postprocess_20231221.mrc
(#48) using 1463 atoms
average map value = 0.003943, steps = 76
shifted from previous position = 10.4
rotated from previous position = 1.46 degrees
atoms outside contour = 823, contour level = 0.0038686
Position of copy of CopZ2_Q9CTG7.pdb (#59) relative to
postprocess_20231221.mrc (#48) coordinates:
Matrix rotation and translation
-0.81851164 0.29517532 -0.49285927 229.55933059
0.42689991 0.88661239 -0.17797463 242.03214924
0.38444141 -0.35607588 -0.85171287 217.28485961
Axis -0.19683266 -0.96956889 0.14557843
Axis point 58.95883072 0.00000000 149.09790106
Rotation angle (degrees) 153.10107885
Shift along axis -248.21962617
> hide #!49 models
> hide #50 models
> hide #51 models
> hide #52 models
> hide #53 models
> hide #54 models
> hide #55 models
> hide #!56 models
> hide #57 models
> hide #58 models
> hide #59 models
> surface dust #48 size 25.5
> hide #!48 models
> show #!1 models
> show #!19 models
> fitmap #1 inMap #19
Fit map postprocess_20231221.mrc in map COPI_golph_linkage3_postprocess.mrc
using 19065 points
correlation = 0.8356, correlation about mean = 0.1176, overlap = 85.08
steps = 40, shift = 0.351, angle = 0.318 degrees
Position of postprocess_20231221.mrc (#1) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.97200722 -0.23376239 -0.02360336 67.45044917
0.21512610 0.84509841 0.48941746 41.67608758
-0.09446023 -0.48079500 0.87173014 268.62599873
Axis -0.90558109 0.06613669 0.41898548
Axis point 0.00000000 490.78061555 77.50615612
Rotation angle (degrees) 32.39038011
Shift along axis 54.22486091
> fitmap #1 inMap #19
Fit map postprocess_20231221.mrc in map COPI_golph_linkage3_postprocess.mrc
using 19065 points
correlation = 0.8356, correlation about mean = 0.1174, overlap = 85.08
steps = 40, shift = 0.0324, angle = 0.0109 degrees
Position of postprocess_20231221.mrc (#1) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.97198583 -0.23385893 -0.02352762 67.44452109
0.21518735 0.84515559 0.48929177 41.70226164
-0.09454075 -0.48064751 0.87180274 268.61429728
Axis -0.90547054 0.06629311 0.41919963
Axis point -0.00000000 490.84193607 77.46193790
Rotation angle (degrees) 32.38458230
Shift along axis 54.29855919
> fitmap #3 inMap #1
Fit molecule CopA_F8WHL2.pdb (#3) to map postprocess_20231221.mrc (#1) using
9810 atoms
average map value = 0.001845, steps = 80
shifted from previous position = 0.5
rotated from previous position = 0.397 degrees
atoms outside contour = 8378, contour level = 0.0036898
Position of CopA_F8WHL2.pdb (#3) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.90011576 0.40415046 0.16264689 162.21985406
-0.20979229 0.72932042 -0.65121342 244.63377968
-0.38180990 0.55204540 0.74126045 239.13299028
Axis 0.82616958 0.37382949 -0.42153925
Axis point 0.00000000 -322.93459090 438.32146602
Rotation angle (degrees) 46.73699309
Shift along axis 124.66848807
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map postprocess_20231221.mrc (#1) using
7501 atoms
average map value = 0.002923, steps = 88
shifted from previous position = 1.13
rotated from previous position = 2.89 degrees
atoms outside contour = 5658, contour level = 0.0036898
Position of CopB_Q9JIF7.pdb (#4) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04137122 -0.73310739 0.67885343 172.36282746
-0.03849848 0.68010022 0.73210761 204.56521857
-0.99840187 0.00415336 -0.05636010 236.23248753
Axis -0.37218186 0.85753190 0.35513335
Axis point 209.31345950 0.00000000 -39.81221265
Rotation angle (degrees) 102.05294948
Shift along axis 195.16491836
> show #4 models
> show #3 models
> show #5 models
> fitmap #5 inMap #1
Fit molecule hArf1_P84078 (#5) to map postprocess_20231221.mrc (#1) using 1457
atoms
average map value = 0.002587, steps = 48
shifted from previous position = 0.374
rotated from previous position = 0.337 degrees
atoms outside contour = 1384, contour level = 0.0036898
Position of hArf1_P84078 (#5) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.15811428 0.02321485 0.98714788 126.72177245
-0.68699131 -0.71550573 0.12686396 200.57906918
0.70925510 -0.69822103 -0.09718328 178.40878833
Axis -0.73435020 0.24733284 -0.63210462
Axis point 0.00000000 138.30490580 -15.40933580
Rotation angle (degrees) 145.82108522
Shift along axis -156.22138629
> show #6 models
> fitmap #6 inMap #1
Fit molecule hArf1_P84078 (#6) to map postprocess_20231221.mrc (#1) using 1457
atoms
average map value = 0.003766, steps = 56
shifted from previous position = 0.304
rotated from previous position = 0.418 degrees
atoms outside contour = 776, contour level = 0.0036898
Position of hArf1_P84078 (#6) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.84435823 -0.49441709 0.20642408 243.00499479
-0.47729838 0.51909518 -0.70903204 195.94467747
0.24340382 -0.69720293 -0.67428677 220.56142381
Axis 0.27877785 -0.87150473 0.40343825
Axis point 151.46502145 0.00000000 157.13713689
Rotation angle (degrees) 178.78431992
Shift along axis -14.03938787
> show #7 models
> fitmap #7 inMap #1
Fit molecule CopBprime_O55029.pdb (#7) to map postprocess_20231221.mrc (#1)
using 7214 atoms
average map value = 0.00312, steps = 48
shifted from previous position = 0.222
rotated from previous position = 0.329 degrees
atoms outside contour = 4437, contour level = 0.0036898
Position of CopBprime_O55029.pdb (#7) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.16289150 -0.17508251 -0.97098531 188.47404673
-0.01383314 -0.98362735 0.17968268 177.44291164
-0.98654701 0.04270056 0.15780260 238.55506119
Axis -0.64568521 0.07335234 0.76007240
Axis point 189.54184111 85.44580340 0.00000000
Rotation angle (degrees) 173.91089427
Shift along axis 72.64006555
> fitmap #7 inMap #1
Fit molecule CopBprime_O55029.pdb (#7) to map postprocess_20231221.mrc (#1)
using 7214 atoms
average map value = 0.00312, steps = 40
shifted from previous position = 0.00485
rotated from previous position = 0.0121 degrees
atoms outside contour = 4437, contour level = 0.0036898
Position of CopBprime_O55029.pdb (#7) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.16281971 -0.17504579 -0.97100397 188.47744403
-0.01403174 -0.98362611 0.17967409 177.43972685
-0.98655605 0.04287936 0.15769752 238.55922073
Axis -0.64571671 0.07341102 0.76003997
Axis point 189.56315070 85.42306787 0.00000000
Rotation angle (degrees) 173.91955374
Shift along axis 72.63754008
> show #8 models
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003728, steps = 48
shifted from previous position = 0.235
rotated from previous position = 0.36 degrees
atoms outside contour = 876, contour level = 0.0036898
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23941733 0.93122644 0.27476658 -92.91539761
-0.88619480 0.09397695 0.45368174 105.66683335
0.39665871 -0.35211598 0.84774773 472.45399925
Axis -0.40456161 -0.06119759 -0.91246083
Axis point -102.47568113 189.84385384 0.00000000
Rotation angle (degrees) 84.80354261
Shift along axis -399.97231985
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003729, steps = 48
shifted from previous position = 0.0486
rotated from previous position = 0.0245 degrees
atoms outside contour = 873, contour level = 0.0036898
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23902942 0.93135641 0.27466377 -93.00941180
-0.88623957 0.09366294 0.45365922 105.73859422
0.39679260 -0.35185580 0.84779310 472.34895334
Axis -0.40440757 -0.06131459 -0.91252125
Axis point -102.45424420 189.79474542 0.00000000
Rotation angle (degrees) 84.82242906
Shift along axis -399.89806748
> show #!9 models
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 60
shifted from previous position = 0.672
rotated from previous position = 0.357 degrees
atoms outside contour = 4570, contour level = 0.0036898
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48917059 -0.51138944 -0.70653589 223.55312567
0.54924443 -0.44865841 0.70500793 282.28695497
-0.67752688 -0.73293005 0.06140730 258.73442159
Axis -0.80465553 -0.01623314 0.59351998
Axis point 0.00000000 245.05249647 103.84569293
Rotation angle (degrees) 116.68212467
Shift along axis -30.90161602
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 44
shifted from previous position = 0.0224
rotated from previous position = 0.0606 degrees
atoms outside contour = 4573, contour level = 0.0036898
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48848080 -0.51208562 -0.70650889 223.58707553
0.54899718 -0.44897481 0.70499909 282.29529538
-0.67822460 -0.73224991 0.06181799 258.73071835
Axis -0.80440475 -0.01583026 0.59387069
Axis point 0.00000000 245.05530168 103.92806394
Rotation angle (degrees) 116.70121957
Shift along axis -30.67072406
> show #10 models
> fitmap #10 inMap #1
Fit molecule CopZ1_P61924.pdb (#10) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 48
shifted from previous position = 0.582
rotated from previous position = 0.356 degrees
atoms outside contour = 728, contour level = 0.0036898
Position of CopZ1_P61924.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16485347 -0.93977365 -0.29941414 230.49392590
-0.38653362 0.21772848 -0.89620649 241.45930184
0.90742223 0.26347638 -0.32736081 218.20262698
Axis 0.65787163 -0.68462114 0.31384521
Axis point 143.38485457 -0.00000000 249.45112759
Rotation angle (degrees) 118.18951155
Shift along axis 54.80912228
> fitmap #10 inMap #1
Fit molecule CopZ1_P61924.pdb (#10) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 44
shifted from previous position = 0.00907
rotated from previous position = 0.0254 degrees
atoms outside contour = 728, contour level = 0.0036898
Position of CopZ1_P61924.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16515139 -0.93969311 -0.29950275 230.49951829
-0.38625432 0.21779168 -0.89631155 241.46263680
0.90748698 0.26371132 -0.32699192 218.19656412
Axis 0.65791855 -0.68455628 0.31388833
Axis point 143.36744648 0.00000000 249.50084586
Rotation angle (degrees) 118.16578701
Shift along axis 54.84450072
> show #11 models
> fitmap #11 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#11) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 40
shifted from previous position = 0.484
rotated from previous position = 0.318 degrees
atoms outside contour = 1695, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#11) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66062637 -0.23615777 0.71260249 198.04212837
-0.68915421 -0.56722905 0.45090762 233.23273346
0.29772350 -0.78897447 -0.53747558 191.33681360
Axis -0.89605993 0.29983209 -0.32737948
Axis point 0.00000000 180.15544061 -4.23442000
Rotation angle (degrees) 136.22309267
Shift along axis -170.16670371
> fitmap #11 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#11) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 40
shifted from previous position = 0.0105
rotated from previous position = 0.0123 degrees
atoms outside contour = 1696, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#11) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66052896 -0.23634807 0.71262969 198.04815956
-0.68927801 -0.56718464 0.45077422 233.23880784
0.29765300 -0.78894941 -0.53755142 191.34107964
Axis -0.89603248 0.29993184 -0.32736323
Axis point 0.00000000 180.17191035 -4.22943965
Rotation angle (degrees) 136.22842742
Shift along axis -170.13987198
> show #12 models
> fitmap #12 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#12) to map postprocess_20231221.mrc (#1) using
1463 atoms
average map value = 0.003943, steps = 48
shifted from previous position = 0.564
rotated from previous position = 0.308 degrees
atoms outside contour = 792, contour level = 0.0036898
Position of CopZ2_Q9CTG7.pdb (#12) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.81874430 0.29468639 -0.49276540 229.57707351
0.42646349 0.88676202 -0.17827520 242.04440837
0.38443036 -0.35610825 -0.85170432 217.26779618
Axis -0.19656816 -0.96961028 0.14566010
Axis point 59.00805506 0.00000000 149.10621012
Rotation angle (degrees) 153.10579582
Shift along axis -248.16903926
> fitmap #12 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#12) to map postprocess_20231221.mrc (#1) using
1463 atoms
average map value = 0.003943, steps = 40
shifted from previous position = 0.0335
rotated from previous position = 0.0211 degrees
atoms outside contour = 791, contour level = 0.0036898
Position of CopZ2_Q9CTG7.pdb (#12) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.81866518 0.29497106 -0.49272652 229.57125241
0.42677568 0.88660223 -0.17832284 242.02908265
0.38425235 -0.35627040 -0.85171684 217.29672636
Axis -0.19673469 -0.96956748 0.14572013
Axis point 58.98526141 0.00000000 149.11804424
Rotation angle (degrees) 153.11169842
Shift along axis -248.16364946
> hide #12 models
> hide #11 models
> hide #10 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> show #!2 models
> fitmap #2 inMap #19
Fit map emdb 3720 in map COPI_golph_linkage3_postprocess.mrc using 59756
points
correlation = 0.9221, correlation about mean = 0.1307, overlap = 7982
steps = 60, shift = 1.8, angle = 1.99 degrees
Position of emdb 3720 (#2) relative to COPI_golph_linkage3_postprocess.mrc
(#19) coordinates:
Matrix rotation and translation
-0.31594025 0.94479671 -0.08683858 142.25623042
-0.83994174 -0.23595976 0.48869302 440.74618377
0.44122515 0.22733714 0.86812338 169.14183802
Axis -0.13905746 -0.28096250 -0.94959102
Axis point 189.74687204 158.49424114 0.00000000
Rotation angle (degrees) 109.99196218
Shift along axis -304.23050762
> fitmap #2 inMap #19
Fit map emdb 3720 in map COPI_golph_linkage3_postprocess.mrc using 59756
points
correlation = 0.9222, correlation about mean = 0.1314, overlap = 7982
steps = 44, shift = 0.0692, angle = 0.0438 degrees
Position of emdb 3720 (#2) relative to COPI_golph_linkage3_postprocess.mrc
(#19) coordinates:
Matrix rotation and translation
-0.31615189 0.94467086 -0.08743537 142.35257321
-0.83978742 -0.23578672 0.48904164 440.66001664
0.44136729 0.22803856 0.86786712 169.00880070
Axis -0.13887768 -0.28137172 -0.94949616
Axis point 189.73292704 158.37878100 0.00000000
Rotation angle (degrees) 110.00095137
Shift along axis -304.23206571
> hide #!1 models
> show #!25 models
> select add #25
2 models selected
> view matrix models
> #25,-0.57191,-0.8201,0.019025,107.88,0.72153,-0.51394,-0.46397,240.5,0.39028,-0.25162,0.88565,97.921
> ui mousemode right "rotate selected models"
> view matrix models
> #25,-0.97643,0.20843,-0.05603,40.105,-0.18476,-0.9414,-0.28218,371.44,-0.11156,-0.26518,0.95772,147.33
> view matrix models
> #25,0.38166,-0.92429,-0.0044408,15.551,0.42044,0.17788,-0.88971,244.28,0.82314,0.3377,0.4565,31.494
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.38166,-0.92429,-0.0044408,463.08,0.42044,0.17788,-0.88971,150.43,0.82314,0.3377,0.4565,69.094
> view matrix models
> #25,0.38166,-0.92429,-0.0044408,472.3,0.42044,0.17788,-0.88971,144.63,0.82314,0.3377,0.4565,54.578
> view matrix models
> #25,0.38166,-0.92429,-0.0044408,462.57,0.42044,0.17788,-0.88971,156.68,0.82314,0.3377,0.4565,47.084
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.9188, correlation about mean = 0.141, overlap = 8478
steps = 84, shift = 4.7, angle = 7.97 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.31594010 -0.94484317 0.08633230 402.08767860
0.84006149 0.23628301 -0.48833090 103.52010046
0.44099725 0.22680775 0.86837762 169.21551421
Axis 0.36574862 -0.18138890 0.91286692
Axis point 62.17270241 271.09250194 0.00000000
Rotation angle (degrees) 77.86004514
Shift along axis 282.75686127
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.9188, correlation about mean = 0.1411, overlap = 8478
steps = 60, shift = 0.0604, angle = 0.0187 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.31589866 -0.94483161 0.08660999 402.09680047
0.84018832 0.23616260 -0.48817090 103.45853133
0.44078525 0.22698124 0.86843992 169.19285447
Axis 0.36575152 -0.18113647 0.91291588
Axis point 62.28097693 271.01210874 0.00000000
Rotation angle (degrees) 77.86296205
Shift along axis 282.78624492
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.9188, correlation about mean = 0.1412, overlap = 8478
steps = 44, shift = 0.06, angle = 0.0158 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.31598273 -0.94482437 0.08638198 402.05546991
0.84007328 0.23630678 -0.48829911 103.48150335
0.44094424 0.22686128 0.86839056 169.18732136
Axis 0.36576293 -0.18133797 0.91287131
Axis point 62.19547617 271.05309880 0.00000000
Rotation angle (degrees) 77.85772053
Shift along axis 282.73811193
> select subtract #25
Nothing selected
> hide #!25 models
> show #!25 models
> show #!37 models
> select add #37
2 models selected
> view matrix models
> #37,-0.61824,-0.62388,-0.47807,233.58,0.7555,-0.30392,-0.58039,107.22,0.2168,-0.72,0.65924,222.03
> ui mousemode right "rotate selected models"
> view matrix models
> #37,-0.97159,0.19811,0.12949,103.65,-0.23662,-0.8022,-0.54817,275.26,-0.0047197,-0.56324,0.82628,208.66
> ui mousemode right "rotate selected models"
> view matrix models
> #37,-0.92877,0.12598,-0.3486,163.85,0.19226,-0.64034,-0.74364,230.44,-0.31691,-0.75769,0.57051,297.42
> ui mousemode right "translate selected models"
> view matrix models
> #37,-0.92877,0.12598,-0.3486,336.71,0.19226,-0.64034,-0.74364,370.23,-0.31691,-0.75769,0.57051,333.6
> view matrix models
> #37,-0.92877,0.12598,-0.3486,339.32,0.19226,-0.64034,-0.74364,351.83,-0.31691,-0.75769,0.57051,326.89
> ui mousemode right "rotate selected models"
> view matrix models
> #37,0.63887,-0.75644,0.14015,209.6,0.57739,0.35108,-0.73713,189,0.50839,0.55186,0.66106,66.313
> ui mousemode right "translate selected models"
> view matrix models
> #37,0.63887,-0.75644,0.14015,238.84,0.57739,0.35108,-0.73713,187.7,0.50839,0.55186,0.66106,80.453
> view matrix models
> #37,0.63887,-0.75644,0.14015,230.99,0.57739,0.35108,-0.73713,188.41,0.50839,0.55186,0.66106,73.947
> ui mousemode right "rotate selected models"
> view matrix models
> #37,0.53263,-0.77516,-0.33975,301.9,0.65601,0.63176,-0.41296,107.7,0.53475,-0.0029237,0.845,115.54
> view matrix models
> #37,0.6883,-0.50769,-0.51817,273.39,0.57831,0.81525,-0.030575,49.438,0.43796,-0.27862,0.85473,158.28
> ui mousemode right "translate selected models"
> view matrix models
> #37,0.6883,-0.50769,-0.51817,271.67,0.57831,0.81525,-0.030575,58.164,0.43796,-0.27862,0.85473,149.69
> fitmap #37 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 93502 points
correlation = 0.8126, correlation about mean = 0.06345, overlap = 7612
steps = 180, shift = 34.6, angle = 32.7 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.53128525 -0.28140419 -0.79909177 250.52694837
0.67839952 0.70628678 0.20231920 51.77405293
0.50745449 -0.64959268 0.56614422 275.41479911
Axis -0.46516877 -0.71341241 0.52408086
Axis point -192.25802356 0.00000000 420.96828822
Rotation angle (degrees) 66.30560952
Shift along axis -9.13393909
> view matrix models
> #37,0.61278,-0.057933,-0.78813,278.4,0.19994,0.97623,0.083696,78.478,0.76454,-0.20887,0.60979,125.69
> view matrix models
> #37,0.61278,-0.057933,-0.78813,290.82,0.19994,0.97623,0.083696,69.562,0.76454,-0.20887,0.60979,135.95
> fitmap #37 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 93502 points
correlation = 0.8127, correlation about mean = 0.06331, overlap = 7612
steps = 88, shift = 19.4, angle = 0.0108 degrees
Position of emd_3720_2017_leaf.map (#37) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.53122006 -0.28153083 -0.79909050 250.54765948
0.67853284 0.70616928 0.20228226 51.80360254
0.50734447 -0.64966555 0.56615921 275.39206228
Axis -0.46516969 -0.71332299 0.52420174
Axis point -192.24664318 0.00000000 421.00099641
Rotation angle (degrees) 66.31085613
Shift along axis -9.13887938
> select subtract #37
Nothing selected
> hide #!37 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/5a1x_COPI_coat_linkage3_2015.cif.gz"
File reader requires uncompressed file;
'/Users/becca/Desktop/Postdoc/Structure files/COPI
structures/5a1x_COPI_coat_linkage3_2015.cif.gz' is compressed
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/5a1x_COPI_coat_linkage3_2015.cif"
5a1x_COPI_coat_linkage3_2015.cif title:
The structure of the COPI coat linkage III [more info...]
Chain information for 5a1x_COPI_coat_linkage3_2015.cif #60
---
Chain | Description | UniProt
A B I J | ADP-RIBOSYLATION FACTOR 1 | ARF1_YEAST 1-181
C K | COATOMER SUBUNIT ALPHA | COPA_MOUSE 1-1224
D L | COATOMER SUBUNIT BETA' | COPB2_MOUSE 1-905
E M | COATOMER SUBUNIT GAMMA-1 | COPG1_MOUSE 1-874
F N | COATOMER SUBUNIT ZETA-1 | COPZ1_MOUSE 1-177
G O | COATOMER SUBUNIT BETA | COPB_MOUSE 1-968
H P Q | COATOMER SUBUNIT DELTA | COPD_MOUSE 1-511
> hide #!60 atoms
> show #!60 cartoons
> hide #60.1 models
> show #60.1 models
> hide #60.1 models
> show #60.1 models
> hide #60.1 models
> show #60.1 models
> select add #60
32592 atoms, 32570 bonds, 5 pseudobonds, 8151 residues, 2 models selected
> view matrix models #60,1,0,0,278.7,0,1,0,292.71,0,0,1,295.39
> hide #!19 models
> view matrix models #60,1,0,0,283.2,0,1,0,309.7,0,0,1,307.52
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.30395,-0.95232,-0.026433,298.99,0.90553,0.29742,-0.30259,232.3,0.29602,0.068037,0.95276,290.94
> view matrix models
> #60,0.30764,-0.9412,-0.1396,298.51,0.87798,0.33735,-0.33961,234.95,0.36674,-0.018089,0.93015,284.01
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.30764,-0.9412,-0.1396,472.74,0.87798,0.33735,-0.33961,184.2,0.36674,-0.018089,0.93015,328.4
> select subtract #60
Nothing selected
> show #50 models
> hide #50 models
> show #50 models
> hide #50 models
> show #50 models
> hide #50 models
> show #50 models
> hide #50 models
> show #50 models
> hide #50 models
> show #50 models
> select add #60
32592 atoms, 32570 bonds, 5 pseudobonds, 8151 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.71806,0.1644,-0.67629,476.17,-0.57073,0.69522,-0.43697,283.37,0.39833,0.69975,0.59303,345.19
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.71806,0.1644,-0.67629,301.94,-0.57073,0.69522,-0.43697,317.81,0.39833,0.69975,0.59303,291
> view matrix models
> #60,0.71806,0.1644,-0.67629,271.07,-0.57073,0.69522,-0.43697,408.75,0.39833,0.69975,0.59303,320.31
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.39633,0.84407,-0.3612,311.83,-0.91749,0.34975,-0.18942,421.58,-0.033549,0.40647,0.91305,340.24
> view matrix models
> #60,0.36213,0.89583,-0.2576,315.92,-0.93213,0.34741,-0.10221,422.85,-0.0020647,0.27713,0.96083,334.85
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.36213,0.89583,-0.2576,282.84,-0.93213,0.34741,-0.10221,406.37,-0.0020647,0.27713,0.96083,302.27
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.29442,0.93069,-0.21709,324.59,-0.93376,-0.32852,-0.14204,387.06,-0.20351,0.16089,0.96576,311.43
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.29442,0.93069,-0.21709,308,-0.93376,-0.32852,-0.14204,396.26,-0.20351,0.16089,0.96576,298.11
> view matrix models
> #60,-0.29442,0.93069,-0.21709,313.22,-0.93376,-0.32852,-0.14204,387.45,-0.20351,0.16089,0.96576,306.51
> hide #50 models
> select subtract #60
Nothing selected
> select add #60
32592 atoms, 32570 bonds, 5 pseudobonds, 8151 residues, 2 models selected
> view matrix models
> #60,-0.29442,0.93069,-0.21709,185.5,-0.93376,-0.32852,-0.14204,270.05,-0.20351,0.16089,0.96576,181.41
> select subtract #60
Nothing selected
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #!56 models
> hide #!56 models
> show #54 models
> hide #54 models
> show #54 models
> hide #54 models
> show #54 models
> hide #!25 models
> show #!25 models
> hide #!2 models
> show #!2 models
> select add #60
32592 atoms, 32570 bonds, 5 pseudobonds, 8151 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.69872,0.078126,-0.71112,97.473,0.24248,0.90932,0.33815,234.97,0.67305,-0.40871,0.61641,109.34
> view matrix models
> #60,0.69338,0.088487,-0.71511,98.077,0.24277,0.90572,0.34747,234.9,0.67844,-0.41454,0.60653,108.79
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.69338,0.088487,-0.71511,288.6,0.24277,0.90572,0.34747,273.74,0.67844,-0.41454,0.60653,261.75
> view matrix models
> #60,0.69338,0.088487,-0.71511,293.77,0.24277,0.90572,0.34747,295.88,0.67844,-0.41454,0.60653,304.94
> select subtract #60
Nothing selected
> hide #!25 models
> hide #!2 models
> select add #60
32592 atoms, 32570 bonds, 5 pseudobonds, 8151 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.86942,-0.22536,0.43968,279.7,0.40591,0.83316,-0.3756,280.16,-0.28168,0.50503,0.81585,391.43
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.86942,-0.22536,0.43968,269.02,0.40591,0.83316,-0.3756,273.58,-0.28168,0.50503,0.81585,316.65
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.099844,-0.98449,-0.14427,292.07,0.84964,0.15982,-0.50257,226.4,0.51783,-0.072399,0.85242,251.03
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.099844,-0.98449,-0.14427,298.05,0.84964,0.15982,-0.50257,272.51,0.51783,-0.072399,0.85242,290.42
> view matrix models
> #60,0.099844,-0.98449,-0.14427,300.25,0.84964,0.15982,-0.50257,276.15,0.51783,-0.072399,0.85242,305.68
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.29969,-0.86037,-0.41226,327.13,0.79371,0.014914,-0.60811,274.96,0.52934,-0.50946,0.67841,291.68
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.29969,-0.86037,-0.41226,330,0.79371,0.014914,-0.60811,274.56,0.52934,-0.50946,0.67841,304.12
> view matrix models
> #60,-0.29969,-0.86037,-0.41226,326.7,0.79371,0.014914,-0.60811,276.86,0.52934,-0.50946,0.67841,295.37
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.16482,-0.96487,0.20459,318.46,-0.25356,-0.15901,-0.95416,334.88,0.95317,-0.20914,-0.21845,273.29
> view matrix models
> #60,-0.22265,-0.9332,-0.28208,320.52,0.95497,-0.15056,-0.25568,263.94,0.19613,-0.3263,0.92469,322.38
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.22265,-0.9332,-0.28208,318.22,0.95497,-0.15056,-0.25568,248.03,0.19613,-0.3263,0.92469,316.64
> view matrix models
> #60,-0.22265,-0.9332,-0.28208,324.94,0.95497,-0.15056,-0.25568,247.07,0.19613,-0.3263,0.92469,301.89
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.10757,-0.99405,0.01717,317.59,0.87094,-0.10255,-0.48057,252.51,0.47948,-0.03674,0.87679,292.39
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.10757,-0.99405,0.01717,309.12,0.87094,-0.10255,-0.48057,265.96,0.47948,-0.03674,0.87679,287.59
> view matrix models
> #60,-0.10757,-0.99405,0.01717,308.58,0.87094,-0.10255,-0.48057,269.36,0.47948,-0.03674,0.87679,297.99
> view matrix models
> #60,-0.10757,-0.99405,0.01717,306.6,0.87094,-0.10255,-0.48057,265.23,0.47948,-0.03674,0.87679,295.2
> hide #54 models
> show #54 models
> hide #54 models
> show #54 models
> view matrix models
> #60,-0.10757,-0.99405,0.01717,195.57,0.87094,-0.10255,-0.48057,229.02,0.47948,-0.03674,0.87679,322.68
> view matrix models
> #60,-0.10757,-0.99405,0.01717,177.13,0.87094,-0.10255,-0.48057,181.04,0.47948,-0.03674,0.87679,302.25
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.67938,-0.71254,0.17532,137.31,0.73214,0.64222,-0.22698,212.05,0.049136,0.28257,0.95799,338.31
> view matrix models
> #60,0.35741,-0.93101,0.074016,150.48,0.88939,0.31509,-0.33122,192.52,0.28505,0.18421,0.94065,320.86
> view matrix models
> #60,0.0062061,-0.99848,0.054808,170.16,0.81786,-0.026469,-0.57481,186.02,0.57538,0.048393,0.81645,298.45
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.0062061,-0.99848,0.054808,300.16,0.81786,-0.026469,-0.57481,269.53,0.57538,0.048393,0.81645,290.76
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.1471,-0.98798,0.047428,309.89,0.96301,-0.15399,-0.22113,258.69,0.22577,0.013147,0.97409,312.14
> view matrix models
> #60,-0.25612,-0.79759,-0.54612,319.1,0.75336,0.1893,-0.62977,279.38,0.60569,-0.57273,0.55239,269.92
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.25612,-0.79759,-0.54612,334.29,0.75336,0.1893,-0.62977,287.43,0.60569,-0.57273,0.55239,310.88
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.28394,-0.86187,0.4202,338.97,-0.030703,-0.42984,-0.90238,316.9,0.95835,-0.26912,0.095586,295.47
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.28394,-0.86187,0.4202,331.17,-0.030703,-0.42984,-0.90238,321.67,0.95835,-0.26912,0.095586,273.13
> view matrix models
> #60,-0.28394,-0.86187,0.4202,309.08,-0.030703,-0.42984,-0.90238,343.32,0.95835,-0.26912,0.095586,285.64
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.38051,-0.71783,-0.58304,267.17,0.76466,0.5988,-0.2382,326.73,0.52011,-0.35519,0.77674,313.64
> view matrix models
> #60,0.089963,-0.91854,-0.38495,280.39,0.93121,0.21466,-0.29458,305.24,0.35322,-0.33196,0.87466,325.09
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.089963,-0.91854,-0.38495,279.17,0.93121,0.21466,-0.29458,308.48,0.35322,-0.33196,0.87466,312.14
> view matrix models
> #60,0.089963,-0.91854,-0.38495,313.17,0.93121,0.21466,-0.29458,275.27,0.35322,-0.33196,0.87466,284.81
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.58428,0.80232,0.12208,406.26,0.81034,0.56857,0.1417,294.96,0.044277,0.18172,-0.98235,309.3
> view matrix models
> #60,-0.98665,0.015404,0.16213,408.94,0.13439,0.63936,0.75708,341.77,-0.091998,0.76876,-0.63289,336.14
> view matrix models
> #60,-0.93577,-0.24632,-0.25233,396.3,-0.29531,0.93848,0.17903,373.95,0.19271,0.24204,-0.95094,302.01
> view matrix models
> #60,-0.93453,-0.24826,-0.255,396.15,-0.29745,0.93826,0.17664,374.07,0.1954,0.24092,-0.95067,301.81
> ui mousemode right "translate selected models"
> view matrix models
> #60,-0.93453,-0.24826,-0.255,320.41,-0.29745,0.93826,0.17664,311,0.1954,0.24092,-0.95067,315.49
> view matrix models
> #60,-0.93453,-0.24826,-0.255,321.63,-0.29745,0.93826,0.17664,283.92,0.1954,0.24092,-0.95067,330.32
> view matrix models
> #60,-0.93453,-0.24826,-0.255,330.19,-0.29745,0.93826,0.17664,277.68,0.1954,0.24092,-0.95067,357.4
> ui mousemode right "rotate selected models"
> view matrix models
> #60,-0.86274,-0.40741,-0.29951,321.01,-0.50398,0.74096,0.44383,286.15,0.041104,0.53386,-0.84457,375.79
> view matrix models
> #60,-0.91726,-0.29906,-0.26304,327.64,-0.36609,0.89321,0.26108,281.05,0.15687,0.33578,-0.92879,362.59
> view matrix models
> #60,0.46859,-0.5126,0.71949,240.83,-0.34056,0.64667,0.68252,274.55,-0.81514,-0.56485,0.12845,402.25
> view matrix models
> #60,-0.511,0.62905,-0.58581,327.33,-0.84789,-0.25685,0.4638,279.12,0.14129,0.73371,0.66462,382.76
> view matrix models
> #60,-0.076799,0.98714,0.14022,314.29,0.81552,0.1431,-0.56076,182.67,-0.57362,0.071289,-0.81602,400.74
> view matrix models
> #60,0.37987,-0.2661,-0.88594,245.37,0.91291,0.26241,0.31262,184.37,0.14929,-0.92754,0.34261,333.43
> view matrix models
> #60,0.24379,-0.61027,-0.75375,244.64,0.96341,0.063127,0.26049,175.33,-0.11139,-0.78967,0.60333,354.74
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.24379,-0.61027,-0.75375,254.27,0.96341,0.063127,0.26049,213.46,-0.11139,-0.78967,0.60333,338.98
> view matrix models
> #60,0.24379,-0.61027,-0.75375,186.67,0.96341,0.063127,0.26049,196.79,-0.11139,-0.78967,0.60333,285.3
> view matrix models
> #60,0.24379,-0.61027,-0.75375,184.49,0.96341,0.063127,0.26049,192.05,-0.11139,-0.78967,0.60333,302.12
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.1646,-0.7403,-0.65181,186.19,0.97953,0.20033,0.019833,193.76,0.11589,-0.64173,0.75812,293.05
> view matrix models
> #60,0.17244,0.13692,-0.97546,209.04,0.54681,0.81038,0.21041,238.78,0.8193,-0.56968,0.064879,248.22
> hide #54 models
> show #54 models
> select subtract #60
Nothing selected
> select add #60
32592 atoms, 32570 bonds, 5 pseudobonds, 8151 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.17244,0.13692,-0.97546,247.1,0.54681,0.81038,0.21041,312.98,0.8193,-0.56968,0.064879,179.83
> view matrix models
> #60,0.17244,0.13692,-0.97546,243.27,0.54681,0.81038,0.21041,317.9,0.8193,-0.56968,0.064879,170.53
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.33024,0.062073,-0.94185,231.57,0.32582,0.92901,0.17547,334.75,0.88588,-0.36482,0.28657,173.34
> view matrix models
> #60,0.091972,0.19299,-0.97688,249.83,0.65733,0.72514,0.20514,308.62,0.74797,-0.661,-0.060164,171.72
> view matrix models
> #60,0.42223,0.037289,-0.90572,225.36,0.1947,0.97211,0.13079,343.85,0.88533,-0.23156,0.40319,177.74
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.42223,0.037289,-0.90572,209.96,0.1947,0.97211,0.13079,368.39,0.88533,-0.23156,0.40319,222.12
> view matrix models
> #60,0.42223,0.037289,-0.90572,213.37,0.1947,0.97211,0.13079,374.19,0.88533,-0.23156,0.40319,214.42
> view matrix models
> #60,0.42223,0.037289,-0.90572,223.35,0.1947,0.97211,0.13079,376.8,0.88533,-0.23156,0.40319,223.94
> view matrix models
> #60,0.42223,0.037289,-0.90572,220.66,0.1947,0.97211,0.13079,374.3,0.88533,-0.23156,0.40319,226.27
> view matrix models
> #60,0.42223,0.037289,-0.90572,219.31,0.1947,0.97211,0.13079,377.5,0.88533,-0.23156,0.40319,221.97
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.46204,0.027203,-0.88644,216.66,0.10583,0.9907,0.085565,383.3,0.88052,-0.13335,0.45486,225.31
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.46204,0.027203,-0.88644,216.5,0.10583,0.9907,0.085565,383.3,0.88052,-0.13335,0.45486,234.52
> select subtract #60
Nothing selected
> hide #54 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!25 models
> show #!19 models
> hide #!25 models
> show #!25 models
> hide #!19 models
> show #30 models
> hide #30 models
> show #30 models
> hide #30 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!60 models
> hide #!25 models
> show #!1 models
> surface dust #2 size 17.8
> surface dust #1 size 25.5
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7167, correlation about mean = 0.2039, overlap = 49.32
steps = 88, shift = 2.05, angle = 2.09 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53789413 0.84247923 -0.02997756 166.41351370
-0.84288398 -0.53809272 0.00168124 370.29314647
-0.01471430 0.02617193 0.99954916 111.75105961
Axis 0.01452927 -0.00905503 -0.99985344
Axis point 185.19765373 138.59553433 0.00000000
Rotation angle (degrees) 122.56246994
Shift along axis -112.66983142
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7166, correlation about mean = 0.2038, overlap = 49.31
steps = 60, shift = 0.0304, angle = 0.00646 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53786301 0.84250231 -0.02988718 166.41268452
-0.84290388 -0.53806172 0.00162510 370.29411574
-0.01471200 0.02606610 0.99955196 111.78773883
Axis 0.01449944 -0.00900256 -0.99985435
Axis point 185.20219904 138.59778405 0.00000000
Rotation angle (degrees) 122.56026340
Shift along axis -112.69216210
> fitmap #2 inMap #1
Fit map emdb 3720 in map postprocess_20231221.mrc using 59756 points
correlation = 0.7166, correlation about mean = 0.2039, overlap = 49.31
steps = 64, shift = 0.0403, angle = 0.0199 degrees
Position of emdb 3720 (#2) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.53813091 0.84232814 -0.02997387 166.43542003
-0.84273361 -0.53832799 0.00174126 370.29897186
-0.01466906 0.02619701 0.99954917 111.76451127
Axis 0.01451114 -0.00908131 -0.99985347
Axis point 185.17478882 138.60667507 0.00000000
Rotation angle (degrees) 122.57851683
Shift along axis -112.69576575
> fitmap #1 inMap #19
Fit map postprocess_20231221.mrc in map COPI_golph_linkage3_postprocess.mrc
using 19065 points
correlation = 0.8356, correlation about mean = 0.1175, overlap = 85.08
steps = 44, shift = 0.0201, angle = 0.00901 degrees
Position of postprocess_20231221.mrc (#1) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.97198715 -0.23384369 -0.02362457 67.46579987
0.21520905 0.84508851 0.48939808 41.67837632
-0.09447780 -0.48077287 0.87174044 268.62322175
Axis -0.90551614 0.06613137 0.41912666
Axis point 0.00000000 490.75832581 77.51050191
Rotation angle (degrees) 32.39143179
Shift along axis 54.25203054
> fitmap #1 inMap #19
Fit map postprocess_20231221.mrc in map COPI_golph_linkage3_postprocess.mrc
using 19065 points
correlation = 0.8357, correlation about mean = 0.1179, overlap = 85.08
steps = 28, shift = 0.0623, angle = 0.00755 degrees
Position of postprocess_20231221.mrc (#1) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.97200433 -0.23378289 -0.02351911 67.46302473
0.21510985 0.84513634 0.48935908 41.68304002
-0.09452693 -0.48071834 0.87176519 268.66471165
Axis -0.90554845 0.06628442 0.41903266
Axis point 0.00000000 490.91186598 77.52461595
Rotation angle (degrees) 32.38663105
Shift along axis 54.25118840
> fitmap #2 inMap #19
Fit map emdb 3720 in map COPI_golph_linkage3_postprocess.mrc using 59756
points
correlation = 0.9222, correlation about mean = 0.1315, overlap = 7982
steps = 60, shift = 2.05, angle = 2.07 degrees
Position of emdb 3720 (#2) relative to COPI_golph_linkage3_postprocess.mrc
(#19) coordinates:
Matrix rotation and translation
-0.31624299 0.94466933 -0.08712193 142.35985490
-0.83977736 -0.23603650 0.48893841 440.70447209
0.44132116 0.22778637 0.86795680 169.02922082
Axis -0.13896370 -0.28119408 -0.94953619
Axis point 189.74284311 158.42726910 0.00000000
Rotation angle (degrees) 110.00860971
Shift along axis -304.20570262
> fitmap #2 inMap #19
Fit map emdb 3720 in map COPI_golph_linkage3_postprocess.mrc using 59756
points
correlation = 0.9221, correlation about mean = 0.1309, overlap = 7982
steps = 96, shift = 0.0548, angle = 0.0155 degrees
Position of emdb 3720 (#2) relative to COPI_golph_linkage3_postprocess.mrc
(#19) coordinates:
Matrix rotation and translation
-0.31605739 0.94474379 -0.08698794 142.29294605
-0.83986531 -0.23596231 0.48882313 440.71948710
0.44128675 0.22755432 0.86803517 169.10135286
Axis -0.13901673 -0.28108605 -0.94956041
Axis point 189.73624545 158.46025452 0.00000000
Rotation angle (degrees) 109.99830030
Shift along axis -304.23315163
> hide #!2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> show #12 models
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map postprocess_20231221.mrc (#1) using
7501 atoms
average map value = 0.002923, steps = 84
shifted from previous position = 0.0382
rotated from previous position = 0.0452 degrees
atoms outside contour = 5658, contour level = 0.0036898
Position of CopB_Q9JIF7.pdb (#4) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04204199 -0.73290824 0.67902723 172.35762146
-0.03854177 0.68031195 0.73190859 204.57850055
-0.99837218 0.00459998 -0.05684925 236.22466685
Axis -0.37189030 0.85769447 0.35504620
Axis point 209.20864402 0.00000000 -39.70487813
Rotation angle (degrees) 102.08072677
Shift along axis 195.23839065
> fitmap #5 inMap #1
Fit molecule hArf1_P84078 (#5) to map postprocess_20231221.mrc (#1) using 1457
atoms
average map value = 0.002588, steps = 60
shifted from previous position = 0.0738
rotated from previous position = 0.0442 degrees
atoms outside contour = 1386, contour level = 0.0036898
Position of hArf1_P84078 (#5) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.15805659 0.02390284 0.98714070 126.72720553
-0.68664804 -0.71576226 0.12727467 200.56733706
0.70960029 -0.69793483 -0.09671810 178.42654262
Axis -0.73431574 0.24697036 -0.63228635
Axis point 0.00000000 138.25648299 -15.42719634
Rotation angle (degrees) 145.81338808
Shift along axis -156.34026119
> fitmap #6 inMap #1
Fit molecule hArf1_P84078 (#6) to map postprocess_20231221.mrc (#1) using 1457
atoms
average map value = 0.003766, steps = 60
shifted from previous position = 0.106
rotated from previous position = 0.0911 degrees
atoms outside contour = 772, contour level = 0.0036898
Position of hArf1_P84078 (#6) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.84467256 -0.49408118 0.20594182 243.02027542
-0.47641085 0.51849497 -0.71006735 195.90966661
0.24405112 -0.69788733 -0.67334412 220.58487971
Axis 0.27848415 -0.87133155 0.40401475
Axis point 151.39777962 0.00000000 157.26095359
Rotation angle (degrees) 178.74693150
Shift along axis -13.90543314
> fitmap #7 inMap #1
Fit molecule CopBprime_O55029.pdb (#7) to map postprocess_20231221.mrc (#1)
using 7214 atoms
average map value = 0.00312, steps = 40
shifted from previous position = 0.0457
rotated from previous position = 0.0115 degrees
atoms outside contour = 4439, contour level = 0.0036898
Position of CopBprime_O55029.pdb (#7) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.16297840 -0.17495258 -0.97099415 188.47156436
-0.01390854 -0.98364743 0.17956694 177.44655545
-0.98653160 0.04277064 0.15787995 238.55752250
Axis -0.64565482 0.07333407 0.76009997
Axis point 189.54120913 85.43977118 0.00000000
Rotation angle (degrees) 173.91889861
Shift along axis 72.65287052
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003729, steps = 44
shifted from previous position = 0.0408
rotated from previous position = 0.102 degrees
atoms outside contour = 873, contour level = 0.0036898
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23790045 0.93128065 0.27589806 -92.98880965
-0.88673422 0.09232665 0.45296603 106.05943164
0.39636576 -0.35240907 0.84776296 472.48610183
Axis -0.40429175 -0.06047381 -0.91262868
Axis point -102.10995577 189.95035402 0.00000000
Rotation angle (degrees) 84.89420555
Shift along axis -400.02357488
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 44
shifted from previous position = 0.0457
rotated from previous position = 0.0581 degrees
atoms outside contour = 4569, contour level = 0.0036898
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48924720 -0.51142655 -0.70645598 223.52473516
0.54885976 -0.44895469 0.70511888 282.30607954
-0.67778325 -0.73272271 0.06105163 258.73819061
Axis -0.80473185 -0.01604757 0.59342154
Axis point 0.00000000 245.03242129 103.85502366
Rotation angle (degrees) 116.70057308
Shift along axis -30.86698566
> fitmap #10 inMap #1
Fit molecule CopZ1_P61924.pdb (#10) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 36
shifted from previous position = 0.0572
rotated from previous position = 0.0173 degrees
atoms outside contour = 728, contour level = 0.0036898
Position of CopZ1_P61924.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16498590 -0.93978539 -0.29930433 230.49900822
-0.38648480 0.21759238 -0.89626060 241.46307367
0.90741895 0.26354694 -0.32731309 218.19582622
Axis 0.65793354 -0.68454782 0.31387536
Axis point 143.40944771 0.00000000 249.46139423
Rotation angle (degrees) 118.18808002
Shift along axis 54.84630101
> fitmap #11 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#11) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 44
shifted from previous position = 0.0573
rotated from previous position = 0.0141 degrees
atoms outside contour = 1696, contour level = 0.0036898
Position of Golph3_ Q9CRA5.pdb (#11) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66065701 -0.23605314 0.71260875 198.04675678
-0.68911945 -0.56720356 0.45099280 233.23742276
0.29773596 -0.78902410 -0.53739582 191.34041376
Axis -0.89606552 0.29979689 -0.32739642
Axis point 0.00000000 180.15753978 -4.24457588
Rotation angle (degrees) 136.21746581
Shift along axis -170.18318361
> fitmap #12 inMap #1
Fit molecule CopZ2_Q9CTG7.pdb (#12) to map postprocess_20231221.mrc (#1) using
1463 atoms
average map value = 0.003943, steps = 28
shifted from previous position = 0.0629
rotated from previous position = 0.0252 degrees
atoms outside contour = 792, contour level = 0.0036898
Position of CopZ2_Q9CTG7.pdb (#12) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.81886103 0.29484741 -0.49247503 229.58746104
0.42642015 0.88682129 -0.17808393 242.05348233
0.38422975 -0.35582726 -0.85191226 217.25273350
Axis -0.19658273 -0.96962860 0.14551842
Axis point 59.03709533 0.00000000 149.06603571
Rotation angle (degrees) 153.12260873
Shift along axis -248.22063449
> hide #12 models
> hide #11 models
> hide #10 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!19 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!25 models
> hide #!19 models
> show #!24 models
> show #26 models
> hide #26 models
> show #26 models
> show #27 models
> show #28 models
> show #29 models
> hide #29 models
> hide #28 models
> hide #27 models
> hide #26 models
> show #26 models
> show #27 models
> show #28 models
> show #29 models
> show #30 models
> show #31 models
> show #!32 models
> show #33 models
> show #34 models
> show #35 models
> hide #35 models
> hide #34 models
> hide #33 models
> hide #!32 models
> hide #31 models
> hide #30 models
> hide #29 models
> hide #28 models
> hide #27 models
> hide #26 models
> select add #24
2 models selected
> select add #26
9810 atoms, 10032 bonds, 1233 residues, 3 models selected
> select add #27
17311 atoms, 17651 bonds, 2186 residues, 4 models selected
> select add #28
18768 atoms, 19134 bonds, 2367 residues, 5 models selected
> select add #29
20225 atoms, 20617 bonds, 2548 residues, 6 models selected
> select add #30
27439 atoms, 27990 bonds, 3453 residues, 7 models selected
> select add #31
28901 atoms, 29471 bonds, 3632 residues, 8 models selected
> select add #32
35574 atoms, 36257 bonds, 1 pseudobond, 4485 residues, 10 models selected
> select add #33
36994 atoms, 37698 bonds, 1 pseudobond, 4662 residues, 11 models selected
> select add #34
39361 atoms, 40096 bonds, 1 pseudobond, 4960 residues, 12 models selected
> select add #35
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 13 models selected
> view matrix models
> #24,-0.16054,-0.65409,-0.73919,747.86,0.86063,-0.45943,0.21963,119.99,-0.48326,-0.60091,0.63669,187.05,#26,0.27527,-0.94991,-0.14796,385.04,0.78709,0.13431,0.60204,199.74,-0.55202,-0.28219,0.78463,113.9,#27,0.76996,-0.33035,-0.54591,411.76,-0.23736,-0.94244,0.23553,226.23,-0.59229,-0.051766,-0.80406,131.24,#28,-0.10092,0.98032,-0.16967,464.43,0.60766,0.19577,0.76969,176.08,0.78776,-0.02542,-0.61546,118.91,#29,0.26753,0.25509,0.92917,417.64,-0.45429,-0.81702,0.3551,287.56,0.84974,-0.51711,-0.1027,92.309,#30,0.76456,0.6398,-0.078118,425.21,-0.35018,0.31057,-0.8837,253.12,-0.54113,0.70299,0.4615,141.24,#31,0.58668,0.23131,-0.77608,343.11,0.44484,0.70875,0.54753,94.817,0.67669,-0.66646,0.31291,475.89,#32,0.063391,0.91735,-0.39301,336.08,0.019728,-0.39487,-0.91852,239.53,-0.99779,0.050473,-0.043129,74.118,#33,-0.44402,-0.18537,0.87663,391.63,0.51881,-0.85086,0.082864,255.36,0.73053,0.4916,0.47397,69.452,#34,0.12403,0.9922,-0.012537,422.1,0.95076,-0.11522,0.28771,225.29,0.28402,-0.047605,-0.95764,73.033,#35,-0.43145,-0.36473,0.82512,392.09,-0.81639,-0.23133,-0.52914,254.09,0.38387,-0.90192,-0.19795,68.983
> view matrix models
> #24,-0.16054,-0.65409,-0.73919,703.34,0.86063,-0.45943,0.21963,40.394,-0.48326,-0.60091,0.63669,261.37,#26,0.27527,-0.94991,-0.14796,340.53,0.78709,0.13431,0.60204,120.14,-0.55202,-0.28219,0.78463,188.22,#27,0.76996,-0.33035,-0.54591,367.25,-0.23736,-0.94244,0.23553,146.63,-0.59229,-0.051766,-0.80406,205.56,#28,-0.10092,0.98032,-0.16967,419.92,0.60766,0.19577,0.76969,96.476,0.78776,-0.02542,-0.61546,193.22,#29,0.26753,0.25509,0.92917,373.13,-0.45429,-0.81702,0.3551,207.96,0.84974,-0.51711,-0.1027,166.62,#30,0.76456,0.6398,-0.078118,380.7,-0.35018,0.31057,-0.8837,173.52,-0.54113,0.70299,0.4615,215.55,#31,0.58668,0.23131,-0.77608,298.6,0.44484,0.70875,0.54753,15.218,0.67669,-0.66646,0.31291,550.2,#32,0.063391,0.91735,-0.39301,291.56,0.019728,-0.39487,-0.91852,159.93,-0.99779,0.050473,-0.043129,148.43,#33,-0.44402,-0.18537,0.87663,347.12,0.51881,-0.85086,0.082864,175.76,0.73053,0.4916,0.47397,143.77,#34,0.12403,0.9922,-0.012537,377.59,0.95076,-0.11522,0.28771,145.69,0.28402,-0.047605,-0.95764,147.35,#35,-0.43145,-0.36473,0.82512,347.57,-0.81639,-0.23133,-0.52914,174.49,0.38387,-0.90192,-0.19795,143.3
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.90809,0.28081,0.31067,454.69,-0.41493,-0.70354,-0.57694,554.12,0.056559,-0.65282,0.7554,123.12,#26,-0.99491,0.0089671,-0.10039,450.36,-0.0052843,-0.99931,-0.03689,176.73,-0.10066,-0.036172,0.99426,153.23,#27,-0.28319,0.85799,-0.42856,429,0.62049,-0.17682,-0.76402,202.38,-0.7313,-0.48228,-0.48229,177.78,#28,-0.11625,-0.43906,-0.8909,451.39,0.00785,0.89655,-0.44287,257.49,0.99319,-0.058476,-0.10077,134.14,#29,0.70867,0.37799,-0.59574,357.56,0.54548,0.242,0.80243,188.18,0.44748,-0.89362,-0.034683,175.57,#30,-0.16277,-0.10384,0.98118,407.43,0.64654,0.73996,0.18557,213.45,-0.74531,0.66459,-0.053313,198.18,#31,-0.21503,-0.97071,-0.10715,719.32,0.66103,-0.063903,-0.74763,246.26,0.71889,-0.23159,0.65541,411.34,#32,-0.50044,0.1108,0.85865,411.32,-0.19814,0.9508,-0.23817,113.48,-0.84279,-0.28932,-0.45387,146.93,#33,0.023605,0.99631,-0.082554,380.94,-0.31959,0.085764,0.94367,162.7,0.94726,0.0041083,0.32044,143.32,#34,-0.70113,-0.19067,-0.68707,399.79,0.038256,0.95214,-0.30327,197.5,0.71201,-0.23892,-0.66028,126.6,#35,0.9827,-0.12958,0.13233,381.67,-0.18193,-0.54138,0.82086,163.22,-0.03472,-0.83073,-0.55559,142.2
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.90809,0.28081,0.31067,423.38,-0.41493,-0.70354,-0.57694,466.16,0.056559,-0.65282,0.7554,172.1,#26,-0.99491,0.0089671,-0.10039,419.05,-0.0052843,-0.99931,-0.03689,88.778,-0.10066,-0.036172,0.99426,202.22,#27,-0.28319,0.85799,-0.42856,397.7,0.62049,-0.17682,-0.76402,114.43,-0.7313,-0.48228,-0.48229,226.76,#28,-0.11625,-0.43906,-0.8909,420.08,0.00785,0.89655,-0.44287,169.54,0.99319,-0.058476,-0.10077,183.12,#29,0.70867,0.37799,-0.59574,326.25,0.54548,0.242,0.80243,100.22,0.44748,-0.89362,-0.034683,224.55,#30,-0.16277,-0.10384,0.98118,376.13,0.64654,0.73996,0.18557,125.49,-0.74531,0.66459,-0.053313,247.16,#31,-0.21503,-0.97071,-0.10715,688.02,0.66103,-0.063903,-0.74763,158.31,0.71889,-0.23159,0.65541,460.33,#32,-0.50044,0.1108,0.85865,380.02,-0.19814,0.9508,-0.23817,25.526,-0.84279,-0.28932,-0.45387,195.91,#33,0.023605,0.99631,-0.082554,349.64,-0.31959,0.085764,0.94367,74.75,0.94726,0.0041083,0.32044,192.31,#34,-0.70113,-0.19067,-0.68707,368.49,0.038256,0.95214,-0.30327,109.54,0.71201,-0.23892,-0.66028,175.59,#35,0.9827,-0.12958,0.13233,350.37,-0.18193,-0.54138,0.82086,75.267,-0.03472,-0.83073,-0.55559,191.19
> view matrix models
> #24,-0.90809,0.28081,0.31067,455.75,-0.41493,-0.70354,-0.57694,495.16,0.056559,-0.65282,0.7554,174.25,#26,-0.99491,0.0089671,-0.10039,451.42,-0.0052843,-0.99931,-0.03689,117.78,-0.10066,-0.036172,0.99426,204.37,#27,-0.28319,0.85799,-0.42856,430.07,0.62049,-0.17682,-0.76402,143.43,-0.7313,-0.48228,-0.48229,228.91,#28,-0.11625,-0.43906,-0.8909,452.45,0.00785,0.89655,-0.44287,198.54,0.99319,-0.058476,-0.10077,185.27,#29,0.70867,0.37799,-0.59574,358.62,0.54548,0.242,0.80243,129.23,0.44748,-0.89362,-0.034683,226.7,#30,-0.16277,-0.10384,0.98118,408.49,0.64654,0.73996,0.18557,154.5,-0.74531,0.66459,-0.053313,249.31,#31,-0.21503,-0.97071,-0.10715,720.39,0.66103,-0.063903,-0.74763,187.31,0.71889,-0.23159,0.65541,462.48,#32,-0.50044,0.1108,0.85865,412.39,-0.19814,0.9508,-0.23817,54.528,-0.84279,-0.28932,-0.45387,198.06,#33,0.023605,0.99631,-0.082554,382.01,-0.31959,0.085764,0.94367,103.75,0.94726,0.0041083,0.32044,194.46,#34,-0.70113,-0.19067,-0.68707,400.86,0.038256,0.95214,-0.30327,138.54,0.71201,-0.23892,-0.66028,177.74,#35,0.9827,-0.12958,0.13233,382.74,-0.18193,-0.54138,0.82086,104.27,-0.03472,-0.83073,-0.55559,193.34
> view matrix models
> #24,-0.90809,0.28081,0.31067,457.66,-0.41493,-0.70354,-0.57694,496.68,0.056559,-0.65282,0.7554,178.02,#26,-0.99491,0.0089671,-0.10039,453.32,-0.0052843,-0.99931,-0.03689,119.3,-0.10066,-0.036172,0.99426,208.14,#27,-0.28319,0.85799,-0.42856,431.97,0.62049,-0.17682,-0.76402,144.95,-0.7313,-0.48228,-0.48229,232.68,#28,-0.11625,-0.43906,-0.8909,454.36,0.00785,0.89655,-0.44287,200.06,0.99319,-0.058476,-0.10077,189.04,#29,0.70867,0.37799,-0.59574,360.53,0.54548,0.242,0.80243,130.74,0.44748,-0.89362,-0.034683,230.47,#30,-0.16277,-0.10384,0.98118,410.4,0.64654,0.73996,0.18557,156.01,-0.74531,0.66459,-0.053313,253.08,#31,-0.21503,-0.97071,-0.10715,722.29,0.66103,-0.063903,-0.74763,188.83,0.71889,-0.23159,0.65541,466.24,#32,-0.50044,0.1108,0.85865,414.29,-0.19814,0.9508,-0.23817,56.047,-0.84279,-0.28932,-0.45387,201.83,#33,0.023605,0.99631,-0.082554,383.91,-0.31959,0.085764,0.94367,105.27,0.94726,0.0041083,0.32044,198.23,#34,-0.70113,-0.19067,-0.68707,402.76,0.038256,0.95214,-0.30327,140.06,0.71201,-0.23892,-0.66028,181.5,#35,0.9827,-0.12958,0.13233,384.64,-0.18193,-0.54138,0.82086,105.79,-0.03472,-0.83073,-0.55559,197.11
> view matrix models
> #24,-0.90809,0.28081,0.31067,456.98,-0.41493,-0.70354,-0.57694,465.87,0.056559,-0.65282,0.7554,205.31,#26,-0.99491,0.0089671,-0.10039,452.65,-0.0052843,-0.99931,-0.03689,88.485,-0.10066,-0.036172,0.99426,235.42,#27,-0.28319,0.85799,-0.42856,431.3,0.62049,-0.17682,-0.76402,114.14,-0.7313,-0.48228,-0.48229,259.96,#28,-0.11625,-0.43906,-0.8909,453.68,0.00785,0.89655,-0.44287,169.24,0.99319,-0.058476,-0.10077,216.33,#29,0.70867,0.37799,-0.59574,359.85,0.54548,0.242,0.80243,99.93,0.44748,-0.89362,-0.034683,257.76,#30,-0.16277,-0.10384,0.98118,409.72,0.64654,0.73996,0.18557,125.2,-0.74531,0.66459,-0.053313,280.37,#31,-0.21503,-0.97071,-0.10715,721.61,0.66103,-0.063903,-0.74763,158.02,0.71889,-0.23159,0.65541,493.53,#32,-0.50044,0.1108,0.85865,413.61,-0.19814,0.9508,-0.23817,25.233,-0.84279,-0.28932,-0.45387,229.12,#33,0.023605,0.99631,-0.082554,383.23,-0.31959,0.085764,0.94367,74.456,0.94726,0.0041083,0.32044,225.51,#34,-0.70113,-0.19067,-0.68707,402.08,0.038256,0.95214,-0.30327,109.25,0.71201,-0.23892,-0.66028,208.79,#35,0.9827,-0.12958,0.13233,383.97,-0.18193,-0.54138,0.82086,74.973,-0.03472,-0.83073,-0.55559,224.39
> view matrix models
> #24,-0.90809,0.28081,0.31067,464.53,-0.41493,-0.70354,-0.57694,464.91,0.056559,-0.65282,0.7554,199.73,#26,-0.99491,0.0089671,-0.10039,460.2,-0.0052843,-0.99931,-0.03689,87.525,-0.10066,-0.036172,0.99426,229.84,#27,-0.28319,0.85799,-0.42856,438.84,0.62049,-0.17682,-0.76402,113.18,-0.7313,-0.48228,-0.48229,254.38,#28,-0.11625,-0.43906,-0.8909,461.23,0.00785,0.89655,-0.44287,168.28,0.99319,-0.058476,-0.10077,210.75,#29,0.70867,0.37799,-0.59574,367.4,0.54548,0.242,0.80243,98.97,0.44748,-0.89362,-0.034683,252.18,#30,-0.16277,-0.10384,0.98118,417.27,0.64654,0.73996,0.18557,124.24,-0.74531,0.66459,-0.053313,274.79,#31,-0.21503,-0.97071,-0.10715,729.16,0.66103,-0.063903,-0.74763,157.06,0.71889,-0.23159,0.65541,487.95,#32,-0.50044,0.1108,0.85865,421.16,-0.19814,0.9508,-0.23817,24.273,-0.84279,-0.28932,-0.45387,223.54,#33,0.023605,0.99631,-0.082554,390.78,-0.31959,0.085764,0.94367,73.496,0.94726,0.0041083,0.32044,219.93,#34,-0.70113,-0.19067,-0.68707,409.63,0.038256,0.95214,-0.30327,108.29,0.71201,-0.23892,-0.66028,203.21,#35,0.9827,-0.12958,0.13233,391.51,-0.18193,-0.54138,0.82086,74.013,-0.03472,-0.83073,-0.55559,218.81
> view matrix models
> #24,-0.90809,0.28081,0.31067,465.49,-0.41493,-0.70354,-0.57694,468.88,0.056559,-0.65282,0.7554,202.27,#26,-0.99491,0.0089671,-0.10039,461.16,-0.0052843,-0.99931,-0.03689,91.492,-0.10066,-0.036172,0.99426,232.39,#27,-0.28319,0.85799,-0.42856,439.8,0.62049,-0.17682,-0.76402,117.14,-0.7313,-0.48228,-0.48229,256.93,#28,-0.11625,-0.43906,-0.8909,462.19,0.00785,0.89655,-0.44287,172.25,0.99319,-0.058476,-0.10077,213.29,#29,0.70867,0.37799,-0.59574,368.36,0.54548,0.242,0.80243,102.94,0.44748,-0.89362,-0.034683,254.72,#30,-0.16277,-0.10384,0.98118,418.23,0.64654,0.73996,0.18557,128.21,-0.74531,0.66459,-0.053313,277.33,#31,-0.21503,-0.97071,-0.10715,730.12,0.66103,-0.063903,-0.74763,161.02,0.71889,-0.23159,0.65541,490.49,#32,-0.50044,0.1108,0.85865,422.12,-0.19814,0.9508,-0.23817,28.241,-0.84279,-0.28932,-0.45387,226.08,#33,0.023605,0.99631,-0.082554,391.74,-0.31959,0.085764,0.94367,77.464,0.94726,0.0041083,0.32044,222.48,#34,-0.70113,-0.19067,-0.68707,410.59,0.038256,0.95214,-0.30327,112.26,0.71201,-0.23892,-0.66028,205.75,#35,0.9827,-0.12958,0.13233,392.47,-0.18193,-0.54138,0.82086,77.981,-0.03472,-0.83073,-0.55559,221.36
> view matrix models
> #24,-0.90809,0.28081,0.31067,465.54,-0.41493,-0.70354,-0.57694,465.93,0.056559,-0.65282,0.7554,196.12,#26,-0.99491,0.0089671,-0.10039,461.21,-0.0052843,-0.99931,-0.03689,88.547,-0.10066,-0.036172,0.99426,226.23,#27,-0.28319,0.85799,-0.42856,439.86,0.62049,-0.17682,-0.76402,114.2,-0.7313,-0.48228,-0.48229,250.77,#28,-0.11625,-0.43906,-0.8909,462.24,0.00785,0.89655,-0.44287,169.31,0.99319,-0.058476,-0.10077,207.14,#29,0.70867,0.37799,-0.59574,368.41,0.54548,0.242,0.80243,99.993,0.44748,-0.89362,-0.034683,248.57,#30,-0.16277,-0.10384,0.98118,418.28,0.64654,0.73996,0.18557,125.26,-0.74531,0.66459,-0.053313,271.18,#31,-0.21503,-0.97071,-0.10715,730.17,0.66103,-0.063903,-0.74763,158.08,0.71889,-0.23159,0.65541,484.34,#32,-0.50044,0.1108,0.85865,422.17,-0.19814,0.9508,-0.23817,25.296,-0.84279,-0.28932,-0.45387,219.93,#33,0.023605,0.99631,-0.082554,391.79,-0.31959,0.085764,0.94367,74.519,0.94726,0.0041083,0.32044,216.32,#34,-0.70113,-0.19067,-0.68707,410.64,0.038256,0.95214,-0.30327,109.31,0.71201,-0.23892,-0.66028,199.6,#35,0.9827,-0.12958,0.13233,392.53,-0.18193,-0.54138,0.82086,75.036,-0.03472,-0.83073,-0.55559,215.2
> view matrix models
> #24,-0.90809,0.28081,0.31067,468.62,-0.41493,-0.70354,-0.57694,473.95,0.056559,-0.65282,0.7554,197.39,#26,-0.99491,0.0089671,-0.10039,464.28,-0.0052843,-0.99931,-0.03689,96.565,-0.10066,-0.036172,0.99426,227.5,#27,-0.28319,0.85799,-0.42856,442.93,0.62049,-0.17682,-0.76402,122.22,-0.7313,-0.48228,-0.48229,252.05,#28,-0.11625,-0.43906,-0.8909,465.32,0.00785,0.89655,-0.44287,177.32,0.99319,-0.058476,-0.10077,208.41,#29,0.70867,0.37799,-0.59574,371.49,0.54548,0.242,0.80243,108.01,0.44748,-0.89362,-0.034683,249.84,#30,-0.16277,-0.10384,0.98118,421.36,0.64654,0.73996,0.18557,133.28,-0.74531,0.66459,-0.053313,272.45,#31,-0.21503,-0.97071,-0.10715,733.25,0.66103,-0.063903,-0.74763,166.1,0.71889,-0.23159,0.65541,485.61,#32,-0.50044,0.1108,0.85865,425.25,-0.19814,0.9508,-0.23817,33.314,-0.84279,-0.28932,-0.45387,221.2,#33,0.023605,0.99631,-0.082554,394.87,-0.31959,0.085764,0.94367,82.537,0.94726,0.0041083,0.32044,217.59,#34,-0.70113,-0.19067,-0.68707,413.72,0.038256,0.95214,-0.30327,117.33,0.71201,-0.23892,-0.66028,200.87,#35,0.9827,-0.12958,0.13233,395.6,-0.18193,-0.54138,0.82086,83.054,-0.03472,-0.83073,-0.55559,216.47
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.98722,0.045709,0.15266,568.15,-0.15935,-0.27526,-0.94807,413.37,-0.0013149,-0.96028,0.27903,376.99,#26,-0.95639,-0.28169,-0.077257,455.69,0.27662,-0.7885,-0.54932,93.473,0.093823,-0.54674,0.83203,208.58,#27,-0.11305,0.75541,-0.64542,443.41,0.96382,-0.074447,-0.25595,105.63,-0.2414,-0.65101,-0.71966,246.24,#28,-0.079507,-0.16234,-0.98353,479.48,-0.50904,0.85492,-0.099964,168.81,0.85706,0.49271,-0.15061,234.01,#29,0.84915,0.40519,-0.33878,370.88,0.035006,0.59685,0.80159,111.6,0.527,-0.69253,0.49263,250.06,#30,0.009283,0.1345,0.99087,426.58,0.96513,0.25802,-0.044066,108.33,-0.2616,0.95673,-0.12742,272.95,#31,0.0068823,-0.95409,-0.29946,740.79,0.18998,0.29526,-0.93634,-52.318,0.98176,-0.050447,0.18329,411.7,#32,-0.56112,0.3726,0.73913,399.85,0.41355,0.89972,-0.13959,54.75,-0.71702,0.22734,-0.65894,177.81,#33,-0.041827,0.97816,0.20361,384.92,-0.77992,-0.15934,0.60526,103.33,0.62448,-0.13348,0.76955,205.67,#34,-0.63863,0.086043,-0.76469,412.53,-0.19828,0.94177,0.27156,136.24,0.74353,0.32505,-0.58438,206.16,#35,0.88652,-0.30527,0.3477,385.74,-0.35103,0.045824,0.93524,104.19,-0.30144,-0.95116,-0.066536,204.87
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.98722,0.045709,0.15266,561.42,-0.15935,-0.27526,-0.94807,411.47,-0.0013149,-0.96028,0.27903,386.23,#26,-0.95639,-0.28169,-0.077257,448.95,0.27662,-0.7885,-0.54932,91.576,0.093823,-0.54674,0.83203,217.83,#27,-0.11305,0.75541,-0.64542,436.68,0.96382,-0.074447,-0.25595,103.73,-0.2414,-0.65101,-0.71966,255.48,#28,-0.079507,-0.16234,-0.98353,472.75,-0.50904,0.85492,-0.099964,166.91,0.85706,0.49271,-0.15061,243.25,#29,0.84915,0.40519,-0.33878,364.14,0.035006,0.59685,0.80159,109.7,0.527,-0.69253,0.49263,259.3,#30,0.009283,0.1345,0.99087,419.84,0.96513,0.25802,-0.044066,106.43,-0.2616,0.95673,-0.12742,282.19,#31,0.0068823,-0.95409,-0.29946,734.06,0.18998,0.29526,-0.93634,-54.215,0.98176,-0.050447,0.18329,420.95,#32,-0.56112,0.3726,0.73913,393.12,0.41355,0.89972,-0.13959,52.853,-0.71702,0.22734,-0.65894,187.06,#33,-0.041827,0.97816,0.20361,378.19,-0.77992,-0.15934,0.60526,101.43,0.62448,-0.13348,0.76955,214.92,#34,-0.63863,0.086043,-0.76469,405.8,-0.19828,0.94177,0.27156,134.34,0.74353,0.32505,-0.58438,215.41,#35,0.88652,-0.30527,0.3477,379.01,-0.35103,0.045824,0.93524,102.29,-0.30144,-0.95116,-0.066536,214.12
> view matrix models
> #24,-0.98722,0.045709,0.15266,448.95,-0.15935,-0.27526,-0.94807,688.08,-0.0013149,-0.96028,0.27903,263.14,#26,-0.95639,-0.28169,-0.077257,336.48,0.27662,-0.7885,-0.54932,368.18,0.093823,-0.54674,0.83203,94.736,#27,-0.11305,0.75541,-0.64542,324.21,0.96382,-0.074447,-0.25595,380.34,-0.2414,-0.65101,-0.71966,132.39,#28,-0.079507,-0.16234,-0.98353,360.28,-0.50904,0.85492,-0.099964,443.52,0.85706,0.49271,-0.15061,120.16,#29,0.84915,0.40519,-0.33878,251.67,0.035006,0.59685,0.80159,386.31,0.527,-0.69253,0.49263,136.21,#30,0.009283,0.1345,0.99087,307.37,0.96513,0.25802,-0.044066,383.04,-0.2616,0.95673,-0.12742,159.1,#31,0.0068823,-0.95409,-0.29946,621.59,0.18998,0.29526,-0.93634,222.39,0.98176,-0.050447,0.18329,297.85,#32,-0.56112,0.3726,0.73913,280.65,0.41355,0.89972,-0.13959,329.46,-0.71702,0.22734,-0.65894,63.965,#33,-0.041827,0.97816,0.20361,265.72,-0.77992,-0.15934,0.60526,378.04,0.62448,-0.13348,0.76955,91.826,#34,-0.63863,0.086043,-0.76469,293.33,-0.19828,0.94177,0.27156,410.95,0.74353,0.32505,-0.58438,92.318,#35,0.88652,-0.30527,0.3477,266.54,-0.35103,0.045824,0.93524,378.9,-0.30144,-0.95116,-0.066536,91.023
> view matrix models
> #24,-0.98722,0.045709,0.15266,422.05,-0.15935,-0.27526,-0.94807,627.72,-0.0013149,-0.96028,0.27903,265.74,#26,-0.95639,-0.28169,-0.077257,309.58,0.27662,-0.7885,-0.54932,307.82,0.093823,-0.54674,0.83203,97.333,#27,-0.11305,0.75541,-0.64542,297.3,0.96382,-0.074447,-0.25595,319.98,-0.2414,-0.65101,-0.71966,134.99,#28,-0.079507,-0.16234,-0.98353,333.38,-0.50904,0.85492,-0.099964,383.15,0.85706,0.49271,-0.15061,122.76,#29,0.84915,0.40519,-0.33878,224.77,0.035006,0.59685,0.80159,325.95,0.527,-0.69253,0.49263,138.81,#30,0.009283,0.1345,0.99087,280.47,0.96513,0.25802,-0.044066,322.67,-0.2616,0.95673,-0.12742,161.7,#31,0.0068823,-0.95409,-0.29946,594.69,0.18998,0.29526,-0.93634,162.03,0.98176,-0.050447,0.18329,300.45,#32,-0.56112,0.3726,0.73913,253.74,0.41355,0.89972,-0.13959,269.1,-0.71702,0.22734,-0.65894,66.562,#33,-0.041827,0.97816,0.20361,238.81,-0.77992,-0.15934,0.60526,317.68,0.62448,-0.13348,0.76955,94.423,#34,-0.63863,0.086043,-0.76469,266.42,-0.19828,0.94177,0.27156,350.59,0.74353,0.32505,-0.58438,94.915,#35,0.88652,-0.30527,0.3477,239.63,-0.35103,0.045824,0.93524,318.54,-0.30144,-0.95116,-0.066536,93.62
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.96236,0.08449,0.25831,385.32,-0.2609,-0.55342,-0.79099,671.07,0.076123,-0.82861,0.55463,161.04,#26,-0.98252,-0.18504,-0.020165,311.64,0.18361,-0.94569,-0.26825,304.21,0.030568,-0.26727,0.96314,103.31,#27,-0.22107,0.76401,-0.60615,297.76,0.82197,-0.18853,-0.53742,326.03,-0.52487,-0.61704,-0.58632,135.68,#28,-0.02722,-0.26325,-0.96434,326.43,-0.2227,0.94205,-0.25088,385.88,0.97451,0.20793,-0.084269,103.46,#29,0.83538,0.33938,-0.43239,224.99,0.29167,0.39308,0.87202,324.77,0.46591,-0.85458,0.22938,139.52,#30,-0.099538,0.09653,0.99034,280.52,0.83057,0.55614,0.029272,335.01,-0.54794,0.82546,-0.13553,160.7,#31,-0.022625,-0.98125,-0.1914,610.01,0.48548,0.15658,-0.86011,261.59,0.87396,-0.11238,0.47283,333.44,#32,-0.59928,0.26506,0.75538,260.86,0.1047,0.96144,-0.2543,251.87,-0.79366,-0.07331,-0.60393,87.653,#33,0.043119,0.99099,0.12678,240.24,-0.54651,-0.082832,0.83335,304.72,0.83634,-0.10522,0.53801,99.501,#34,-0.61742,-0.025179,-0.78623,263.88,-0.027069,0.99958,-0.010754,339.01,0.78617,0.014643,-0.61784,88.988,#35,0.92328,-0.30109,0.23854,240.96,-0.32622,-0.28667,0.90078,305.37,-0.20284,-0.90948,-0.3629,98.448
> volume #24 level 0.003763
> view matrix models
> #24,-0.42877,0.67009,-0.60592,345.79,-0.43491,-0.74097,-0.51168,683.83,-0.79184,0.04413,0.60913,153.01,#26,-0.29506,-0.019261,-0.95529,295.26,-0.040339,-0.99865,0.032595,309.65,-0.95463,0.048153,0.29388,181,#27,0.5969,0.7675,0.23377,265.82,0.55762,-0.18735,-0.80868,336.41,-0.57687,0.61306,-0.5398,169.45,#28,-0.95796,-0.06691,-0.27899,317.74,0.076679,0.87734,-0.47371,388.81,0.27646,-0.47518,-0.83533,170.22,#29,-0.10497,0.98231,-0.15505,239.24,0.59608,0.18695,0.78085,320.09,0.79603,-0.010458,-0.60516,103.58,#30,0.65811,-0.60998,0.44138,239.28,0.58594,0.78307,0.20852,348.32,-0.47282,0.1214,0.87276,156.88,#31,-0.70761,-0.16854,-0.68621,166.56,0.70521,-0.10761,-0.70078,405.21,0.044265,-0.9798,0.195,524.66,#32,0.56895,0.36243,0.7382,282.32,-0.27268,0.93001,-0.24644,245.04,-0.77585,-0.061084,0.62795,146.04,#33,-0.87964,0.38888,-0.27386,276.56,-0.2492,0.11361,0.96176,293.01,0.40512,0.91426,-0.0030221,114.02,#34,-0.92542,0.1988,0.3226,301.23,0.070259,0.92659,-0.36946,327.01,-0.37237,-0.31924,-0.87145,123.04,#35,0.40428,0.683,0.60834,277.91,-0.15647,-0.60366,0.78173,293.46,0.90115,-0.41123,-0.13718,114.24
> view matrix models
> #24,-0.8369,0.39245,-0.38155,438.18,0.27643,-0.29862,-0.91346,533.65,-0.47243,-0.86995,0.14144,376.12,#26,-0.6898,-0.26294,-0.67457,307.18,0.66048,-0.61018,-0.43755,287,-0.29656,-0.74736,0.59456,120.49,#27,0.40063,0.87879,-0.25927,284.07,0.91201,-0.40963,0.020834,304.41,-0.087896,-0.2448,-0.96558,150.15,#28,-0.67282,-0.034265,-0.73901,342.77,-0.39938,0.85768,0.32384,345.78,0.62274,0.51303,-0.59075,167.02,#29,0.42676,0.88342,-0.19353,227.54,-0.31347,0.34522,0.88462,340.83,0.8483,-0.31686,0.42425,122.06,#30,0.50702,-0.25578,0.82311,259.01,0.86045,0.20616,-0.46596,314.86,-0.050508,0.9445,0.32462,166.47,#31,-0.39449,-0.6112,-0.68616,376.86,0.19979,0.6718,-0.71328,40.133,0.89692,-0.41847,-0.1429,399.76,#32,0.064856,0.53145,0.84461,263.14,0.59036,0.66195,-0.46185,274.81,-0.80453,0.52857,-0.27081,61.526,#33,-0.6359,0.77142,0.023203,256.78,-0.66768,-0.56497,0.48478,325.97,0.38708,0.29278,0.87433,88.002,#34,-0.9372,0.27541,-0.21405,290.98,0.1162,0.82512,0.55287,343.98,0.32888,0.49328,-0.8053,106.75,#35,0.7062,0.2365,0.66735,258.14,-0.70454,0.1415,0.69541,326.37,0.070036,-0.96127,0.26655,87.822
> view matrix models
> #24,-0.82146,0.50944,0.25628,269.61,-0.3073,-0.016865,-0.95146,607.02,-0.48039,-0.86034,0.1704,369.41,#26,-0.94416,0.1807,-0.27551,322.25,0.090507,-0.66179,-0.7442,325.52,-0.31681,-0.72758,0.60849,121.76,#27,-0.24134,0.94976,-0.1993,292.78,0.96338,0.20975,-0.16705,325.83,-0.11686,-0.23232,-0.96559,150.87,#28,-0.29807,-0.56275,-0.77102,313.44,-0.71229,0.66884,-0.21281,394.93,0.63545,0.48576,-0.60021,166.39,#29,0.51323,0.49181,-0.70336,226.33,0.035911,0.80651,0.59014,319.17,0.8575,-0.32814,0.39626,121.68,#30,-0.12642,-0.34622,0.9296,266.27,0.98891,0.029635,0.14552,319.11,-0.07793,0.93769,0.33863,166.87,#31,-0.45094,-0.88675,-0.10165,523.42,-0.061702,0.14459,-0.98757,180.5,0.89042,-0.43906,-0.11992,408.64,#32,-0.29569,0.0036975,0.95528,296.08,0.48538,0.86187,0.14691,287.38,-0.82279,0.50711,-0.25664,63.238,#33,-0.099921,0.95011,-0.29548,259.17,-0.90735,0.034866,0.41894,324.52,0.40834,0.30997,0.85859,88.092,#34,-0.8175,-0.29789,-0.49291,274.78,-0.47504,0.83266,0.28464,360.19,0.32564,0.46684,-0.8222,106.24,#35,0.98841,0.11809,0.095423,260.01,-0.12094,0.23248,0.96505,325.67,0.091774,-0.9654,0.24407,87.898
> view matrix models
> #24,-0.93632,0.19207,0.29395,350.03,-0.34833,-0.40246,-0.84658,670.96,-0.044296,-0.89506,0.44374,224.43,#26,-0.9953,-0.076393,-0.05958,315.41,0.094467,-0.90166,-0.422,313.55,-0.021483,-0.42564,0.90464,104.39,#27,-0.26189,0.81825,-0.51174,297.38,0.87528,-0.022002,-0.48312,328.6,-0.40657,-0.57444,-0.71043,138.52,#28,-0.071659,-0.36452,-0.92843,322.37,-0.37964,0.87073,-0.31257,395.05,0.92235,0.33007,-0.20078,118.47,#29,0.77077,0.35752,-0.52735,224.96,0.27998,0.55343,0.78443,320.72,0.5723,-0.75226,0.32647,136.16,#30,-0.14044,-0.012317,0.99001,277.72,0.89752,0.42059,0.13255,331.93,-0.41802,0.90717,-0.048015,163.15,#31,-0.12725,-0.98184,-0.14068,600.28,0.33339,0.091236,-0.93836,258.86,0.93416,-0.16631,0.31573,348.64,#32,-0.55164,0.17733,0.81501,270.98,0.18251,0.97912,-0.08951,260.44,-0.81387,0.09937,-0.57249,76.672,#33,0.038121,0.99921,0.010898,244.7,-0.66975,0.017455,0.74238,308.78,0.74161,-0.035599,0.66989,94.891,#34,-0.66367,-0.12047,-0.73826,265.65,-0.20538,0.97836,0.024977,346.15,0.71928,0.1682,-0.67405,91.819,#35,0.96154,-0.21067,0.17624,245.42,-0.21157,-0.15886,0.96437,309.65,-0.17517,-0.96456,-0.19733,94.016
> view matrix models
> #24,-0.98931,0.016977,0.14485,429.9,-0.11261,-0.72008,-0.6847,650.38,0.09268,-0.69369,0.71429,94.648,#26,-0.94925,-0.3078,-0.064668,308.2,0.31144,-0.94857,-0.056799,292.23,-0.043859,-0.074057,0.99629,110.79,#27,-0.10406,0.73736,-0.66743,297.08,0.71612,-0.41014,-0.56477,321.92,-0.69018,-0.53673,-0.48536,137.46,#28,-0.065652,-0.13638,-0.98848,333.81,-0.0093562,0.99066,-0.13605,369.51,0.9978,0.00031621,-0.066314,94.713,#29,0.86271,0.39675,-0.31357,224.77,0.27179,0.15914,0.94911,330.9,0.42646,-0.90403,0.029464,138.8,#30,0.017727,0.16279,0.9865,280.97,0.70393,0.69865,-0.12794,338.06,-0.71005,0.6967,-0.10221,159.46,#31,0.034803,-0.95032,-0.30931,596.06,0.65566,0.25529,-0.71059,260.26,0.75426,-0.17807,0.63197,355.56,#32,-0.57263,0.39228,0.71987,251,0.013664,0.88253,-0.47005,244.78,-0.8197,-0.25933,-0.51072,104.36,#33,-0.038137,0.97184,0.23255,237.55,-0.36116,-0.23039,0.9036,301.16,0.93173,-0.049526,0.35977,104.34,#34,-0.62255,0.109,-0.77495,265.67,0.2174,0.97536,-0.037457,329.15,0.75178,-0.19179,-0.63091,87.887,#35,0.87297,-0.3286,0.36048,238.36,-0.47792,-0.42846,0.76682,301.48,-0.097522,-0.84169,-0.53108,103.2
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.98931,0.016977,0.14485,375.13,-0.11261,-0.72008,-0.6847,541.14,0.09268,-0.69369,0.71429,117.18,#26,-0.94925,-0.3078,-0.064668,253.43,0.31144,-0.94857,-0.056799,182.99,-0.043859,-0.074057,0.99629,133.32,#27,-0.10406,0.73736,-0.66743,242.31,0.71612,-0.41014,-0.56477,212.68,-0.69018,-0.53673,-0.48536,159.99,#28,-0.065652,-0.13638,-0.98848,279.04,-0.0093562,0.99066,-0.13605,260.27,0.9978,0.00031621,-0.066314,117.24,#29,0.86271,0.39675,-0.31357,170,0.27179,0.15914,0.94911,221.66,0.42646,-0.90403,0.029464,161.33,#30,0.017727,0.16279,0.9865,226.2,0.70393,0.69865,-0.12794,228.82,-0.71005,0.6967,-0.10221,181.99,#31,0.034803,-0.95032,-0.30931,541.29,0.65566,0.25529,-0.71059,151.02,0.75426,-0.17807,0.63197,378.09,#32,-0.57263,0.39228,0.71987,196.23,0.013664,0.88253,-0.47005,135.54,-0.8197,-0.25933,-0.51072,126.89,#33,-0.038137,0.97184,0.23255,182.78,-0.36116,-0.23039,0.9036,191.92,0.93173,-0.049526,0.35977,126.87,#34,-0.62255,0.109,-0.77495,210.9,0.2174,0.97536,-0.037457,219.91,0.75178,-0.19179,-0.63091,110.42,#35,0.87297,-0.3286,0.36048,183.59,-0.47792,-0.42846,0.76682,192.24,-0.097522,-0.84169,-0.53108,125.73
> view matrix models
> #24,-0.98931,0.016977,0.14485,423.79,-0.11261,-0.72008,-0.6847,480.35,0.09268,-0.69369,0.71429,65.778,#26,-0.94925,-0.3078,-0.064668,302.09,0.31144,-0.94857,-0.056799,122.2,-0.043859,-0.074057,0.99629,81.923,#27,-0.10406,0.73736,-0.66743,290.96,0.71612,-0.41014,-0.56477,151.89,-0.69018,-0.53673,-0.48536,108.59,#28,-0.065652,-0.13638,-0.98848,327.7,-0.0093562,0.99066,-0.13605,199.48,0.9978,0.00031621,-0.066314,65.842,#29,0.86271,0.39675,-0.31357,218.65,0.27179,0.15914,0.94911,160.87,0.42646,-0.90403,0.029464,109.93,#30,0.017727,0.16279,0.9865,274.86,0.70393,0.69865,-0.12794,168.03,-0.71005,0.6967,-0.10221,130.59,#31,0.034803,-0.95032,-0.30931,589.95,0.65566,0.25529,-0.71059,90.231,0.75426,-0.17807,0.63197,326.69,#32,-0.57263,0.39228,0.71987,244.89,0.013664,0.88253,-0.47005,74.753,-0.8197,-0.25933,-0.51072,75.489,#33,-0.038137,0.97184,0.23255,231.43,-0.36116,-0.23039,0.9036,131.13,0.93173,-0.049526,0.35977,75.47,#34,-0.62255,0.109,-0.77495,259.56,0.2174,0.97536,-0.037457,159.12,0.75178,-0.19179,-0.63091,59.017,#35,0.87297,-0.3286,0.36048,232.24,-0.47792,-0.42846,0.76682,131.45,-0.097522,-0.84169,-0.53108,74.333
> view matrix models
> #24,-0.98931,0.016977,0.14485,437.27,-0.11261,-0.72008,-0.6847,518.06,0.09268,-0.69369,0.71429,168.29,#26,-0.94925,-0.3078,-0.064668,315.57,0.31144,-0.94857,-0.056799,159.91,-0.043859,-0.074057,0.99629,184.43,#27,-0.10406,0.73736,-0.66743,304.44,0.71612,-0.41014,-0.56477,189.6,-0.69018,-0.53673,-0.48536,211.1,#28,-0.065652,-0.13638,-0.98848,341.17,-0.0093562,0.99066,-0.13605,237.19,0.9978,0.00031621,-0.066314,168.35,#29,0.86271,0.39675,-0.31357,232.13,0.27179,0.15914,0.94911,198.58,0.42646,-0.90403,0.029464,212.44,#30,0.017727,0.16279,0.9865,288.34,0.70393,0.69865,-0.12794,205.74,-0.71005,0.6967,-0.10221,233.1,#31,0.034803,-0.95032,-0.30931,603.43,0.65566,0.25529,-0.71059,127.94,0.75426,-0.17807,0.63197,429.2,#32,-0.57263,0.39228,0.71987,258.36,0.013664,0.88253,-0.47005,112.46,-0.8197,-0.25933,-0.51072,178,#33,-0.038137,0.97184,0.23255,244.91,-0.36116,-0.23039,0.9036,168.84,0.93173,-0.049526,0.35977,177.98,#34,-0.62255,0.109,-0.77495,273.03,0.2174,0.97536,-0.037457,196.83,0.75178,-0.19179,-0.63091,161.53,#35,0.87297,-0.3286,0.36048,245.72,-0.47792,-0.42846,0.76682,169.16,-0.097522,-0.84169,-0.53108,176.84
> view matrix models
> #24,-0.98931,0.016977,0.14485,536.59,-0.11261,-0.72008,-0.6847,508.95,0.09268,-0.69369,0.71429,127.66,#26,-0.94925,-0.3078,-0.064668,414.89,0.31144,-0.94857,-0.056799,150.8,-0.043859,-0.074057,0.99629,143.81,#27,-0.10406,0.73736,-0.66743,403.76,0.71612,-0.41014,-0.56477,180.49,-0.69018,-0.53673,-0.48536,170.47,#28,-0.065652,-0.13638,-0.98848,440.49,-0.0093562,0.99066,-0.13605,228.09,0.9978,0.00031621,-0.066314,127.73,#29,0.86271,0.39675,-0.31357,331.45,0.27179,0.15914,0.94911,189.48,0.42646,-0.90403,0.029464,171.82,#30,0.017727,0.16279,0.9865,387.66,0.70393,0.69865,-0.12794,196.64,-0.71005,0.6967,-0.10221,192.48,#31,0.034803,-0.95032,-0.30931,702.75,0.65566,0.25529,-0.71059,118.84,0.75426,-0.17807,0.63197,388.58,#32,-0.57263,0.39228,0.71987,357.69,0.013664,0.88253,-0.47005,103.36,-0.8197,-0.25933,-0.51072,137.37,#33,-0.038137,0.97184,0.23255,344.23,-0.36116,-0.23039,0.9036,159.73,0.93173,-0.049526,0.35977,137.36,#34,-0.62255,0.109,-0.77495,372.35,0.2174,0.97536,-0.037457,187.73,0.75178,-0.19179,-0.63091,120.9,#35,0.87297,-0.3286,0.36048,345.04,-0.47792,-0.42846,0.76682,160.05,-0.097522,-0.84169,-0.53108,136.22
> view matrix models
> #24,-0.98931,0.016977,0.14485,527.42,-0.11261,-0.72008,-0.6847,440.8,0.09268,-0.69369,0.71429,180.79,#26,-0.94925,-0.3078,-0.064668,405.72,0.31144,-0.94857,-0.056799,82.645,-0.043859,-0.074057,0.99629,196.94,#27,-0.10406,0.73736,-0.66743,394.59,0.71612,-0.41014,-0.56477,112.34,-0.69018,-0.53673,-0.48536,223.6,#28,-0.065652,-0.13638,-0.98848,431.33,-0.0093562,0.99066,-0.13605,159.93,0.9978,0.00031621,-0.066314,180.86,#29,0.86271,0.39675,-0.31357,322.28,0.27179,0.15914,0.94911,121.32,0.42646,-0.90403,0.029464,224.94,#30,0.017727,0.16279,0.9865,378.49,0.70393,0.69865,-0.12794,128.48,-0.71005,0.6967,-0.10221,245.6,#31,0.034803,-0.95032,-0.30931,693.58,0.65566,0.25529,-0.71059,50.679,0.75426,-0.17807,0.63197,441.7,#32,-0.57263,0.39228,0.71987,348.52,0.013664,0.88253,-0.47005,35.202,-0.8197,-0.25933,-0.51072,190.5,#33,-0.038137,0.97184,0.23255,335.06,-0.36116,-0.23039,0.9036,91.575,0.93173,-0.049526,0.35977,190.48,#34,-0.62255,0.109,-0.77495,363.19,0.2174,0.97536,-0.037457,119.57,0.75178,-0.19179,-0.63091,174.03,#35,0.87297,-0.3286,0.36048,335.87,-0.47792,-0.42846,0.76682,91.895,-0.097522,-0.84169,-0.53108,189.35
> view matrix models
> #24,-0.98931,0.016977,0.14485,544.07,-0.11261,-0.72008,-0.6847,456.24,0.09268,-0.69369,0.71429,217.95,#26,-0.94925,-0.3078,-0.064668,422.37,0.31144,-0.94857,-0.056799,98.086,-0.043859,-0.074057,0.99629,234.09,#27,-0.10406,0.73736,-0.66743,411.24,0.71612,-0.41014,-0.56477,127.78,-0.69018,-0.53673,-0.48536,260.76,#28,-0.065652,-0.13638,-0.98848,447.98,-0.0093562,0.99066,-0.13605,175.37,0.9978,0.00031621,-0.066314,218.01,#29,0.86271,0.39675,-0.31357,338.93,0.27179,0.15914,0.94911,136.76,0.42646,-0.90403,0.029464,262.1,#30,0.017727,0.16279,0.9865,395.14,0.70393,0.69865,-0.12794,143.92,-0.71005,0.6967,-0.10221,282.76,#31,0.034803,-0.95032,-0.30931,710.23,0.65566,0.25529,-0.71059,66.12,0.75426,-0.17807,0.63197,478.86,#32,-0.57263,0.39228,0.71987,365.17,0.013664,0.88253,-0.47005,50.643,-0.8197,-0.25933,-0.51072,227.66,#33,-0.038137,0.97184,0.23255,351.71,-0.36116,-0.23039,0.9036,107.02,0.93173,-0.049526,0.35977,227.64,#34,-0.62255,0.109,-0.77495,379.84,0.2174,0.97536,-0.037457,135.01,0.75178,-0.19179,-0.63091,211.19,#35,0.87297,-0.3286,0.36048,352.52,-0.47792,-0.42846,0.76682,107.34,-0.097522,-0.84169,-0.53108,226.5
> view matrix models
> #24,-0.98931,0.016977,0.14485,568.38,-0.11261,-0.72008,-0.6847,445.69,0.09268,-0.69369,0.71429,198.08,#26,-0.94925,-0.3078,-0.064668,446.68,0.31144,-0.94857,-0.056799,87.54,-0.043859,-0.074057,0.99629,214.22,#27,-0.10406,0.73736,-0.66743,435.56,0.71612,-0.41014,-0.56477,117.23,-0.69018,-0.53673,-0.48536,240.89,#28,-0.065652,-0.13638,-0.98848,472.29,-0.0093562,0.99066,-0.13605,164.83,0.9978,0.00031621,-0.066314,198.14,#29,0.86271,0.39675,-0.31357,363.25,0.27179,0.15914,0.94911,126.21,0.42646,-0.90403,0.029464,242.23,#30,0.017727,0.16279,0.9865,419.45,0.70393,0.69865,-0.12794,133.38,-0.71005,0.6967,-0.10221,262.89,#31,0.034803,-0.95032,-0.30931,734.54,0.65566,0.25529,-0.71059,55.574,0.75426,-0.17807,0.63197,458.99,#32,-0.57263,0.39228,0.71987,389.48,0.013664,0.88253,-0.47005,40.096,-0.8197,-0.25933,-0.51072,207.79,#33,-0.038137,0.97184,0.23255,376.03,-0.36116,-0.23039,0.9036,96.469,0.93173,-0.049526,0.35977,207.77,#34,-0.62255,0.109,-0.77495,404.15,0.2174,0.97536,-0.037457,124.47,0.75178,-0.19179,-0.63091,191.32,#35,0.87297,-0.3286,0.36048,376.84,-0.47792,-0.42846,0.76682,96.79,-0.097522,-0.84169,-0.53108,206.63
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.97564,0.21001,-0.06349,572.38,-0.096474,-0.67055,-0.73556,443.5,-0.19705,-0.71151,0.67448,271.29,#26,-0.89787,-0.27651,-0.34258,450.3,0.335,-0.93401,-0.12413,87.914,-0.28565,-0.22622,0.93125,226.55,#27,0.095913,0.85775,-0.50503,432.18,0.76431,-0.3885,-0.51468,115.93,-0.63767,-0.33664,-0.69285,251.11,#28,-0.34385,-0.12886,-0.93014,479.56,-0.076894,0.99108,-0.10888,165.53,0.93587,0.034085,-0.35069,223.96,#29,0.70838,0.63548,-0.30718,362.44,0.22216,0.21235,0.95161,126.42,0.66996,-0.74234,0.009246,232.76,#30,0.21834,-0.038402,0.97512,410.57,0.7508,0.64493,-0.14272,130.87,-0.6234,0.76327,0.16965,268.82,#31,-0.17751,-0.86125,-0.47618,657.56,0.60095,0.28831,-0.74548,32.623,0.77933,-0.41849,0.46639,539.25,#32,-0.31874,0.45127,0.83352,397.12,0.083221,0.88932,-0.44966,42.328,-0.94418,-0.073957,-0.32102,200.89,#33,-0.2996,0.946,0.12379,384.34,-0.42381,-0.24821,0.87108,98.855,0.85477,0.20851,0.47529,201.2,#34,-0.80851,0.16063,-0.56613,416.01,0.1788,0.9836,0.023723,127.28,0.56066,-0.082046,-0.82397,195.38,#35,0.86412,-0.079317,0.497,385.43,-0.48954,-0.3617,0.79343,99.235,0.11683,-0.92892,-0.35138,200.36
> view matrix models
> #24,-0.98154,0.19029,0.019121,559.31,-0.13926,-0.64266,-0.75339,450.74,-0.13107,-0.74215,0.65729,267.51,#26,-0.93061,-0.24768,-0.26947,451.2,0.29744,-0.94081,-0.16248,90.772,-0.21328,-0.23135,0.9492,221.87,#27,0.014445,0.84902,-0.52817,433.58,0.78282,-0.33823,-0.5223,117.29,-0.62208,-0.40591,-0.66951,248.38,#28,-0.27262,-0.17253,-0.94653,476.53,-0.11548,0.98255,-0.14583,169.76,0.95516,0.069549,-0.28779,219.33,#29,0.74289,0.57056,-0.35011,362.29,0.24065,0.26041,0.93502,124.8,0.62466,-0.77887,0.056152,235.22,#30,0.13808,-0.014425,0.99032,412.6,0.77495,0.62422,-0.098957,130.74,-0.61675,0.78111,0.097369,267.95,#31,-0.14982,-0.90135,-0.40636,682.49,0.57315,0.25572,-0.77853,38.333,0.80564,-0.34955,0.47829,517.77,#32,-0.38845,0.40262,0.82885,398.54,0.089699,0.91174,-0.40085,43.262,-0.91709,-0.081363,-0.39028,198.77,#33,-0.21799,0.96902,0.11614,383.17,-0.45783,-0.20663,0.8647,99.077,0.8619,0.13532,0.48869,201.48,#34,-0.77422,0.10803,-0.62363,412.98,0.12599,0.99191,0.015412,129.14,0.62025,-0.06664,-0.78157,194.23,#35,0.89226,-0.12792,0.43301,384.19,-0.44945,-0.34325,0.82473,99.53,0.043137,-0.93049,-0.36377,200.58
> view matrix models
> #24,-0.97911,0.19244,0.065625,548.05,-0.17488,-0.63246,-0.75459,456.39,-0.1037,-0.75031,0.65291,264.41,#26,-0.94664,-0.21946,-0.23601,451.98,0.26371,-0.94845,-0.1758,92.856,-0.18526,-0.22865,0.95572,220.16,#27,-0.032168,0.8489,-0.52758,434.16,0.7851,-0.3052,-0.53895,118.61,-0.61853,-0.43154,-0.65665,247.29,#28,-0.24071,-0.20646,-0.94838,474.31,-0.12897,0.97525,-0.17957,172.74,0.96199,0.079089,-0.26139,217.28,#29,0.75113,0.53805,-0.38249,362.3,0.26558,0.28414,0.92127,123.53,0.60437,-0.79357,0.070534,236.2,#30,0.091772,-0.014971,0.99567,413.27,0.78178,0.62039,-0.06273,131.2,-0.61676,0.78415,0.068638,267.51,#31,-0.14764,-0.91978,-0.3636,693.42,0.56426,0.2236,-0.79474,47.892,0.81229,-0.3225,0.48599,509.1,#32,-0.41761,0.36634,0.8315,400.46,0.078691,0.92626,-0.36857,43.522,-0.90521,-0.088486,-0.41564,198.35,#33,-0.17622,0.97944,0.098234,383.13,-0.46873,-0.17125,0.86658,98.721,0.86559,0.10667,0.48927,201.76,#34,-0.76024,0.069547,-0.64591,411.6,0.095072,0.99546,-0.0047163,129.89,0.64265,-0.064994,-0.7634,193.81,#35,0.90905,-0.14182,0.39181,384.1,-0.4164,-0.34431,0.84147,99.214,0.015563,-0.92808,-0.37205,200.84
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.97911,0.19244,0.065625,555.1,-0.17488,-0.63246,-0.75459,467.12,-0.1037,-0.75031,0.65291,270.09,#26,-0.94664,-0.21946,-0.23601,459.03,0.26371,-0.94845,-0.1758,103.59,-0.18526,-0.22865,0.95572,225.84,#27,-0.032168,0.8489,-0.52758,441.21,0.7851,-0.3052,-0.53895,129.34,-0.61853,-0.43154,-0.65665,252.96,#28,-0.24071,-0.20646,-0.94838,481.35,-0.12897,0.97525,-0.17957,183.47,0.96199,0.079089,-0.26139,222.96,#29,0.75113,0.53805,-0.38249,369.34,0.26558,0.28414,0.92127,134.26,0.60437,-0.79357,0.070534,241.88,#30,0.091772,-0.014971,0.99567,420.32,0.78178,0.62039,-0.06273,141.94,-0.61676,0.78415,0.068638,273.19,#31,-0.14764,-0.91978,-0.3636,700.47,0.56426,0.2236,-0.79474,58.624,0.81229,-0.3225,0.48599,514.77,#32,-0.41761,0.36634,0.8315,407.51,0.078691,0.92626,-0.36857,54.254,-0.90521,-0.088486,-0.41564,204.03,#33,-0.17622,0.97944,0.098234,390.18,-0.46873,-0.17125,0.86658,109.45,0.86559,0.10667,0.48927,207.44,#34,-0.76024,0.069547,-0.64591,418.65,0.095072,0.99546,-0.0047163,140.63,0.64265,-0.064994,-0.7634,199.49,#35,0.90905,-0.14182,0.39181,391.15,-0.4164,-0.34431,0.84147,109.95,0.015563,-0.92808,-0.37205,206.51
> view matrix models
> #24,-0.97911,0.19244,0.065625,534.22,-0.17488,-0.63246,-0.75459,468.5,-0.1037,-0.75031,0.65291,261.02,#26,-0.94664,-0.21946,-0.23601,438.15,0.26371,-0.94845,-0.1758,104.97,-0.18526,-0.22865,0.95572,216.78,#27,-0.032168,0.8489,-0.52758,420.33,0.7851,-0.3052,-0.53895,130.72,-0.61853,-0.43154,-0.65665,243.9,#28,-0.24071,-0.20646,-0.94838,460.48,-0.12897,0.97525,-0.17957,184.85,0.96199,0.079089,-0.26139,213.9,#29,0.75113,0.53805,-0.38249,348.47,0.26558,0.28414,0.92127,135.64,0.60437,-0.79357,0.070534,232.82,#30,0.091772,-0.014971,0.99567,399.44,0.78178,0.62039,-0.06273,143.31,-0.61676,0.78415,0.068638,264.13,#31,-0.14764,-0.91978,-0.3636,679.59,0.56426,0.2236,-0.79474,60.002,0.81229,-0.3225,0.48599,505.71,#32,-0.41761,0.36634,0.8315,386.63,0.078691,0.92626,-0.36857,55.632,-0.90521,-0.088486,-0.41564,194.97,#33,-0.17622,0.97944,0.098234,369.3,-0.46873,-0.17125,0.86658,110.83,0.86559,0.10667,0.48927,198.38,#34,-0.76024,0.069547,-0.64591,397.77,0.095072,0.99546,-0.0047163,142,0.64265,-0.064994,-0.7634,190.43,#35,0.90905,-0.14182,0.39181,370.28,-0.4164,-0.34431,0.84147,111.32,0.015563,-0.92808,-0.37205,197.45
> view matrix models
> #24,-0.97911,0.19244,0.065625,532.75,-0.17488,-0.63246,-0.75459,471.05,-0.1037,-0.75031,0.65291,262.31,#26,-0.94664,-0.21946,-0.23601,436.68,0.26371,-0.94845,-0.1758,107.52,-0.18526,-0.22865,0.95572,218.07,#27,-0.032168,0.8489,-0.52758,418.86,0.7851,-0.3052,-0.53895,133.27,-0.61853,-0.43154,-0.65665,245.19,#28,-0.24071,-0.20646,-0.94838,459.01,-0.12897,0.97525,-0.17957,187.4,0.96199,0.079089,-0.26139,215.19,#29,0.75113,0.53805,-0.38249,347,0.26558,0.28414,0.92127,138.19,0.60437,-0.79357,0.070534,234.11,#30,0.091772,-0.014971,0.99567,397.97,0.78178,0.62039,-0.06273,145.87,-0.61676,0.78415,0.068638,265.41,#31,-0.14764,-0.91978,-0.3636,678.13,0.56426,0.2236,-0.79474,62.557,0.81229,-0.3225,0.48599,507,#32,-0.41761,0.36634,0.8315,385.16,0.078691,0.92626,-0.36857,58.186,-0.90521,-0.088486,-0.41564,196.25,#33,-0.17622,0.97944,0.098234,367.83,-0.46873,-0.17125,0.86658,113.39,0.86559,0.10667,0.48927,199.67,#34,-0.76024,0.069547,-0.64591,396.3,0.095072,0.99546,-0.0047163,144.56,0.64265,-0.064994,-0.7634,191.71,#35,0.90905,-0.14182,0.39181,368.81,-0.4164,-0.34431,0.84147,113.88,0.015563,-0.92808,-0.37205,198.74
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.97974,0.1466,-0.13649,587.06,-0.031522,-0.78578,-0.61771,441.89,-0.1978,-0.60089,0.77447,224.61,#26,-0.86036,-0.36471,-0.35605,431.35,0.37262,-0.9267,0.048836,96.839,-0.34776,-0.090653,0.93319,230.73,#27,0.17141,0.81731,-0.5501,415.94,0.6484,-0.51398,-0.56161,129.79,-0.74175,-0.26042,-0.61805,250.56,#28,-0.35276,-0.032618,-0.93514,467.98,0.096137,0.99284,-0.070896,170.07,0.93076,-0.11491,-0.3471,217.23,#29,0.72431,0.65548,-0.21384,347.6,0.25095,0.038246,0.96725,144.02,0.64219,-0.75425,-0.13679,229.63,#30,0.29192,0.021565,0.9562,395.81,0.62557,0.75194,-0.20794,149.19,-0.72349,0.65888,0.20601,265.48,#31,-0.12119,-0.82798,-0.54751,631.27,0.72426,0.30343,-0.61918,69.206,0.67879,-0.47158,0.5629,551.77,#32,-0.30609,0.53532,0.78723,374.1,-0.028165,0.82147,-0.56956,53.209,-0.95159,-0.19651,-0.23636,211.15,#33,-0.34196,0.9169,0.2058,366.83,-0.2616,-0.30323,0.91631,110.11,0.90257,0.2595,0.34355,202.88,#34,-0.7893,0.25518,-0.55846,401.13,0.3362,0.9407,-0.045343,134.22,0.51377,-0.22355,-0.82829,193.49,#35,0.81239,-0.11082,0.57249,367.97,-0.54662,-0.48659,0.68149,110.26,0.20304,-0.86657,-0.45588,202.02
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.97974,0.1466,-0.13649,598.55,-0.031522,-0.78578,-0.61771,434.37,-0.1978,-0.60089,0.77447,224.04,#26,-0.86036,-0.36471,-0.35605,442.83,0.37262,-0.9267,0.048836,89.316,-0.34776,-0.090653,0.93319,230.15,#27,0.17141,0.81731,-0.5501,427.43,0.6484,-0.51398,-0.56161,122.27,-0.74175,-0.26042,-0.61805,249.98,#28,-0.35276,-0.032618,-0.93514,479.47,0.096137,0.99284,-0.070896,162.55,0.93076,-0.11491,-0.3471,216.65,#29,0.72431,0.65548,-0.21384,359.08,0.25095,0.038246,0.96725,136.5,0.64219,-0.75425,-0.13679,229.06,#30,0.29192,0.021565,0.9562,407.3,0.62557,0.75194,-0.20794,141.66,-0.72349,0.65888,0.20601,264.91,#31,-0.12119,-0.82798,-0.54751,642.75,0.72426,0.30343,-0.61918,61.683,0.67879,-0.47158,0.5629,551.19,#32,-0.30609,0.53532,0.78723,385.59,-0.028165,0.82147,-0.56956,45.685,-0.95159,-0.19651,-0.23636,210.58,#33,-0.34196,0.9169,0.2058,378.32,-0.2616,-0.30323,0.91631,102.59,0.90257,0.2595,0.34355,202.31,#34,-0.7893,0.25518,-0.55846,412.62,0.3362,0.9407,-0.045343,126.69,0.51377,-0.22355,-0.82829,192.91,#35,0.81239,-0.11082,0.57249,379.45,-0.54662,-0.48659,0.68149,102.73,0.20304,-0.86657,-0.45588,201.44
> view matrix models
> #24,-0.97974,0.1466,-0.13649,602.11,-0.031522,-0.78578,-0.61771,441.2,-0.1978,-0.60089,0.77447,223.29,#26,-0.86036,-0.36471,-0.35605,446.4,0.37262,-0.9267,0.048836,96.149,-0.34776,-0.090653,0.93319,229.4,#27,0.17141,0.81731,-0.5501,430.99,0.6484,-0.51398,-0.56161,129.1,-0.74175,-0.26042,-0.61805,249.23,#28,-0.35276,-0.032618,-0.93514,483.03,0.096137,0.99284,-0.070896,169.38,0.93076,-0.11491,-0.3471,215.9,#29,0.72431,0.65548,-0.21384,362.65,0.25095,0.038246,0.96725,143.33,0.64219,-0.75425,-0.13679,228.31,#30,0.29192,0.021565,0.9562,410.87,0.62557,0.75194,-0.20794,148.49,-0.72349,0.65888,0.20601,264.16,#31,-0.12119,-0.82798,-0.54751,646.32,0.72426,0.30343,-0.61918,68.516,0.67879,-0.47158,0.5629,550.44,#32,-0.30609,0.53532,0.78723,389.15,-0.028165,0.82147,-0.56956,52.518,-0.95159,-0.19651,-0.23636,209.83,#33,-0.34196,0.9169,0.2058,381.89,-0.2616,-0.30323,0.91631,109.42,0.90257,0.2595,0.34355,201.56,#34,-0.7893,0.25518,-0.55846,416.18,0.3362,0.9407,-0.045343,133.52,0.51377,-0.22355,-0.82829,192.16,#35,0.81239,-0.11082,0.57249,383.02,-0.54662,-0.48659,0.68149,109.56,0.20304,-0.86657,-0.45588,200.69
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.92771,0.27918,-0.24781,588.87,0.12527,-0.39253,-0.91117,393.26,-0.35165,-0.87635,0.32918,410.47,#26,-0.79884,-0.30844,-0.51644,447.41,0.54328,-0.73852,-0.39929,99.671,-0.25825,-0.59954,0.75753,217.76,#27,0.27526,0.86888,-0.41142,427.54,0.91965,-0.36269,-0.15066,119.3,-0.28012,-0.3369,-0.89891,248.36,#28,-0.51454,-0.048629,-0.85609,483.11,-0.35724,0.91977,0.16247,167.82,0.77951,0.38943,-0.49063,248.89,#29,0.59004,0.77623,-0.22208,363.47,-0.14046,0.36957,0.91853,145.81,0.79506,-0.51077,0.32709,225.92,#30,0.39143,-0.12273,0.91199,404.4,0.88409,0.3251,-0.3357,129.87,-0.25529,0.93768,0.23575,267.24,#31,-0.26563,-0.74261,-0.61479,588.53,0.29922,0.5427,-0.78482,-94.256,0.91646,-0.39243,0.078041,511.49,#32,-0.1324,0.53076,0.83712,396.16,0.46333,0.77974,-0.4211,74.712,-0.87624,0.33211,-0.34915,169.65,#33,-0.48569,0.86744,0.10796,388.37,-0.65417,-0.44261,0.61331,128.56,0.57979,0.22725,0.78243,189.61,#34,-0.87938,0.25553,-0.40174,422.86,0.081619,0.91219,0.40156,152.2,0.46907,0.32034,-0.82302,199.45,#35,0.7836,0.061687,0.6182,389.63,-0.61995,0.012767,0.78454,129.05,0.040504,-0.99801,0.048247,189.14
> view matrix models
> #24,-0.92217,0.27128,-0.27571,595.51,0.14647,-0.41479,-0.89805,390.44,-0.35798,-0.86854,0.34277,407.19,#26,-0.78154,-0.32736,-0.53107,446.34,0.56203,-0.73894,-0.37161,97.984,-0.27078,-0.5889,0.76149,218.61,#27,0.30319,0.85933,-0.41186,426.93,0.90653,-0.39332,-0.1533,118.69,-0.29373,-0.32689,-0.89826,248.79,#28,-0.52803,-0.023377,-0.8489,483.89,-0.32928,0.92705,0.17929,165.56,0.78279,0.3742,-0.49721,248.8,#29,0.58233,0.78884,-0.19653,363.75,-0.14456,0.33838,0.92984,146.68,0.79999,-0.51307,0.31108,225.63,#30,0.41816,-0.11712,0.90079,404.02,0.86801,0.34385,-0.35823,130.23,-0.26778,0.93169,0.24545,267.4,#31,-0.26063,-0.72478,-0.63778,580.5,0.3218,0.55761,-0.76519,-95.137,0.91023,-0.40467,0.0879,516.11,#32,-0.11512,0.55191,0.82592,394.59,0.45258,0.76928,-0.45098,73.745,-0.88426,0.32188,-0.33834,170.67,#33,-0.50703,0.85317,0.12254,388.29,-0.63016,-0.46392,0.62263,128.12,0.58806,0.23847,0.77286,189.72,#34,-0.87859,0.28072,-0.38637,423.42,0.11488,0.90948,0.39957,150.9,0.46356,0.30667,-0.8313,199.33,#35,0.76498,0.066234,0.64064,389.56,-0.64177,-0.0053799,0.76688,128.56,0.05424,-0.99779,0.038391,189.25
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.92217,0.27128,-0.27571,587.68,0.14647,-0.41479,-0.89805,391.66,-0.35798,-0.86854,0.34277,412.03,#26,-0.78154,-0.32736,-0.53107,438.51,0.56203,-0.73894,-0.37161,99.205,-0.27078,-0.5889,0.76149,223.46,#27,0.30319,0.85933,-0.41186,419.1,0.90653,-0.39332,-0.1533,119.91,-0.29373,-0.32689,-0.89826,253.64,#28,-0.52803,-0.023377,-0.8489,476.06,-0.32928,0.92705,0.17929,166.78,0.78279,0.3742,-0.49721,253.64,#29,0.58233,0.78884,-0.19653,355.93,-0.14456,0.33838,0.92984,147.9,0.79999,-0.51307,0.31108,230.47,#30,0.41816,-0.11712,0.90079,396.19,0.86801,0.34385,-0.35823,131.45,-0.26778,0.93169,0.24545,272.24,#31,-0.26063,-0.72478,-0.63778,572.67,0.3218,0.55761,-0.76519,-93.916,0.91023,-0.40467,0.0879,520.95,#32,-0.11512,0.55191,0.82592,386.76,0.45258,0.76928,-0.45098,74.966,-0.88426,0.32188,-0.33834,175.52,#33,-0.50703,0.85317,0.12254,380.46,-0.63016,-0.46392,0.62263,129.34,0.58806,0.23847,0.77286,194.56,#34,-0.87859,0.28072,-0.38637,415.59,0.11488,0.90948,0.39957,152.12,0.46356,0.30667,-0.8313,204.18,#35,0.76498,0.066234,0.64064,381.73,-0.64177,-0.0053799,0.76688,129.78,0.05424,-0.99779,0.038391,194.09
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.95958,0.23013,-0.16201,578.69,0.059806,-0.39576,-0.9164,410.02,-0.27501,-0.88905,0.366,393.67,#26,-0.85001,-0.30973,-0.4261,440.58,0.48705,-0.77025,-0.41171,103.77,-0.20068,-0.55749,0.80557,219.09,#27,0.19283,0.85925,-0.47382,422.1,0.92773,-0.31692,-0.19717,122.89,-0.31958,-0.40156,-0.85827,250.86,#28,-0.42503,-0.07414,-0.90214,474.36,-0.36911,0.92421,0.09795,174.71,0.8265,0.37462,-0.42019,245.82,#29,0.66123,0.70669,-0.25172,354.86,-0.084911,0.40389,0.91086,144.88,0.74536,-0.58091,0.32707,233.37,#30,0.31265,-0.06523,0.94763,399.97,0.89994,0.33952,-0.27355,132.47,-0.30389,0.93833,0.16485,271.42,#31,-0.20749,-0.8051,-0.55566,617.35,0.30445,0.48667,-0.81882,-74.021,0.92966,-0.33907,0.14413,503.58,#32,-0.23306,0.50621,0.83032,387.21,0.4331,0.81851,-0.37745,74.575,-0.8707,0.27164,-0.41,175.92,#33,-0.39412,0.90934,0.13328,377.71,-0.66846,-0.38315,0.63746,128.31,0.63074,0.16214,0.75887,195.44,#34,-0.84111,0.22317,-0.49268,411.35,0.039009,0.93356,0.35628,154.24,0.53945,0.28045,-0.79394,201.9,#35,0.82172,-0.021711,0.56948,378.9,-0.56973,-0.0075706,0.8218,128.87,-0.013531,-0.99974,-0.01859,194.86
> view matrix models
> #24,-0.95978,0.23023,-0.16071,578.43,0.057941,-0.39767,-0.9157,410.65,-0.27473,-0.88818,0.36833,392.92,#26,-0.8507,-0.30902,-0.42523,440.61,0.4855,-0.772,-0.41025,103.8,-0.2015,-0.55545,0.80677,219.15,#27,0.19154,0.85946,-0.47396,422.13,0.92718,-0.31685,-0.19987,122.97,-0.32196,-0.40116,-0.85756,250.89,#28,-0.42421,-0.075115,-0.90245,474.32,-0.3676,0.92504,0.095798,174.84,0.8276,0.37237,-0.42002,245.69,#29,0.66167,0.70593,-0.2527,354.85,-0.082254,0.40333,0.91135,144.84,0.74527,-0.58223,0.32494,233.37,#30,0.3114,-0.065229,0.94804,400,0.89958,0.34175,-0.27197,132.57,-0.30625,0.93752,0.1651,271.43,#31,-0.20745,-0.80586,-0.55458,617.73,0.30648,0.48484,-0.81915,-73.077,0.929,-0.3399,0.1464,504,#32,-0.23399,0.50532,0.8306,387.27,0.43066,0.81981,-0.37743,74.426,-0.87166,0.26939,-0.40944,176.08,#33,-0.39301,0.90989,0.13284,377.71,-0.66739,-0.38163,0.6395,128.2,0.63256,0.16268,0.75723,195.47,#34,-0.84092,0.22214,-0.49347,411.31,0.0393,0.93453,0.35371,154.19,0.53974,0.27805,-0.79459,201.85,#35,0.82242,-0.02215,0.56845,378.89,-0.56875,-0.010064,0.82245,128.75,-0.012497,-0.9997,-0.020875,194.88
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.95978,0.23023,-0.16071,579.09,0.057941,-0.39767,-0.9157,408.67,-0.27473,-0.88818,0.36833,388.94,#26,-0.8507,-0.30902,-0.42523,441.28,0.4855,-0.772,-0.41025,101.82,-0.2015,-0.55545,0.80677,215.18,#27,0.19154,0.85946,-0.47396,422.8,0.92718,-0.31685,-0.19987,120.99,-0.32196,-0.40116,-0.85756,246.91,#28,-0.42421,-0.075115,-0.90245,474.99,-0.3676,0.92504,0.095798,172.86,0.8276,0.37237,-0.42002,241.72,#29,0.66167,0.70593,-0.2527,355.52,-0.082254,0.40333,0.91135,142.86,0.74527,-0.58223,0.32494,229.39,#30,0.3114,-0.065229,0.94804,400.66,0.89958,0.34175,-0.27197,130.6,-0.30625,0.93752,0.1651,267.45,#31,-0.20745,-0.80586,-0.55458,618.4,0.30648,0.48484,-0.81915,-75.051,0.929,-0.3399,0.1464,500.03,#32,-0.23399,0.50532,0.8306,387.93,0.43066,0.81981,-0.37743,72.453,-0.87166,0.26939,-0.40944,172.1,#33,-0.39301,0.90989,0.13284,378.38,-0.66739,-0.38163,0.6395,126.23,0.63256,0.16268,0.75723,191.49,#34,-0.84092,0.22214,-0.49347,411.98,0.0393,0.93453,0.35371,152.21,0.53974,0.27805,-0.79459,197.88,#35,0.82242,-0.02215,0.56845,379.56,-0.56875,-0.010064,0.82245,126.78,-0.012497,-0.9997,-0.020875,190.91
> view matrix models
> #24,-0.95978,0.23023,-0.16071,578.33,0.057941,-0.39767,-0.9157,406.48,-0.27473,-0.88818,0.36833,390.5,#26,-0.8507,-0.30902,-0.42523,440.52,0.4855,-0.772,-0.41025,99.631,-0.2015,-0.55545,0.80677,216.74,#27,0.19154,0.85946,-0.47396,422.04,0.92718,-0.31685,-0.19987,118.8,-0.32196,-0.40116,-0.85756,248.47,#28,-0.42421,-0.075115,-0.90245,474.23,-0.3676,0.92504,0.095798,170.67,0.8276,0.37237,-0.42002,243.28,#29,0.66167,0.70593,-0.2527,354.76,-0.082254,0.40333,0.91135,140.67,0.74527,-0.58223,0.32494,230.96,#30,0.3114,-0.065229,0.94804,399.91,0.89958,0.34175,-0.27197,128.41,-0.30625,0.93752,0.1651,269.02,#31,-0.20745,-0.80586,-0.55458,617.64,0.30648,0.48484,-0.81915,-77.243,0.929,-0.3399,0.1464,501.59,#32,-0.23399,0.50532,0.8306,387.17,0.43066,0.81981,-0.37743,70.26,-0.87166,0.26939,-0.40944,173.66,#33,-0.39301,0.90989,0.13284,377.62,-0.66739,-0.38163,0.6395,124.03,0.63256,0.16268,0.75723,193.06,#34,-0.84092,0.22214,-0.49347,411.22,0.0393,0.93453,0.35371,150.02,0.53974,0.27805,-0.79459,199.44,#35,0.82242,-0.02215,0.56845,378.8,-0.56875,-0.010064,0.82245,124.59,-0.012497,-0.9997,-0.020875,192.47
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7376, correlation about mean = 0.2518, overlap = 17.37
steps = 104, shift = 6.57, angle = 11 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53717394 -0.84339058 -0.01168334 402.36094944
0.84310057 -0.53729695 0.02221345 56.76569545
-0.02501204 0.00208226 0.99968499 -108.79516868
Axis -0.01193551 0.00790240 0.99989754
Axis point 184.71498739 138.81057099 0.00000000
Rotation angle (degrees) 122.50634127
Shift along axis -113.13782048
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7376, correlation about mean = 0.2518, overlap = 17.37
steps = 104, shift = 6.57, angle = 11 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53717394 -0.84339058 -0.01168334 402.36094944
0.84310057 -0.53729695 0.02221345 56.76569545
-0.02501204 0.00208226 0.99968499 -108.79516868
Axis -0.01193551 0.00790240 0.99989754
Axis point 184.71498739 138.81057099 0.00000000
Rotation angle (degrees) 122.50634127
Shift along axis -113.13782048
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7376, correlation about mean = 0.2518, overlap = 17.37
steps = 104, shift = 6.57, angle = 11 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53717394 -0.84339058 -0.01168334 402.36094944
0.84310057 -0.53729695 0.02221345 56.76569545
-0.02501204 0.00208226 0.99968499 -108.79516868
Axis -0.01193551 0.00790240 0.99989754
Axis point 184.71498739 138.81057099 0.00000000
Rotation angle (degrees) 122.50634127
Shift along axis -113.13782048
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.96175,0.24118,-0.12989,569.68,0.068309,-0.24805,-0.96634,385.04,-0.26528,-0.93825,0.22208,431.17,#26,-0.86655,-0.28482,-0.40984,441.6,0.48276,-0.68666,-0.54354,104.36,-0.1266,-0.66886,0.73253,211.72,#27,0.16042,0.86849,-0.46903,422.56,0.97152,-0.2229,-0.080438,117.79,-0.1744,-0.44277,-0.87951,245.98,#28,-0.41017,-0.10451,-0.906,473.02,-0.50461,0.85351,0.12999,171.52,0.75969,0.51049,-0.40282,249.01,#29,0.66562,0.6911,-0.28165,354.57,-0.17469,0.5112,0.84152,139.9,0.72556,-0.51093,0.461,231.85,#30,0.28116,-0.074334,0.95678,400.17,0.94575,0.1906,-0.26311,123.38,-0.1628,0.97885,0.12389,267.69,#31,-0.21534,-0.82201,-0.52719,625.02,0.15245,0.50494,-0.84959,-108.49,0.96457,-0.26332,0.016578,466.37,#32,-0.24983,0.47883,0.84161,389.14,0.5522,0.78443,-0.28238,80.271,-0.7954,0.39419,-0.46039,164.47,#33,-0.36961,0.92223,0.1135,377.88,-0.76951,-0.37227,0.51891,130.06,0.52081,0.10446,0.84726,191.9,#34,-0.84058,0.19207,-0.50649,410.63,-0.071964,0.88714,0.45585,155.84,0.53689,0.41963,-0.73189,202.32,#35,0.84054,-0.023977,0.54121,379.04,-0.53285,0.14368,0.83392,130.74,-0.097758,-0.98933,0.108,191.42
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.96175,0.24118,-0.12989,573.17,0.068309,-0.24805,-0.96634,385.07,-0.26528,-0.93825,0.22208,436.15,#26,-0.86655,-0.28482,-0.40984,445.09,0.48276,-0.68666,-0.54354,104.39,-0.1266,-0.66886,0.73253,216.7,#27,0.16042,0.86849,-0.46903,426.05,0.97152,-0.2229,-0.080438,117.82,-0.1744,-0.44277,-0.87951,250.96,#28,-0.41017,-0.10451,-0.906,476.51,-0.50461,0.85351,0.12999,171.54,0.75969,0.51049,-0.40282,253.99,#29,0.66562,0.6911,-0.28165,358.06,-0.17469,0.5112,0.84152,139.92,0.72556,-0.51093,0.461,236.83,#30,0.28116,-0.074334,0.95678,403.66,0.94575,0.1906,-0.26311,123.41,-0.1628,0.97885,0.12389,272.68,#31,-0.21534,-0.82201,-0.52719,628.51,0.15245,0.50494,-0.84959,-108.47,0.96457,-0.26332,0.016578,471.35,#32,-0.24983,0.47883,0.84161,392.63,0.5522,0.78443,-0.28238,80.296,-0.7954,0.39419,-0.46039,169.45,#33,-0.36961,0.92223,0.1135,381.36,-0.76951,-0.37227,0.51891,130.09,0.52081,0.10446,0.84726,196.89,#34,-0.84058,0.19207,-0.50649,414.11,-0.071964,0.88714,0.45585,155.86,0.53689,0.41963,-0.73189,207.3,#35,0.84054,-0.023977,0.54121,382.53,-0.53285,0.14368,0.83392,130.77,-0.097758,-0.98933,0.108,196.4
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 152, shift = 8.12, angle = 18.7 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53704927 -0.84347043 -0.01165063 402.33042921
0.84318173 -0.53717160 0.02216432 56.75380643
-0.02495334 0.00207973 0.99968646 -108.78435477
Axis -0.01190675 0.00788624 0.99989801
Axis point 184.70237821 138.81569158 0.00000000
Rotation angle (degrees) 122.49779840
Shift along axis -113.11613255
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 152, shift = 8.12, angle = 18.7 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53704927 -0.84347043 -0.01165063 402.33042921
0.84318173 -0.53717160 0.02216432 56.75380643
-0.02495334 0.00207973 0.99968646 -108.78435477
Axis -0.01190675 0.00788624 0.99989801
Axis point 184.70237821 138.81569158 0.00000000
Rotation angle (degrees) 122.49779840
Shift along axis -113.11613255
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 152, shift = 8.12, angle = 18.7 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53704927 -0.84347043 -0.01165063 402.33042921
0.84318173 -0.53717160 0.02216432 56.75380643
-0.02495334 0.00207973 0.99968646 -108.78435477
Axis -0.01190675 0.00788624 0.99989801
Axis point 184.70237821 138.81569158 0.00000000
Rotation angle (degrees) 122.49779840
Shift along axis -113.11613255
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.9551,0.15287,-0.2538,617.26,0.19462,-0.32217,-0.92646,364.85,-0.2234,-0.93426,0.27795,414.17,#26,-0.79469,-0.41492,-0.44308,439.02,0.59677,-0.66761,-0.44516,96.067,-0.1111,-0.61817,0.77815,215.84,#27,0.28727,0.80303,-0.52214,423.96,0.92931,-0.36574,-0.051206,113.63,-0.23208,-0.47052,-0.85132,250.21,#28,-0.43641,0.045328,-0.8986,481.63,-0.4054,0.8817,0.24136,159.58,0.80324,0.46963,-0.36641,248.08,#29,0.67195,0.72835,-0.13412,359.14,-0.23631,0.38249,0.89323,144.67,0.70189,-0.56851,0.42913,238.13,#30,0.40356,0.0060483,0.91493,403.78,0.88691,0.24309,-0.39281,123.37,-0.22479,0.96998,0.092739,272.62,#31,-0.13951,-0.75483,-0.64091,603.72,0.22512,0.60611,-0.76286,-129.42,0.96429,-0.25071,0.08537,472.42,#32,-0.21108,0.60586,0.76706,381.23,0.54624,0.72389,-0.42144,77.711,-0.8106,0.33004,-0.48374,172.41,#33,-0.44677,0.86423,0.2313,378.63,-0.68384,-0.49659,0.53457,129.79,0.57685,0.080651,0.81286,197.71,#34,-0.8123,0.33838,-0.47505,415.22,0.074464,0.868,0.49095,151,0.57847,0.36342,-0.73027,205.23,#35,0.74984,-0.056281,0.65922,379.85,-0.65259,0.10108,0.75094,130.27,-0.10889,-0.99329,0.039062,197.13
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2516, overlap = 17.37
steps = 132, shift = 7.97, angle = 15.7 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53715115 -0.84340573 -0.01163786 402.33544824
0.84311660 -0.53727309 0.02218203 56.78127972
-0.02496116 0.00210302 0.99968622 -108.78802057
Axis -0.01190435 0.00789906 0.99989794
Axis point 184.69932070 138.81584890 0.00000000
Rotation angle (degrees) 122.50471451
Shift along axis -113.11794171
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2516, overlap = 17.37
steps = 132, shift = 7.97, angle = 15.7 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53715115 -0.84340573 -0.01163786 402.33544824
0.84311660 -0.53727309 0.02218203 56.78127972
-0.02496116 0.00210302 0.99968622 -108.78802057
Axis -0.01190435 0.00789906 0.99989794
Axis point 184.69932070 138.81584890 0.00000000
Rotation angle (degrees) 122.50471451
Shift along axis -113.11794171
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2516, overlap = 17.37
steps = 132, shift = 7.97, angle = 15.7 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53715115 -0.84340573 -0.01163786 402.33544824
0.84311660 -0.53727309 0.02218203 56.78127972
-0.02496116 0.00210302 0.99968622 -108.78802057
Axis -0.01190435 0.00789906 0.99989794
Axis point 184.69932070 138.81584890 0.00000000
Rotation angle (degrees) 122.50471451
Shift along axis -113.11794171
> view matrix models
> #24,-0.94277,0.073832,-0.32515,646.62,0.29536,-0.26761,-0.91714,330.54,-0.15473,-0.96069,0.23049,415.69,#26,-0.73973,-0.50696,-0.44248,433.98,0.67241,-0.58194,-0.4574,93.676,-0.025612,-0.63588,0.77136,210.69,#27,0.36105,0.73993,-0.56758,422.41,0.9137,-0.40243,0.056599,110.05,-0.18653,-0.53904,-0.82137,246.94,#28,-0.43083,0.15199,-0.88954,483.96,-0.42029,0.83849,0.34683,150.64,0.79859,0.52329,-0.29737,244.53,#29,0.68186,0.73097,-0.027412,360.26,-0.34514,0.35454,0.86901,147.59,0.64494,-0.58308,0.49403,240.69,#30,0.47306,0.078574,0.87752,404.42,0.86057,0.17218,-0.47935,119.95,-0.18875,0.98193,0.013833,271.07,#31,-0.068129,-0.70639,-0.70454,589.69,0.16786,0.68799,-0.70604,-163.37,0.98345,-0.16637,0.071704,441.95,#32,-0.20008,0.68732,0.69826,372.56,0.61914,0.64104,-0.45358,83.737,-0.75936,0.34156,-0.55381,169.54,#33,-0.47889,0.81674,0.32187,376.18,-0.6799,-0.57701,0.45254,133.91,0.55533,-0.0021241,0.83163,198.32,#34,-0.77098,0.43663,-0.46362,414.94,0.10626,0.80597,0.58234,151.15,0.62793,0.39971,-0.66778,205.1,#35,0.67863,-0.097371,0.728,377.41,-0.70823,0.1759,0.68372,134.32,-0.19463,-0.97958,0.050411,197.71
> view matrix models
> #24,-0.98044,0.073253,-0.18266,623.02,0.13546,-0.42211,-0.89637,390.95,-0.14276,-0.90358,0.40393,363.06,#26,-0.82796,-0.44396,-0.34262,438.21,0.55301,-0.7478,-0.36739,95.318,-0.093102,-0.49365,0.86466,215.45,#27,0.22038,0.76775,-0.60166,425.87,0.90559,-0.39021,-0.16623,116.2,-0.3624,-0.50822,-0.78127,249.04,#28,-0.33529,0.05209,-0.94067,480.9,-0.32482,0.93086,0.16732,163.51,0.88435,0.36165,-0.29519,235.82,#29,0.74864,0.64994,-0.13084,358.83,-0.13136,0.33885,0.93162,143.45,0.64983,-0.68027,0.33905,240.42,#30,0.33861,0.091849,0.93643,407.62,0.86824,0.35304,-0.34859,127.76,-0.36262,0.93109,0.039798,272.21,#31,-0.052589,-0.8027,-0.59405,637.71,0.32966,0.54757,-0.76908,-93.517,0.94264,-0.23628,0.23582,476.87,#32,-0.31541,0.60244,0.7332,377.25,0.44204,0.77697,-0.44825,70.16,-0.83971,0.18273,-0.51136,180.59,#33,-0.35559,0.88952,0.28689,374.85,-0.62762,-0.45471,0.63193,124.69,0.69256,0.044647,0.71997,200.09,#34,-0.75303,0.33339,-0.56727,411.01,0.11313,0.9149,0.38751,147.84,0.64819,0.22763,-0.72666,201.35,#35,0.76395,-0.15966,0.62521,375.98,-0.63522,-0.015717,0.77217,125.14,-0.11346,-0.98705,-0.11343,199.33
> view matrix models
> #24,-0.97204,0.010694,-0.23459,645.53,0.21319,-0.37869,-0.90064,366.75,-0.098468,-0.92546,0.36582,366.69,#26,-0.78741,-0.51484,-0.33899,434.36,0.61548,-0.68705,-0.38619,93.329,-0.034082,-0.51273,0.85787,211.8,#27,0.27429,0.71882,-0.6388,424.76,0.90494,-0.41768,-0.081431,113.27,-0.32535,-0.55574,-0.76505,246.82,#28,-0.32786,0.13331,-0.93527,482.66,-0.34533,0.90457,0.24999,157.1,0.87935,0.40494,-0.25053,233.87,#29,0.75873,0.64951,-0.049725,359.67,-0.21876,0.32596,0.91973,145.71,0.61358,-0.68695,0.3894,242.12,#30,0.38936,0.14968,0.90884,408.22,0.8592,0.29654,-0.41693,124.9,-0.33191,0.94322,-0.01315,271.22,#31,0.0043923,-0.76757,-0.64096,628.18,0.28308,0.6157,-0.73538,-122.78,0.95909,-0.17821,0.21998,455.78,#32,-0.31044,0.66428,0.67997,370.55,0.50679,0.72084,-0.47282,74.49,-0.80423,0.19782,-0.56042,178.08,#33,-0.37712,0.85439,0.35749,372.86,-0.63549,-0.5195,0.57121,127.96,0.67375,-0.011766,0.73887,200.33,#34,-0.71986,0.40789,-0.56163,410.66,0.13335,0.87532,0.46479,148.34,0.68119,0.25969,-0.68451,201.36,#35,0.71043,-0.19419,0.67644,374,-0.68199,0.047263,0.72983,128.36,-0.1737,-0.97982,-0.098863,199.56
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2517, overlap = 17.37
steps = 120, shift = 7.43, angle = 12.6 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53707590 -0.84345346 -0.01165140 402.34012599
0.84316858 -0.53719856 0.02201090 56.80819392
-0.02482429 0.00199743 0.99968984 -108.80732978
Axis -0.01186481 0.00780943 0.99989911
Axis point 184.69738864 138.83872102 0.00000000
Rotation angle (degrees) 122.49950368
Shift along axis -113.12640341
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2517, overlap = 17.37
steps = 120, shift = 7.43, angle = 12.6 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53707590 -0.84345346 -0.01165140 402.34012599
0.84316858 -0.53719856 0.02201090 56.80819392
-0.02482429 0.00199743 0.99968984 -108.80732978
Axis -0.01186481 0.00780943 0.99989911
Axis point 184.69738864 138.83872102 0.00000000
Rotation angle (degrees) 122.49950368
Shift along axis -113.12640341
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2517, overlap = 17.37
steps = 120, shift = 7.43, angle = 12.6 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53707590 -0.84345346 -0.01165140 402.34012599
0.84316858 -0.53719856 0.02201090 56.80819392
-0.02482429 0.00199743 0.99968984 -108.80732978
Axis -0.01186481 0.00780943 0.99989911
Axis point 184.69738864 138.83872102 0.00000000
Rotation angle (degrees) 122.49950368
Shift along axis -113.12640341
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2517, overlap = 17.37
steps = 120, shift = 7.43, angle = 12.6 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53707590 -0.84345346 -0.01165140 402.34012599
0.84316858 -0.53719856 0.02201090 56.80819392
-0.02482429 0.00199743 0.99968984 -108.80732978
Axis -0.01186481 0.00780943 0.99989911
Axis point 184.69738864 138.83872102 0.00000000
Rotation angle (degrees) 122.49950368
Shift along axis -113.12640341
> view matrix models
> #24,-0.91179,0.065394,-0.40541,659.65,0.37281,-0.28214,-0.88398,309.91,-0.17219,-0.95714,0.23287,418.1,#26,-0.67941,-0.54488,-0.49142,430.78,0.73249,-0.5429,-0.41075,89.985,-0.042981,-0.63904,0.76797,211.7,#27,0.44021,0.71114,-0.54818,420.09,0.87792,-0.46894,0.096668,107.62,-0.18832,-0.52381,-0.83076,247.63,#28,-0.47708,0.21477,-0.85221,484.9,-0.3745,0.82756,0.4182,142.82,0.79507,0.51867,-0.31438,245.86,#29,0.64017,0.76724,0.039069,361.46,-0.39555,0.28559,0.87291,150.25,0.65858,-0.57427,0.48631,240.08,#30,0.54733,0.078007,0.83327,402.64,0.81546,0.17432,-0.55194,119.25,-0.18832,0.98159,0.031801,271.39,#31,-0.068538,-0.64273,-0.76302,560.54,0.18249,0.74384,-0.64297,-177.11,0.98082,-0.18331,0.066312,447.54,#32,-0.13517,0.73406,0.66549,369.37,0.62656,0.58364,-0.51652,84.899,-0.76757,0.34715,-0.53882,169.66,#33,-0.54334,0.76466,0.34652,376.8,-0.63143,-0.64424,0.43156,134.86,0.55324,0.015687,0.83287,198.08,#34,-0.7686,0.49745,-0.40224,416.78,0.17735,0.76981,0.61314,148.81,0.61465,0.39992,-0.6799,205.34,#35,0.61884,-0.067176,0.78264,378.07,-0.76511,0.1741,0.61992,135.16,-0.1779,-0.98243,0.056343,197.48
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2514, overlap = 17.37
steps = 180, shift = 8.43, angle = 23.4 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53705460 -0.84346654 -0.01168611 402.33850239
0.84317691 -0.53717775 0.02219872 56.72588531
-0.02500139 0.00206846 0.99968528 -108.77679599
Axis -0.01193388 0.00789374 0.99989763
Axis point 184.71253914 138.80253508 0.00000000
Rotation angle (degrees) 122.49822817
Shift along axis -113.11933930
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2514, overlap = 17.37
steps = 180, shift = 8.43, angle = 23.4 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53705460 -0.84346654 -0.01168611 402.33850239
0.84317691 -0.53717775 0.02219872 56.72588531
-0.02500139 0.00206846 0.99968528 -108.77679599
Axis -0.01193388 0.00789374 0.99989763
Axis point 184.71253914 138.80253508 0.00000000
Rotation angle (degrees) 122.49822817
Shift along axis -113.11933930
> view matrix models
> #24,-0.99402,-0.016471,-0.10792,627.58,0.10379,-0.44888,-0.88754,401.09,-0.033823,-0.89344,0.44791,328.4,#26,-0.8499,-0.47362,-0.23099,436.49,0.52676,-0.77526,-0.34856,95.88,-0.013993,-0.41792,0.90838,211.46,#27,0.14979,0.717,-0.68079,427.39,0.89914,-0.38518,-0.20783,117.48,-0.41124,-0.58099,-0.70237,245.62,#28,-0.2228,0.063847,-0.97277,479.08,-0.30519,0.94313,0.1318,165.84,0.92586,0.32624,-0.19065,224.84,#29,0.8211,0.55795,-0.1204,358.99,-0.089699,0.33444,0.93814,142.59,0.5637,-0.7595,0.32466,243.92,#30,0.26834,0.18568,0.94526,411.53,0.86506,0.3853,-0.32126,129.29,-0.42387,0.90391,-0.057235,270.38,#31,0.044276,-0.84086,-0.53944,670.05,0.35834,0.51741,-0.7771,-78.867,0.93254,-0.1589,0.32422,453.76,#32,-0.42197,0.59491,0.68412,372.79,0.40587,0.79871,-0.44421,67.945,-0.81068,0.090225,-0.57849,184.52,#33,-0.2553,0.90251,0.34685,370.92,-0.61447,-0.42842,0.66248,122.99,0.74649,-0.043995,0.66394,202.58,#34,-0.67795,0.32853,-0.65761,406.26,0.11327,0.93058,0.34813,147.15,0.72633,0.16152,-0.6681,199.04,#35,0.76549,-0.2698,0.58414,371.94,-0.61733,-0.05195,0.78499,123.44,-0.18145,-0.96151,-0.20633,201.69
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 108, shift = 6.93, angle = 8.53 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53706199 -0.84346186 -0.01168449 402.33865259
0.84317250 -0.53718512 0.02218803 56.72804860
-0.02499150 0.00206430 0.99968554 -108.77872519
Axis -0.01193007 0.00788887 0.99989771
Axis point 184.71252822 138.80238569 0.00000000
Rotation angle (degrees) 122.49872094
Shift along axis -113.12000798
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 108, shift = 6.93, angle = 8.53 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53706199 -0.84346186 -0.01168449 402.33865259
0.84317250 -0.53718512 0.02218803 56.72804860
-0.02499150 0.00206430 0.99968554 -108.77872519
Axis -0.01193007 0.00788887 0.99989771
Axis point 184.71252822 138.80238569 0.00000000
Rotation angle (degrees) 122.49872094
Shift along axis -113.12000798
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 108, shift = 6.93, angle = 8.53 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53706199 -0.84346186 -0.01168449 402.33865259
0.84317250 -0.53718512 0.02218803 56.72804860
-0.02499150 0.00206430 0.99968554 -108.77872519
Axis -0.01193007 0.00788887 0.99989771
Axis point 184.71252822 138.80238569 0.00000000
Rotation angle (degrees) 122.49872094
Shift along axis -113.12000798
> view matrix models
> #24,-0.99922,0.0022816,-0.039311,609.63,0.032689,-0.50853,-0.86042,422.14,-0.021954,-0.86104,0.50806,305.97,#26,-0.88473,-0.42418,-0.1932,438.69,0.46493,-0.83254,-0.30118,97.289,-0.033096,-0.35629,0.93379,213.26,#27,0.080787,0.73386,-0.67448,428.58,0.87733,-0.37351,-0.30131,120.48,-0.47304,-0.5674,-0.67401,246.07,#28,-0.18782,0.0024265,-0.9822,476.48,-0.25626,0.96524,0.051388,170.76,0.94818,0.26135,-0.18067,221.14,#29,0.83325,0.52242,-0.18102,358.59,0.0054018,0.3197,0.9475,140.66,0.55287,-0.79049,0.26357,243.98,#30,0.20124,0.17109,0.96448,412.29,0.85071,0.45759,-0.25867,132.82,-0.4856,0.87255,-0.053463,270.28,#31,0.03233,-0.87711,-0.4792,687.29,0.42298,0.44641,-0.78855,-44.148,0.90556,-0.1772,0.38543,462.24,#32,-0.46072,0.53888,0.70523,376.72,0.31997,0.84199,-0.43436,63.278,-0.82786,0.025538,-0.56035,189.45,#33,-0.20117,0.92951,0.30909,371.26,-0.5785,-0.36737,0.72827,119.16,0.79048,-0.032302,0.61163,203.83,#34,-0.67386,0.26498,-0.68971,404.77,0.11542,0.95977,0.25597,145.4,0.72979,0.092883,-0.67733,198.02,#35,0.8041,-0.2791,0.52491,372.24,-0.57414,-0.13549,0.80747,119.62,-0.15424,-0.95066,-0.26918,202.89
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 96, shift = 6.77, angle = 7.86 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53711631 -0.84342763 -0.01165873 402.33694809
0.84313678 -0.53723864 0.02224909 56.75185351
-0.02502902 0.00212044 0.99968448 -108.77613969
Axis -0.01193348 0.00792671 0.99989737
Axis point 184.70501377 138.80739150 0.00000000
Rotation angle (degrees) 122.50242003
Shift along axis -113.11640090
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 96, shift = 6.77, angle = 7.86 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53711631 -0.84342763 -0.01165873 402.33694809
0.84313678 -0.53723864 0.02224909 56.75185351
-0.02502902 0.00212044 0.99968448 -108.77613969
Axis -0.01193348 0.00792671 0.99989737
Axis point 184.70501377 138.80739150 0.00000000
Rotation angle (degrees) 122.50242003
Shift along axis -113.11640090
> view matrix models
> #24,-0.99188,0.1263,-0.015154,577.45,-0.065958,-0.61252,-0.7877,447.89,-0.10877,-0.7803,0.61587,283.79,#26,-0.91338,-0.31744,-0.25488,443.82,0.3702,-0.90812,-0.19561,98.985,-0.16937,-0.27302,0.94698,222.54,#27,0.051569,0.81292,-0.58008,428.75,0.81285,-0.37162,-0.44852,125.14,-0.58018,-0.44839,-0.67995,250.91,#28,-0.25465,-0.10304,-0.96153,474.41,-0.1489,0.98663,-0.066295,176.13,0.9555,0.12629,-0.26659,223.4,#29,0.77379,0.56634,-0.28375,357.82,0.15601,0.26376,0.95189,138.1,0.61394,-0.78083,0.11574,240.31,#30,0.17447,0.048855,0.98345,409.26,0.79646,0.58027,-0.17012,138.87,-0.57897,0.81296,0.062328,271.78,#31,-0.089026,-0.89063,-0.44592,678.68,0.5371,0.33411,-0.77453,15.14,0.83881,-0.30846,0.44861,508.2,#32,-0.40541,0.46175,0.78894,387.44,0.16535,0.88585,-0.4335,56.434,-0.89906,-0.045292,-0.43548,198.55,#33,-0.22603,0.95584,0.18782,375.99,-0.48854,-0.27804,0.82706,112.92,0.84276,0.095181,0.52981,204.66,#34,-0.7472,0.17382,-0.64146,407.59,0.14348,0.98462,0.099678,141.28,0.64892,-0.017555,-0.76065,198.11,#35,0.86027,-0.17553,0.47868,377.02,-0.50979,-0.28268,0.81253,113.35,-0.0073119,-0.94302,-0.33267,203.75
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 100, shift = 6.9, angle = 9.9 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53709987 -0.84343794 -0.01167000 402.33815969
0.84314628 -0.53722242 0.02228108 56.73246859
-0.02506209 0.00212765 0.99968364 -108.77255181
Axis -0.01194803 0.00793955 0.99989710
Axis point 184.70940740 138.80074964 0.00000000
Rotation angle (degrees) 122.50133899
Shift along axis -113.11807635
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 100, shift = 6.9, angle = 9.9 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53709987 -0.84343794 -0.01167000 402.33815969
0.84314628 -0.53722242 0.02228108 56.73246859
-0.02506209 0.00212765 0.99968364 -108.77255181
Axis -0.01194803 0.00793955 0.99989710
Axis point 184.70940740 138.80074964 0.00000000
Rotation angle (degrees) 122.50133899
Shift along axis -113.11807635
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 100, shift = 6.9, angle = 9.9 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53709987 -0.84343794 -0.01167000 402.33815969
0.84314628 -0.53722242 0.02228108 56.73246859
-0.02506209 0.00212765 0.99968364 -108.77255181
Axis -0.01194803 0.00793955 0.99989710
Axis point 184.70940740 138.80074964 0.00000000
Rotation angle (degrees) 122.50133899
Shift along axis -113.11807635
> view matrix models
> #24,-0.99282,0.076835,-0.091661,604.7,0.03504,-0.54588,-0.83713,424.09,-0.11436,-0.83433,0.53927,312.97,#26,-0.87462,-0.39612,-0.27952,440.52,0.46599,-0.84597,-0.25921,96.058,-0.13379,-0.35696,0.92449,219.27,#27,0.1299,0.77965,-0.6126,427.64,0.85542,-0.40054,-0.32837,120.71,-0.50138,-0.48137,-0.71896,249.98,#28,-0.27514,-0.014265,-0.9613,477.97,-0.21372,0.97578,0.046689,169.67,0.93735,0.21829,-0.27152,227.37,#29,0.77954,0.59447,-0.19728,358.28,0.0269,0.28291,0.95877,141.01,0.62577,-0.75271,0.20455,240.65,#30,0.2508,0.094394,0.96343,409.31,0.82787,0.49492,-0.264,134.15,-0.50174,0.8638,0.045979,272.05,#31,-0.047045,-0.85406,-0.51804,664.41,0.46225,0.44113,-0.76924,-35.134,0.8855,-0.27565,0.37404,495.79,#32,-0.38117,0.54049,0.75005,380.72,0.28483,0.84049,-0.46092,61.241,-0.87954,0.037945,-0.47432,191.41,#33,-0.27646,0.92588,0.25753,374.39,-0.54253,-0.37155,0.7534,117.72,0.79324,0.068567,0.60503,202.79,#34,-0.73656,0.26247,-0.62336,408.49,0.14963,0.96203,0.22827,143.57,0.65961,0.074858,-0.74787,198.93,#35,0.81056,-0.19248,0.55312,375.46,-0.58305,-0.17619,0.7931,118.14,-0.0552,-0.96535,-0.25504,201.93
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 64, shift = 6.9, angle = 3.2 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53703159 -0.84348159 -0.01165744 402.33132509
0.84319357 -0.53715415 0.02213663 56.74756624
-0.02493368 0.00205859 0.99968700 -108.78731108
Axis -0.01190270 0.00787045 0.99989819
Axis point 184.70483206 138.81482616 0.00000000
Rotation angle (degrees) 122.49658715
Shift along axis -113.11843685
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2515, overlap = 17.37
steps = 64, shift = 6.9, angle = 3.2 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53703159 -0.84348159 -0.01165744 402.33132509
0.84319357 -0.53715415 0.02213663 56.74756624
-0.02493368 0.00205859 0.99968700 -108.78731108
Axis -0.01190270 0.00787045 0.99989819
Axis point 184.70483206 138.81482616 0.00000000
Rotation angle (degrees) 122.49658715
Shift along axis -113.11843685
> view matrix models
> #24,-0.99028,0.060441,-0.1253,614.97,0.076335,-0.5169,-0.85264,412.97,-0.1163,-0.85391,0.50726,324.47,#26,-0.85603,-0.42562,-0.29336,439.15,0.50299,-0.81669,-0.28286,95.013,-0.11919,-0.38969,0.9132,218.01,#27,0.16401,0.76649,-0.62096,427.05,0.86806,-0.41116,-0.27824,118.96,-0.46858,-0.4934,-0.73279,249.58,#28,-0.28735,0.021005,-0.9576,479.27,-0.23807,0.96682,0.092647,166.83,0.92777,0.2546,-0.27281,228.98,#29,0.77702,0.60815,-0.16245,358.53,-0.025574,0.28836,0.95718,142.17,0.62895,-0.7396,0.23961,240.78,#30,0.2838,0.10863,0.95271,409.12,0.83604,0.45851,-0.30133,132.25,-0.46956,0.88202,0.039305,272.07,#31,-0.034025,-0.83574,-0.54807,656.68,0.43037,0.48268,-0.76276,-54.663,0.90201,-0.26182,0.34325,490.17,#32,-0.36613,0.5712,0.73463,378.23,0.33144,0.81772,-0.47062,63.517,-0.86954,0.071184,-0.48871,188.67,#33,-0.30021,0.91108,0.2825,373.95,-0.56101,-0.40817,0.72019,119.73,0.77145,0.057727,0.63366,202.13,#34,-0.73361,0.29772,-0.61088,409,0.15235,0.9481,0.2791,144.41,0.66227,0.11168,-0.7409,199.35,#35,0.78856,-0.19431,0.58345,375.04,-0.61046,-0.13278,0.78084,120.14,-0.074255,-0.97191,-0.22333,201.29
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2514, overlap = 17.37
steps = 52, shift = 6.95, angle = 2.48 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53711118 -0.84343043 -0.01169252 402.34326612
0.84313715 -0.53723416 0.02234320 56.71029643
-0.02512655 0.00214238 0.99968199 -108.76329695
Axis -0.01197623 0.00796449 0.99989656
Axis point 184.71605435 138.78965469 0.00000000
Rotation angle (degrees) 122.50217823
Shift along axis -113.11893456
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7375, correlation about mean = 0.2514, overlap = 17.37
steps = 52, shift = 6.95, angle = 2.48 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53711118 -0.84343043 -0.01169252 402.34326612
0.84313715 -0.53723416 0.02234320 56.71029643
-0.02512655 0.00214238 0.99968199 -108.76329695
Axis -0.01197623 0.00796449 0.99989656
Axis point 184.71605435 138.78965469 0.00000000
Rotation angle (degrees) 122.50217823
Shift along axis -113.11893456
> view matrix models
> #24,-0.97307,0.12581,-0.19317,613.1,0.12312,-0.42483,-0.89686,394.2,-0.1949,-0.89649,0.3979,373.89,#26,-0.82833,-0.40846,-0.38344,439.82,0.54267,-0.75505,-0.36799,95.783,-0.1392,-0.5129,0.84709,218.11,#27,0.22854,0.79804,-0.55758,425.48,0.90671,-0.38302,-0.17657,116.65,-0.35448,-0.46521,-0.81113,250.9,#28,-0.37766,0.021979,-0.92568,480.58,-0.32525,0.93286,0.15485,164.56,0.86694,0.35956,-0.34516,240.38,#29,0.71479,0.68091,-0.1595,358.67,-0.11976,0.34388,0.93134,143.06,0.68901,-0.64661,0.32735,238.63,#30,0.34705,0.038416,0.93706,405.89,0.87078,0.35786,-0.33717,128.09,-0.34829,0.93299,0.090743,273.03,#31,-0.10615,-0.7955,-0.59659,627.45,0.33279,0.53696,-0.77519,-89.595,0.93701,-0.28082,0.20773,490.55,#32,-0.27582,0.58278,0.76439,381.09,0.43485,0.78486,-0.44148,69.757,-0.85722,0.21063,-0.4699,180.2,#33,-0.38425,0.89121,0.24104,377.02,-0.62905,-0.44383,0.63821,124.33,0.67576,0.093606,0.73116,199.29,#34,-0.78747,0.31013,-0.53264,412.79,0.1067,0.91973,0.37776,147.92,0.60705,0.24064,-0.75736,202.35,#35,0.77629,-0.10714,0.62121,378.19,-0.62647,-0.021597,0.77914,124.79,-0.07006,-0.99401,-0.083884,198.59
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7374, correlation about mean = 0.2514, overlap = 17.37
steps = 92, shift = 7.44, angle = 7.78 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53702676 -0.84348427 -0.01168654 402.33384056
0.84319403 -0.53714987 0.02222297 56.72606806
-0.02502215 0.00208031 0.99968474 -108.76693197
Axis -0.01194099 0.00790562 0.99989745
Axis point 184.70886211 138.80604607 0.00000000
Rotation angle (degrees) 122.49635404
Shift along axis -113.11158615
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7374, correlation about mean = 0.2514, overlap = 17.37
steps = 92, shift = 7.44, angle = 7.78 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53702676 -0.84348427 -0.01168654 402.33384056
0.84319403 -0.53714987 0.02222297 56.72606806
-0.02502215 0.00208031 0.99968474 -108.76693197
Axis -0.01194099 0.00790562 0.99989745
Axis point 184.70886211 138.80604607 0.00000000
Rotation angle (degrees) 122.49635404
Shift along axis -113.11158615
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7374, correlation about mean = 0.2514, overlap = 17.37
steps = 92, shift = 7.44, angle = 7.78 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53702676 -0.84348427 -0.01168654 402.33384056
0.84319403 -0.53714987 0.02222297 56.72606806
-0.02502215 0.00208031 0.99968474 -108.76693197
Axis -0.01194099 0.00790562 0.99989745
Axis point 184.70886211 138.80604607 0.00000000
Rotation angle (degrees) 122.49635404
Shift along axis -113.11158615
> fitmap #24 inMap #25
Fit map postprocess_20231221.mrc in map emd_3720_2017_leaf.map using 18014
points
correlation = 0.7374, correlation about mean = 0.2514, overlap = 17.37
steps = 92, shift = 7.44, angle = 7.78 degrees
Position of postprocess_20231221.mrc (#24) relative to emd_3720_2017_leaf.map
(#25) coordinates:
Matrix rotation and translation
-0.53702676 -0.84348427 -0.01168654 402.33384056
0.84319403 -0.53714987 0.02222297 56.72606806
-0.02502215 0.00208031 0.99968474 -108.76693197
Axis -0.01194099 0.00790562 0.99989745
Axis point 184.70886211 138.80604607 0.00000000
Rotation angle (degrees) 122.49635404
Shift along axis -113.11158615
> select subtract #24
40824 atoms, 41582 bonds, 1 pseudobond, 5145 residues, 11 models selected
> select subtract #26
31014 atoms, 31550 bonds, 1 pseudobond, 3912 residues, 10 models selected
> select subtract #27
23513 atoms, 23931 bonds, 1 pseudobond, 2959 residues, 9 models selected
> select subtract #28
22056 atoms, 22448 bonds, 1 pseudobond, 2778 residues, 8 models selected
> select subtract #29
20599 atoms, 20965 bonds, 1 pseudobond, 2597 residues, 7 models selected
> select subtract #30
13385 atoms, 13592 bonds, 1 pseudobond, 1692 residues, 6 models selected
> select subtract #31
11923 atoms, 12111 bonds, 1 pseudobond, 1513 residues, 5 models selected
> select subtract #32
5250 atoms, 5325 bonds, 660 residues, 3 models selected
> select subtract #33
3830 atoms, 3884 bonds, 483 residues, 2 models selected
> select subtract #34
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> select subtract #35
Nothing selected
> fitmap #24 inMap #19
Fit map postprocess_20231221.mrc in map COPI_golph_linkage3_postprocess.mrc
using 18014 points
correlation = 0.8382, correlation about mean = 0.1145, overlap = 82.66
steps = 48, shift = 1.49, angle = 2.19 degrees
Position of postprocess_20231221.mrc (#24) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.97203359 0.23353650 0.02472742 476.65176931
-0.21547145 -0.84502445 -0.48939328 502.69321473
-0.09339591 -0.48103475 0.87171257 268.47354093
Axis 0.01800007 0.25437826 -0.96693728
Axis point 273.32590072 257.51648836 0.00000000
Rotation angle (degrees) 166.57451956
Shift along axis -123.14308766
> fitmap #24 inMap #19
Fit map postprocess_20231221.mrc in map COPI_golph_linkage3_postprocess.mrc
using 18014 points
correlation = 0.8382, correlation about mean = 0.1144, overlap = 82.66
steps = 28, shift = 0.02, angle = 0.00798 degrees
Position of postprocess_20231221.mrc (#24) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
-0.97202596 0.23357940 0.02462192 476.67328677
-0.21546556 -0.84506605 -0.48932404 502.68220492
-0.09348887 -0.48094083 0.87175443 268.44685604
Axis 0.01805192 0.25433313 -0.96694818
Axis point 273.34423552 257.49733342 0.00000000
Rotation angle (degrees) 166.57354635
Shift along axis -123.12059435
> fitmap #25 inMap #19
Fit map emd_3720_2017_leaf.map in map COPI_golph_linkage3_postprocess.mrc
using 65799 points
correlation = 0.9188, correlation about mean = 0.1408, overlap = 8478
steps = 48, shift = 0.0726, angle = 0.0389 degrees
Position of emd_3720_2017_leaf.map (#25) relative to
COPI_golph_linkage3_postprocess.mrc (#19) coordinates:
Matrix rotation and translation
0.31545792 -0.94500968 0.08627300 402.21544873
0.84037390 0.23598354 -0.48793802 103.41959547
0.44074713 0.22642549 0.86860433 169.26232870
Axis 0.36532989 -0.18128025 0.91305615
Axis point 62.41634809 271.10376062 0.00000000
Rotation angle (degrees) 77.87630625
Shift along axis 282.73940752
> show #26 models
> hide #!25 models
> show #27 models
> show #28 models
> show #29 models
> show #30 models
> show #31 models
> show #!32 models
> show #33 models
> show #34 models
> show #35 models
> fitmap #26 inMap #24
Fit molecule copy of CopA_F8WHL2.pdb (#26) to map postprocess_20231221.mrc
(#24) using 9810 atoms
average map value = 0.002302, steps = 180
shifted from previous position = 34.2
rotated from previous position = 9.99 degrees
atoms outside contour = 8643, contour level = 0.0037635
Position of copy of CopA_F8WHL2.pdb (#26) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.86507267 0.48271071 0.13652705 179.72237680
-0.27280766 0.68108410 -0.67948541 229.59514250
-0.42098128 0.55055863 0.72087442 210.15298064
Axis 0.79487947 0.36027322 -0.48823133
Axis point 0.00000000 -284.74933541 406.34125041
Rotation angle (degrees) 50.69002383
Shift along axis 122.97133949
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002923, steps = 140
shifted from previous position = 6.91
rotated from previous position = 7.67 degrees
atoms outside contour = 5721, contour level = 0.0037635
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.04160222 -0.73260006 0.67938679 172.38172893
-0.03782789 0.68064286 0.73163813 204.57811403
-0.99841790 0.00473800 -0.05602897 236.25128780
Axis -0.37161686 0.85775265 0.35519192
Axis point 209.22857536 0.00000000 -39.79684346
Rotation angle (degrees) 102.03412099
Shift along axis 195.33201108
> fitmap #28 inMap #24
Fit molecule copy of hArf1_P84078 (#28) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.002597, steps = 112
shifted from previous position = 12.3
rotated from previous position = 22.5 degrees
atoms outside contour = 1394, contour level = 0.0037635
Position of copy of hArf1_P84078 (#28) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.01934794 -0.31091515 0.95024071 127.82557022
-0.57176123 -0.77623084 -0.26562147 202.08556806
0.82019189 -0.54845003 -0.16275076 178.70102583
Axis -0.69639109 0.32021108 -0.64226499
Axis point 0.00000000 137.01484769 12.23739255
Rotation angle (degrees) 168.28361402
Shift along axis -139.07996225
> fitmap #29 inMap #24
Fit molecule copy of hArf1_P84078 (#29) to map postprocess_20231221.mrc (#24)
using 1457 atoms
average map value = 0.003766, steps = 72
shifted from previous position = 8.51
rotated from previous position = 7.54 degrees
atoms outside contour = 800, contour level = 0.0037635
Position of copy of hArf1_P84078 (#29) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.84474773 -0.49401404 0.20579450 243.02037754
-0.47618409 0.51835648 -0.71032053 195.90856907
0.24423341 -0.69803773 -0.67312209 220.58528669
Axis 0.27841319 -0.87129151 0.40414996
Axis point 151.37874481 0.00000000 157.29169422
Rotation angle (degrees) 178.73603375
Shift along axis -13.88386023
> fitmap #30 inMap #24
Fit molecule copy of CopBprime_O55029.pdb (#30) to map
postprocess_20231221.mrc (#24) using 7214 atoms
average map value = 0.00312, steps = 76
shifted from previous position = 4.92
rotated from previous position = 7.62 degrees
atoms outside contour = 4513, contour level = 0.0037635
Position of copy of CopBprime_O55029.pdb (#30) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.16284683 -0.17501121 -0.97100565 188.50517873
-0.01397505 -0.98363475 0.17963119 177.42546588
-0.98655238 0.04282222 0.15773601 238.57597049
Axis -0.64570587 0.07337687 0.76005247
Axis point 189.58052565 85.42232155 0.00000000
Rotation angle (degrees) 173.91881574
Shift along axis 72.63028077
> fitmap #31 inMap #24
Fit molecule copy of CopD_Q5XJY5 (#31) to map postprocess_20231221.mrc (#24)
using 1462 atoms
average map value = 0.003202, steps = 100
shifted from previous position = 7.75
rotated from previous position = 7.61 degrees
atoms outside contour = 960, contour level = 0.0037635
Position of copy of CopD_Q5XJY5 (#31) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.03867793 0.89478393 0.44482103 -96.24491555
-0.99472967 -0.07677989 0.06795391 102.81750945
0.09495737 -0.43984836 0.89303781 477.62018193
Axis -0.25548593 0.17602371 -0.95065377
Axis point -29.87862257 190.33459261 0.00000000
Rotation angle (degrees) 96.38507173
Shift along axis -411.36388547
> fitmap #44 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#44) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.002327, steps = 164
shifted from previous position = 38.1
rotated from previous position = 44.4 degrees
atoms outside contour = 6645, contour level = 0.0037635
Position of copy of CopG_Q9QZE5 (#44) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.61216261 0.43919834 -0.65754218 285.46162094
0.78865790 0.27893520 -0.54791771 122.96214473
-0.05723289 -0.85399059 -0.51713095 227.88169761
Axis -0.40322559 -0.79085760 0.46038394
Axis point 76.81675526 0.00000000 179.91059694
Rotation angle (degrees) 157.69539113
Shift along axis -107.43790246
> fitmap #32 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#32) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.002304, steps = 104
shifted from previous position = 3.4
rotated from previous position = 5.66 degrees
atoms outside contour = 5586, contour level = 0.0037635
Position of copy of CopG_Q9QZE5 (#32) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.44817827 -0.52631563 -0.72258431 218.97399207
0.39316596 -0.60988406 0.68808572 281.99701496
-0.80284293 -0.59248062 -0.06640739 239.02861561
Axis -0.81124288 0.05084409 0.58249453
Axis point -0.00000000 224.12582577 112.77046133
Rotation angle (degrees) 127.88340258
Shift along axis -24.07034965
> fitmap #32 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#32) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.002303, steps = 48
shifted from previous position = 0.0255
rotated from previous position = 0.0915 degrees
atoms outside contour = 5582, contour level = 0.0037635
Position of copy of CopG_Q9QZE5 (#32) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.44809247 -0.52626317 -0.72267572 218.97081694
0.39194556 -0.61089371 0.68788629 281.98590138
-0.80348728 -0.59148621 -0.06747036 238.97648505
Axis -0.81135093 0.05124898 0.58230852
Axis point -0.00000000 224.01146973 112.86762893
Rotation angle (degrees) 127.96178856
Shift along axis -24.05264225
> fitmap #32 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#32) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.002304, steps = 80
shifted from previous position = 0.0367
rotated from previous position = 0.0701 degrees
atoms outside contour = 5583, contour level = 0.0037635
Position of copy of CopG_Q9QZE5 (#32) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.44780713 -0.52609803 -0.72297277 218.96331223
0.39304791 -0.61043876 0.68766115 282.00765981
-0.80310778 -0.59210250 -0.06657710 238.98972733
Axis -0.81117269 0.05079323 0.58259670
Axis point 0.00000000 224.05099040 112.83280987
Rotation angle (degrees) 127.92317871
Shift along axis -24.05835120
> select add #32
6673 atoms, 6786 bonds, 1 pseudobond, 853 residues, 2 models selected
> view matrix models
> #32,-0.41942,0.54138,0.7287,377.77,0.2351,0.84011,-0.48883,67.254,-0.87682,-0.033707,-0.47964,184.63
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.41942,0.54138,0.7287,372.72,0.2351,0.84011,-0.48883,69.446,-0.87682,-0.033707,-0.47964,189.37
> fitmap #32 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#32) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.002906, steps = 92
shifted from previous position = 6.32
rotated from previous position = 14.1 degrees
atoms outside contour = 5059, contour level = 0.0037635
Position of copy of CopG_Q9QZE5 (#32) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.47154726 -0.63850037 -0.60824374 228.85343617
0.47824571 -0.39433582 0.78471670 278.61322647
-0.74089420 -0.66092097 0.11941209 254.29113821
Axis -0.78929614 0.07242513 0.60972634
Axis point 0.00000000 256.41512245 100.06668007
Rotation angle (degrees) 113.68376066
Shift along axis -5.40652946
> select add #27
14174 atoms, 14405 bonds, 1 pseudobond, 1806 residues, 3 models selected
> view matrix models
> #27,0.20363,0.781,-0.5904,416.85,0.85589,-0.43481,-0.27999,112.99,-0.47538,-0.4483,-0.75699,248.91,#32,-0.29559,0.70066,0.64939,365.21,0.41175,0.70682,-0.5752,63.578,-0.86202,0.097362,-0.49743,186.55
> select subtract #32
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> fitmap #32 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#32) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.002906, steps = 88
shifted from previous position = 3.25
rotated from previous position = 0.0132 degrees
atoms outside contour = 5051, contour level = 0.0037635
Position of copy of CopG_Q9QZE5 (#32) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.47154883 -0.63865736 -0.60807769 228.89663626
0.47818092 -0.39418923 0.78482983 278.60638802
-0.74093502 -0.66085674 0.11951430 254.30830924
Axis -0.78927551 0.07253373 0.60974013
Axis point 0.00000000 256.45192148 100.07902507
Rotation angle (degrees) 113.67592865
Shift along axis -5.39216813
> view matrix models
> #27,0.20363,0.781,-0.5904,418.54,0.85589,-0.43481,-0.27999,112.19,-0.47538,-0.4483,-0.75699,248.61
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.2004,0.78409,-0.5874,418.53,0.85683,-0.43099,-0.28299,112.19,-0.47506,-0.44659,-0.7582,248.61
> view matrix models
> #27,0.13564,0.76181,-0.63344,419.17,0.84703,-0.42082,-0.32473,112.45,-0.51394,-0.4925,-0.70236,248.58
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002923, steps = 96
shifted from previous position = 2.49
rotated from previous position = 5.09 degrees
atoms outside contour = 5726, contour level = 0.0037635
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.04206488 -0.73251848 0.67944626 172.36870294
-0.03855814 0.68073178 0.73151727 204.56621725
-0.99837058 0.00457300 -0.05687945 236.23830332
Axis -0.37168909 0.85787350 0.35482430
Axis point 209.20227656 0.00000000 -39.64656356
Rotation angle (degrees) 102.06998275
Shift along axis 195.24745974
> select subtract #27
Nothing selected
> fitmap #45 inMap #24
Fit molecule copy of CopZ1_P61924.pdb (#45) to map postprocess_20231221.mrc
(#24) using 1420 atoms
average map value = 0.002959, steps = 124
shifted from previous position = 17.3
rotated from previous position = 17.7 degrees
atoms outside contour = 1345, contour level = 0.0037635
Position of copy of CopZ1_P61924.pdb (#45) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.31392983 0.72637183 -0.61141803 307.16343514
-0.34921927 -0.68716881 -0.63705958 155.19780204
-0.88288954 0.01352695 0.46938583 206.76789307
Axis 0.50589018 0.21109378 -0.83636986
Axis point 249.20040984 38.50227007 0.00000000
Rotation angle (degrees) 139.98324224
Shift along axis 15.21782070
> fitmap #46 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#46) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.002774, steps = 124
shifted from previous position = 31.5
rotated from previous position = 41.2 degrees
atoms outside contour = 2316, contour level = 0.0037635
Position of copy of Golph3_ Q9CRA5.pdb (#46) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.36575003 0.51539000 -0.77498389 313.59398497
0.84259247 0.17030390 0.51091533 160.67810942
0.39530344 -0.83986290 -0.37197509 212.29582825
Axis -0.74343976 -0.64410139 0.18008531
Axis point 0.00000000 59.12484614 157.71167950
Rotation angle (degrees) 114.70589747
Shift along axis -298.39986990
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.002794, steps = 104
shifted from previous position = 8.54
rotated from previous position = 26.1 degrees
atoms outside contour = 2100, contour level = 0.0037635
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.89576384 -0.28618485 0.34015492 192.67335380
-0.44437077 -0.59697332 0.66795020 233.15319187
0.01190618 -0.74948054 -0.66191930 176.70751843
Axis -0.96851040 0.22428772 -0.10808620
Axis point 0.00000000 174.85960953 17.49295541
Rotation angle (degrees) 132.96601105
Shift along axis -153.41239267
> fitmap #33 inMap #24
Fit molecule copy of CopZ1_P61924.pdb (#33) to map postprocess_20231221.mrc
(#24) using 1420 atoms
average map value = 0.002877, steps = 96
shifted from previous position = 4.46
rotated from previous position = 7.12 degrees
atoms outside contour = 1168, contour level = 0.0037635
Position of copy of CopZ1_P61924.pdb (#33) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.19308292 -0.94842799 -0.25140277 223.58566804
-0.36413319 0.16866212 -0.91594766 236.56681043
0.91111251 0.26839794 -0.31278833 203.43218272
Axis 0.67315004 -0.66074228 0.33209737
Axis point -0.00000000 147.00955006 169.39527246
Rotation angle (degrees) 118.39331975
Shift along axis 61.75630170
> fitmap #35 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#35) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.00336, steps = 132
shifted from previous position = 11.2
rotated from previous position = 26.5 degrees
atoms outside contour = 958, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#35) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.97216939 0.18672263 -0.14149687 227.77682409
0.23376735 0.81303421 -0.53322437 243.08158768
0.01547674 -0.55146175 -0.83405662 215.39437003
Axis -0.11060779 -0.95202821 0.28532122
Axis point 93.88911333 0.00000000 148.59418013
Rotation angle (degrees) 175.27107242
Shift along axis -195.15783710
> fitmap #26 inMap #24
Fit molecule copy of CopA_F8WHL2.pdb (#26) to map postprocess_20231221.mrc
(#24) using 9810 atoms
average map value = 0.002302, steps = 180
shifted from previous position = 34.2
rotated from previous position = 9.99 degrees
atoms outside contour = 8643, contour level = 0.0037635
Position of copy of CopA_F8WHL2.pdb (#26) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.86507267 0.48271071 0.13652705 179.72237680
-0.27280766 0.68108410 -0.67948541 229.59514250
-0.42098128 0.55055863 0.72087442 210.15298064
Axis 0.79487947 0.36027322 -0.48823133
Axis point -0.00000000 -284.74933541 406.34125041
Rotation angle (degrees) 50.69002383
Shift along axis 122.97133949
> hide #!2 models
> show #!1 models
> show #3 models
> select add #3
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #26
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> view matrix models
> #26,-0.92759,-0.099393,-0.36013,435.15,0.2534,-0.87571,-0.41101,89.291,-0.27452,-0.4725,0.83748,214.4
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.92759,-0.099393,-0.36013,432.49,0.2534,-0.87571,-0.41101,84.793,-0.27452,-0.4725,0.83748,214.71
> fitmap #26 inMap #24
Fit molecule copy of CopA_F8WHL2.pdb (#26) to map postprocess_20231221.mrc
(#24) using 9810 atoms
average map value = 0.001845, steps = 156
shifted from previous position = 5.27
rotated from previous position = 19.5 degrees
atoms outside contour = 8454, contour level = 0.0037635
Position of copy of CopA_F8WHL2.pdb (#26) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.90002629 0.40434962 0.16264703 162.22591413
-0.20990448 0.72920305 -0.65130868 244.63191611
-0.38195913 0.55205460 0.74117672 239.12991736
Axis 0.82608622 0.37386187 -0.42167387
Axis point 0.00000000 -322.87328569 438.29947047
Rotation angle (degrees) 46.74842327
Shift along axis 124.63630121
> select subtract #26
Nothing selected
> show #7 models
> hide #7 models
> hide #3 models
> hide #34 models
> show #34 models
> select add #34
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> view matrix models
> #34,-0.92224,0.3509,-0.16231,406.9,0.30997,0.922,0.23202,135.33,0.23107,0.16366,-0.95907,195.55
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.0031, steps = 88
shifted from previous position = 4.7
rotated from previous position = 25.9 degrees
atoms outside contour = 1757, contour level = 0.0037635
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.66107851 -0.23538394 0.71243919 198.01764748
-0.68861771 -0.56740177 0.45150955 233.20995810
0.29796116 -0.78908151 -0.53718667 191.32717908
Axis -0.89618830 0.29941402 -0.32741071
Axis point 0.00000000 180.09123814 -4.24809178
Rotation angle (degrees) 136.19956454
Shift along axis -170.27733453
> view matrix models
> #34,-0.76193,0.31034,-0.56847,404.93,0.17789,0.94425,0.27705,137.7,0.62275,0.10996,-0.77465,200.4
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.0031, steps = 52
shifted from previous position = 1.73
rotated from previous position = 0.0207 degrees
atoms outside contour = 1754, contour level = 0.0037635
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.66094921 -0.23568640 0.71245916 198.02627283
-0.68875214 -0.56745433 0.45123837 233.21711085
0.29793729 -0.78895342 -0.53738801 191.32745999
Axis -0.89615863 0.29953218 -0.32738385
Axis point 0.00000000 180.10275225 -4.22827857
Rotation angle (degrees) 136.21542708
Shift along axis -170.24444387
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.0031, steps = 48
shifted from previous position = 0.0567
rotated from previous position = 0.0732 degrees
atoms outside contour = 1752, contour level = 0.0037635
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.66030485 -0.23676096 0.71270032 198.05890200
-0.68954027 -0.56712613 0.45044662 233.25118019
0.29754280 -0.78886767 -0.53773235 191.34786805
Axis -0.89597093 0.30014103 -0.32733997
Axis point 0.00000000 180.20298211 -4.21611868
Rotation angle (degrees) 136.24278023
Shift along axis -170.08257377
> hide #33 models
> show #33 models
> hide #33 models
> fitmap #33 inMap #24
Fit molecule copy of CopZ1_P61924.pdb (#33) to map postprocess_20231221.mrc
(#24) using 1420 atoms
average map value = 0.002876, steps = 64
shifted from previous position = 0.0956
rotated from previous position = 0.924 degrees
atoms outside contour = 1155, contour level = 0.0037635
Position of copy of CopZ1_P61924.pdb (#33) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.20518131 -0.94864591 -0.24077288 223.66436577
-0.36049158 0.15546011 -0.91971625 236.63008510
0.90991563 0.27550518 -0.31008135 203.48243798
Axis 0.67899746 -0.65369860 0.33412662
Axis point 0.00000000 146.12330338 169.42808387
Rotation angle (degrees) 118.34111838
Shift along axis 65.17168050
> fitmap #33 inMap #24
Fit molecule copy of CopZ1_P61924.pdb (#33) to map postprocess_20231221.mrc
(#24) using 1420 atoms
average map value = 0.002876, steps = 44
shifted from previous position = 0.0477
rotated from previous position = 0.598 degrees
atoms outside contour = 1155, contour level = 0.0037635
Position of copy of CopZ1_P61924.pdb (#33) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.21320758 -0.94850364 -0.23427202 223.69238124
-0.35729733 0.14747903 -0.92227358 236.63459720
0.90933006 0.28034049 -0.30745417 203.53949161
Axis 0.68263920 -0.64914225 0.33558613
Axis point 0.00000000 145.45071387 169.56450289
Rotation angle (degrees) 118.25417022
Shift along axis 67.39670363
> show #33 models
> hide #33 models
> show #33 models
> hide #33 models
> hide #35 models
> show #35 models
> fitmap #47 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.002919, steps = 144
shifted from previous position = 18.9
rotated from previous position = 12.6 degrees
atoms outside contour = 1339, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.98590061 0.16552841 0.02450138 307.81924023
-0.16531855 0.94089384 0.29561554 159.17828977
0.02587958 -0.29549808 0.95499273 207.30718464
Axis -0.87261537 -0.00203453 -0.48840380
Axis point 0.00000000 166.27214456 -502.67125256
Rotation angle (degrees) 19.79782964
Shift along axis -370.18127105
> show #33 models
> select add #33
3787 atoms, 3839 bonds, 475 residues, 2 models selected
> select subtract #34
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> view matrix models
> #33,-0.39359,0.89806,0.19642,372.14,-0.55439,-0.40232,0.72855,119.05,0.73331,0.17786,0.65622,194
> fitmap #33 inMap #24
Fit molecule copy of CopZ1_P61924.pdb (#33) to map postprocess_20231221.mrc
(#24) using 1420 atoms
average map value = 0.003163, steps = 92
shifted from previous position = 8.33
rotated from previous position = 16.8 degrees
atoms outside contour = 1006, contour level = 0.0037635
Position of copy of CopZ1_P61924.pdb (#33) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.16627480 -0.98606611 -0.00513179 236.52760618
-0.15296672 -0.02065199 -0.98801553 241.60078095
0.97414264 0.16506708 -0.15426920 209.38805539
Axis 0.66766798 -0.56702805 0.48238849
Axis point 0.00000000 156.51281645 152.82714666
Rotation angle (degrees) 120.28643466
Shift along axis 121.93387863
> hide #34 models
> select subtract #33
Nothing selected
> hide #!32 models
> hide #31 models
> hide #30 models
> hide #29 models
> hide #28 models
> hide #27 models
> hide #26 models
> hide #!24 models
> hide #33 models
> show #33 models
> hide #33 models
> show #33 models
> show #!24 models
> hide #35 models
> hide #33 models
> show #35 models
> select add #35
1463 atoms, 1486 bonds, 185 residues, 1 model selected
> view matrix models
> #35,0.97333,-0.01674,0.2288,371.38,-0.22779,0.047549,0.97255,117.35,-0.027159,-0.99873,0.042467,198.86
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.93449,0.019851,0.35544,371.99,-0.35592,0.031667,0.93398,117.66,0.0072849,-0.9993,0.036658,198.72
> view matrix models
> #35,0.86128,-0.068194,0.50354,374.52,-0.50035,0.058928,0.86381,117.2,-0.088579,-0.99593,0.016632,198.82
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.86128,-0.068194,0.50354,370.11,-0.50035,0.058928,0.86381,117.04,-0.088579,-0.99593,0.016632,198.08
> fitmap #47 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.002919, steps = 56
shifted from previous position = 0.0384
rotated from previous position = 0.065 degrees
atoms outside contour = 1343, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.98576158 0.16643347 0.02395818 307.78824771
-0.16603286 0.94089140 0.29522269 159.19368056
0.02659290 -0.29499703 0.95512803 207.32720157
Axis -0.87127375 -0.00388933 -0.49078195
Axis point 0.00000000 162.67625162 -501.78041708
Rotation angle (degrees) 19.79835088
Shift along axis -370.53942680
> fitmap #47 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.002919, steps = 64
shifted from previous position = 0.0488
rotated from previous position = 0.102 degrees
atoms outside contour = 1340, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.98595218 0.16512297 0.02515331 307.82261447
-0.16513598 0.94106697 0.29516614 159.19782246
0.02506776 -0.29517341 0.95511478 207.28684221
Axis -0.87271466 0.00012646 -0.48823059
Axis point 0.00000000 167.50093651 -506.06500811
Rotation angle (degrees) 19.76847979
Shift along axis -369.82495205
> fitmap #47 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.002919, steps = 64
shifted from previous position = 0.0295
rotated from previous position = 0.055 degrees
atoms outside contour = 1341, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.98589432 0.16555539 0.02457203 307.82081110
-0.16536131 0.94084161 0.29575782 159.21269344
0.02584592 -0.29564922 0.95494686 207.31580657
Axis -0.87267505 -0.00187973 -0.48829779
Axis point 0.00000000 166.46445678 -502.67182785
Rotation angle (degrees) 19.80665676
Shift along axis -370.15866765
> fitmap #47 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.002919, steps = 64
shifted from previous position = 0.0105
rotated from previous position = 0.0177 degrees
atoms outside contour = 1340, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.98590281 0.16550848 0.02454742 307.81864064
-0.16531710 0.94094037 0.29546820 159.21440921
0.02580484 -0.29536104 0.95503714 207.30437908
Axis -0.87252894 -0.00185695 -0.48855890
Axis point 0.00000000 166.20704661 -503.30600137
Rotation angle (degrees) 19.78994934
Shift along axis -370.15672507
> view matrix models
> #35,0.86128,-0.068194,0.50354,368.76,-0.50035,0.058928,0.86381,116.92,-0.088579,-0.99593,0.016632,197.82
> view matrix models
> #35,0.86128,-0.068194,0.50354,368.77,-0.50035,0.058928,0.86381,117.15,-0.088579,-0.99593,0.016632,199.22
> fitmap #47 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.002919, steps = 48
shifted from previous position = 0.0117
rotated from previous position = 0.0284 degrees
atoms outside contour = 1341, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.98595545 0.16514513 0.02487809 307.82426994
-0.16506674 0.94097017 0.29551327 159.20472438
0.02539304 -0.29546947 0.95501464 207.29997700
Axis -0.87297040 -0.00076065 -0.48777259
Axis point 0.00000000 167.63452220 -504.30181862
Rotation angle (degrees) 19.78487695
Shift along axis -369.95782203
> fitmap #47 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#47) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.002919, steps = 48
shifted from previous position = 0.0395
rotated from previous position = 0.0746 degrees
atoms outside contour = 1339, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#47) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.98600822 0.16470981 0.02566038 307.83169797
-0.16490528 0.94127963 0.29461651 159.19101872
0.02437263 -0.29472583 0.95527098 207.25830383
Axis -0.87276733 0.00190705 -0.48813272
Axis point 0.00000000 168.46706398 -509.14759745
Rotation angle (degrees) 19.73245852
Shift along axis -369.53142265
> fitmap #35 inMap #24
Fit molecule copy of CopZ2_Q9CTG7.pdb (#35) to map postprocess_20231221.mrc
(#24) using 1463 atoms
average map value = 0.003943, steps = 76
shifted from previous position = 3.19
rotated from previous position = 15.6 degrees
atoms outside contour = 807, contour level = 0.0037635
Position of copy of CopZ2_Q9CTG7.pdb (#35) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
-0.81856676 0.29507642 -0.49282696 229.55206706
0.42680317 0.88664782 -0.17803010 242.02712600
0.38443146 -0.35606962 -0.85171997 217.29612729
Axis -0.19677594 -0.96957876 0.14558933
Axis point 58.96405572 0.00000000 149.10399676
Rotation angle (degrees) 153.10277520
Shift along axis -248.19868563
> select subtract #35
Nothing selected
> show #33 models
> select add #33
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> view matrix models
> #33,-0.33953,0.93867,-0.060093,373.46,-0.72219,-0.21922,0.65604,118.03,0.60263,0.26614,0.75233,193.62
> ui mousemode right "rotate selected models"
> view matrix models
> #33,-0.61937,0.78508,-0.0050767,371.62,-0.66718,-0.52292,0.5305,115.73,0.41383,0.33196,0.84767,193.73
> ui mousemode right "translate selected models"
> view matrix models
> #33,-0.61937,0.78508,-0.0050767,367.56,-0.66718,-0.52292,0.5305,116.75,0.41383,0.33196,0.84767,193.62
> view matrix models
> #33,-0.61937,0.78508,-0.0050767,366.43,-0.66718,-0.52292,0.5305,117.56,0.41383,0.33196,0.84767,199.06
> view matrix models
> #33,-0.61937,0.78508,-0.0050767,366.75,-0.66718,-0.52292,0.5305,114.55,0.41383,0.33196,0.84767,197.9
> fitmap #33 inMap #24
Fit molecule copy of CopZ1_P61924.pdb (#33) to map postprocess_20231221.mrc
(#24) using 1420 atoms
average map value = 0.003933, steps = 72
shifted from previous position = 2.52
rotated from previous position = 27.2 degrees
atoms outside contour = 737, contour level = 0.0037635
Position of copy of CopZ1_P61924.pdb (#33) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.16509917 -0.93968387 -0.29956050 230.49601442
-0.38636569 0.21783235 -0.89625366 241.46100099
0.90744908 0.26371063 -0.32709767 218.19937857
Axis 0.65790876 -0.68459192 0.31383111
Axis point 143.36250261 0.00000000 249.48356769
Rotation angle (degrees) 118.16959859
Shift along axis 54.82085118
> select subtract #33
Nothing selected
> hide #!24 models
> show #!24 models
> hide #35 models
> hide #33 models
> show #34 models
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.0031, steps = 44
shifted from previous position = 0.0773
rotated from previous position = 0.123 degrees
atoms outside contour = 1759, contour level = 0.0037635
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.66134655 -0.23494320 0.71233590 198.01384438
-0.68835567 -0.56736615 0.45195367 233.20446720
0.29797183 -0.78923846 -0.53695013 191.32633148
Axis -0.89625794 0.29920999 -0.32740662
Axis point 0.00000000 180.07319061 -4.27043840
Rotation angle (degrees) 136.17721024
Shift along axis -170.33588153
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.0031, steps = 44
shifted from previous position = 0.0313
rotated from previous position = 0.053 degrees
atoms outside contour = 1755, contour level = 0.0037635
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.66103116 -0.23578123 0.71235175 198.04144717
-0.68874957 -0.56738370 0.45133110 233.20691681
0.29776137 -0.78897589 -0.53745252 191.32116399
Axis -0.89618237 0.29956180 -0.32729175
Axis point 0.00000000 180.10706491 -4.22572784
Rotation angle (degrees) 136.21178130
Shift along axis -170.23920897
> fitmap #34 inMap #24
Fit molecule copy of Golph3_ Q9CRA5.pdb (#34) to map postprocess_20231221.mrc
(#24) using 2367 atoms
average map value = 0.0031, steps = 48
shifted from previous position = 0.0543
rotated from previous position = 0.062 degrees
atoms outside contour = 1751, contour level = 0.0037635
Position of copy of Golph3_ Q9CRA5.pdb (#34) relative to
postprocess_20231221.mrc (#24) coordinates:
Matrix rotation and translation
0.66039269 -0.23659311 0.71267468 198.05627709
-0.68944268 -0.56713155 0.45058916 233.24789908
0.29757401 -0.78891413 -0.53764692 191.34687900
Axis -0.89599403 0.30006191 -0.32734928
Axis point 0.00000000 180.19357918 -4.22356963
Rotation angle (degrees) 136.23582773
Shift along axis -170.10569549
> hide #34 models
> show #!32 models
> select add #32
6673 atoms, 6786 bonds, 1 pseudobond, 853 residues, 2 models selected
> view matrix models
> #32,-0.29559,0.70082,0.64922,370.15,0.41182,0.70668,-0.57534,61.218,-0.86199,0.097298,-0.4975,190.36
> fitmap #32 inMap #24
Fit molecule copy of CopG_Q9QZE5 (#32) to map postprocess_20231221.mrc (#24)
using 6673 atoms
average map value = 0.002906, steps = 120
shifted from previous position = 4.38
rotated from previous position = 0.0271 degrees
atoms outside contour = 5053, contour level = 0.0037635
Position of copy of CopG_Q9QZE5 (#32) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
0.47195635 -0.63843665 -0.60799329 228.86598331
0.47812803 -0.39405195 0.78493098 278.59789211
-0.74070965 -0.66115180 0.11927914 254.30588618
Axis -0.78943333 0.07245140 0.60954558
Axis point 0.00000000 256.45096103 100.02298261
Rotation angle (degrees) 113.66624324
Shift along axis -5.47859762
> select subtract #32
Nothing selected
> hide #!32 models
> show #26 models
> hide #26 models
> show #27 models
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002923, steps = 136
shifted from previous position = 0.0167
rotated from previous position = 0.0633 degrees
atoms outside contour = 5723, contour level = 0.0037635
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.04120464 -0.73285767 0.67913314 172.36563468
-0.03806305 0.68036835 0.73188122 204.54939790
-0.99842545 0.00430702 -0.05592913 236.23896056
Axis -0.37195243 0.85760601 0.35519477
Axis point 209.29692826 0.00000000 -39.84186820
Rotation angle (degrees) 102.02759160
Shift along axis 195.22181885
> fitmap #27 inMap #24
Fit molecule copy of CopB_Q9JIF7.pdb (#27) to map postprocess_20231221.mrc
(#24) using 7501 atoms
average map value = 0.002923, steps = 96
shifted from previous position = 0.0318
rotated from previous position = 0.0229 degrees
atoms outside contour = 5718, contour level = 0.0037635
Position of copy of CopB_Q9JIF7.pdb (#27) relative to postprocess_20231221.mrc
(#24) coordinates:
Matrix rotation and translation
-0.04158996 -0.73289933 0.67906469 172.37761621
-0.03813008 0.68032190 0.73192090 204.57940442
-0.99840692 0.00454777 -0.05624008 236.23956794
Axis -0.37187976 0.85763098 0.35521056
Axis point 209.25825333 0.00000000 -39.80666611
Rotation angle (degrees) 102.04934748
Shift along axis 195.26467926
> hide #27 models
> show #26 models
> hide #26 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> show #12 models
> show #26 models
> show #27 models
> show #28 models
> show #29 models
> show #30 models
> show #31 models
> show #!32 models
> show #33 models
> show #34 models
> show #35 models
> show #!36 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!36 models
> show #!37 models
> hide #!37 models
> show #38 models
> show #39 models
> show #40 models
> hide #40 models
> show #40 models
> hide #40 models
> show #40 models
> show #41 models
> show #42 models
> show #43 models
> hide #43 models
> show #43 models
> show #!44 models
> hide #!44 models
> show #!44 models
> show #45 models
> show #46 models
> show #47 models
> volume #36 level 0.003958
> hide #47 models
> hide #46 models
> hide #45 models
> hide #!44 models
> hide #43 models
> hide #42 models
> hide #41 models
> hide #40 models
> hide #39 models
> hide #38 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #!19 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240126_linkage_3_fitting_v1.cxs"
——— End of log from Fri Jan 26 14:05:24 2024 ———
opened ChimeraX session
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #3 models
> show #3 models
> hide #!19 models
> show #!23 models
> hide #!23 models
> show #!21 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #!9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #!21 models
> show #!21 models
> hide #!24 models
> show #!24 models
> hide #26 models
> hide #27 models
> hide #28 models
> hide #29 models
> hide #30 models
> hide #31 models
> hide #!32 models
> hide #33 models
> hide #34 models
> hide #35 models
> show #!36 models
> show #!48 models
> hide #!48 models
> show #!48 models
> hide #!48 models
> close #60
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_linkage_4_fitting_v1.cxs"
> hide #!24 models
> show #!24 models
> show #!25 models
> hide #!24 models
> hide #!36 models
> select add #25
2 models selected
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/5nzv_COPI_coat_linkage4.cif"
5nzv_COPI_coat_linkage4.cif title:
The structure of the COPI coat linkage IV [more info...]
Chain information for 5nzv_COPI_coat_linkage4.cif #60
---
Chain | Description | UniProt
A H | Coatomer subunit alpha | COPA_MOUSE 1-1224
B I | Coatomer subunit beta | COPB_MOUSE 16-968
C J | Coatomer subunit beta' | COPB2_MOUSE 1-905
D N | Coatomer subunit delta | COPD_MOUSE 1-511
E O | Coatomer subunit epsilon | COPE_MOUSE 1-308
F M P R T | ADP-ribosylation factor 1 | ARF1_YEAST 1-181
G K Q | Coatomer subunit gamma-1 | COPG1_MOUSE 1-874
L S U Z | Coatomer subunit zeta-1 | COPZ1_MOUSE 1-177
> hide #!60 atoms
> show #!60 cartoons
[Repeated 1 time(s)]
> hide #!60 models
> show #!60 models
> select subtract #25
Nothing selected
> select #60/A
4503 atoms, 4501 bonds, 1 pseudobond, 1126 residues, 2 models selected
> color sel blue
> select #60/H
4503 atoms, 4501 bonds, 1 pseudobond, 1126 residues, 2 models selected
> color sel blue
> select #60/B
3198 atoms, 3193 bonds, 4 pseudobonds, 800 residues, 2 models selected
> color sel dark green
> select #60/I
3198 atoms, 3193 bonds, 4 pseudobonds, 800 residues, 2 models selected
> color sel dark green
> select #60/C
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> color sel cyan
> select #60/J
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> color sel cyan
> select #60/D
1707 atoms, 1704 bonds, 2 pseudobonds, 427 residues, 2 models selected
> color sel sienna
> select #60/N
706 atoms, 704 bonds, 1 pseudobond, 177 residues, 2 models selected
> color sel sienna
[Repeated 1 time(s)]
> select #60/E
1169 atoms, 1168 bonds, 292 residues, 1 model selected
> color sel orange
> select #60/O
1169 atoms, 1168 bonds, 292 residues, 1 model selected
> color sel orange
> select #60/G
3190 atoms, 3188 bonds, 1 pseudobond, 798 residues, 2 models selected
> color sel lime green
> select #60/K
2239 atoms, 2237 bonds, 1 pseudobond, 560 residues, 2 models selected
> color sel lime green
> select #60/Q
2239 atoms, 2237 bonds, 1 pseudobond, 560 residues, 2 models selected
> color sel lime green
> select #60/L
555 atoms, 554 bonds, 139 residues, 1 model selected
> color sel yellow
> select #60/S
555 atoms, 554 bonds, 139 residues, 1 model selected
> color sel yellow
> select #60/U
555 atoms, 554 bonds, 139 residues, 1 model selected
> color sel yellow
> select #60/Z
555 atoms, 554 bonds, 139 residues, 1 model selected
> color sel yellow
> select #60/F
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #60/M
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #60/P
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #60/P
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #60/R
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #60/T
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
[Repeated 1 time(s)]
> select add #60
39958 atoms, 39920 bonds, 16 pseudobonds, 9995 residues, 2 models selected
> select subtract #60
Nothing selected
> hide #!25 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_linkage_4_fitting_v2.cxs"
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> hide #!21 models
> select add #60
39958 atoms, 39920 bonds, 16 pseudobonds, 9995 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #60,1,0,0,37.035,0,1,0,148.62,0,0,1,164.59
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.88046,-0.40119,-0.25267,199.92,0.41104,0.9115,-0.014964,65.488,0.23631,-0.090682,0.96744,129.73
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.88046,-0.40119,-0.25267,168.79,0.41104,0.9115,-0.014964,111.56,0.23631,-0.090682,0.96744,138.66
> view matrix models
> #60,0.88046,-0.40119,-0.25267,173.29,0.41104,0.9115,-0.014964,98.13,0.23631,-0.090682,0.96744,98.534
> ui mousemode right "rotate selected models"
> view matrix models
> #60,0.75569,-0.38828,-0.52742,256.19,0.54343,0.82121,0.17406,46.108,0.36553,-0.41815,0.83159,160.09
> view matrix models
> #60,0.76494,-0.3632,-0.53193,249.54,0.52274,0.83256,0.18326,47.209,0.37631,-0.41825,0.82672,158.33
> ui mousemode right "translate selected models"
> view matrix models
> #60,0.76494,-0.3632,-0.53193,227.87,0.52274,0.83256,0.18326,56.959,0.37631,-0.41825,0.82672,126.46
> view matrix models
> #60,0.76494,-0.3632,-0.53193,220.4,0.52274,0.83256,0.18326,55.122,0.37631,-0.41825,0.82672,131.33
> select subtract #60
Nothing selected
> ui tool show "Fit in Map"
> show #!21 models
> hide #!1 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #8 models
> hide #!9 models
> hide #10 models
> hide #11 models
> select add #60
39958 atoms, 39920 bonds, 16 pseudobonds, 9995 residues, 2 models selected
> view matrix models
> #60,0.76494,-0.3632,-0.53193,216.67,0.52274,0.83256,0.18326,47.042,0.37631,-0.41825,0.82672,132
> view matrix models
> #60,0.76494,-0.3632,-0.53193,218.27,0.52274,0.83256,0.18326,38.966,0.37631,-0.41825,0.82672,133.84
> view matrix models
> #60,0.76494,-0.3632,-0.53193,228.16,0.52274,0.83256,0.18326,37.074,0.37631,-0.41825,0.82672,136.97
> fitmap #60 inMap #21
Fit molecule 5nzv_COPI_coat_linkage4.cif (#60) to map
COPI_golph_linkage4_postprocess.mrc (#21) using 39958 atoms
average map value = 0.5448, steps = 116
shifted from previous position = 17.2
rotated from previous position = 12.4 degrees
atoms outside contour = 14338, contour level = 0.49979
Position of 5nzv_COPI_coat_linkage4.cif (#60) relative to
COPI_golph_linkage4_postprocess.mrc (#21) coordinates:
Matrix rotation and translation
-0.86035372 0.50969732 -0.00033404 340.70998833
-0.50956209 -0.86014019 -0.02247969 533.98917184
-0.01174515 -0.01917027 0.99974725 172.36839673
Axis 0.00324666 0.01119474 -0.99993207
Axis point 244.03857465 221.21265529 0.00000000
Rotation angle (degrees) 149.35852660
Shift along axis -165.27264720
> combine #60
> select subtract #60
Nothing selected
> select add #61
39958 atoms, 39920 bonds, 16 pseudobonds, 9995 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #61,-0.88507,0.10712,-0.45297,545.09,-0.17602,-0.97792,0.11267,612.88,-0.4309,0.17945,0.88438,214.46
> ui mousemode right "translate selected models"
> view matrix models
> #61,-0.88507,0.10712,-0.45297,432.57,-0.17602,-0.97792,0.11267,530.18,-0.4309,0.17945,0.88438,194.95
> view matrix models
> #61,-0.88507,0.10712,-0.45297,453.48,-0.17602,-0.97792,0.11267,515.8,-0.4309,0.17945,0.88438,159.62
> view matrix models
> #61,-0.88507,0.10712,-0.45297,427.53,-0.17602,-0.97792,0.11267,521.08,-0.4309,0.17945,0.88438,143.87
> ui mousemode right "rotate selected models"
> view matrix models
> #61,-0.46993,0.75114,-0.46363,191.02,-0.72552,-0.62785,-0.28183,665.59,-0.50278,0.20393,0.84001,165.76
> view matrix models
> #61,-0.60124,0.60127,-0.52629,267.65,-0.48832,-0.79781,-0.35362,654.59,-0.6325,0.044382,0.77329,244.78
> ui mousemode right "translate selected models"
> view matrix models
> #61,-0.60124,0.60127,-0.52629,276.46,-0.48832,-0.79781,-0.35362,684.67,-0.6325,0.044382,0.77329,254.69
> ui mousemode right "translate selected models"
> view matrix models
> #61,-0.60124,0.60127,-0.52629,288.26,-0.48832,-0.79781,-0.35362,672.13,-0.6325,0.044382,0.77329,229.78
> ui mousemode right "rotate selected models"
> view matrix models
> #61,-0.58591,0.54673,-0.59816,309.75,-0.38735,-0.83729,-0.38588,660.98,-0.7118,0.0056101,0.70236,271.85
> view matrix models
> #61,-0.68594,0.43226,-0.58535,356.31,-0.40681,-0.89478,-0.18404,638.22,-0.60331,0.11188,0.78962,205.2
> ui mousemode right "translate selected models"
> view matrix models
> #61,-0.68594,0.43226,-0.58535,373.1,-0.40681,-0.89478,-0.18404,638.85,-0.60331,0.11188,0.78962,220.16
> fitmap #61 inMap #21
Fit molecule copy of 5nzv_COPI_coat_linkage4.cif (#61) to map
COPI_golph_linkage4_postprocess.mrc (#21) using 39958 atoms
average map value = 0.5448, steps = 104
shifted from previous position = 22.2
rotated from previous position = 16.4 degrees
atoms outside contour = 14328, contour level = 0.49979
Position of copy of 5nzv_COPI_coat_linkage4.cif (#61) relative to
COPI_golph_linkage4_postprocess.mrc (#21) coordinates:
Matrix rotation and translation
0.86035795 -0.50969014 0.00039665 203.60052554
0.50955528 0.86014769 0.02234648 10.35119498
-0.01173096 -0.01902386 0.99975021 172.32402514
Axis -0.04055292 0.01188799 0.99910667
Axis point 89.96540407 387.86258211 0.00000000
Rotation angle (degrees) 30.66905056
Shift along axis 164.03654079
> select subtract #61
Nothing selected
> hide #!61 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> hide #7 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_linkage_4_fitting_v3.cxs"
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!24 models
> hide #!24 models
> close #24
> close #25
> close #26-31,33-35,38-43,45-47,50-55,57-59#32,36-37,44,48-49,56,60-61
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v1.cxs"
> show #!1 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #!9 models
> show #10 models
> show #11 models
> show #12 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/3kn1_Golph3_xtal.cif"
3kn1_Golph3_xtal.cif title:
Crystal Structure of Golgi Phosphoprotein 3 N-term Truncation Variant [more
info...]
Chain information for 3kn1_Golph3_xtal.cif #24
---
Chain | Description | UniProt
A | Golgi phosphoprotein 3 | GOLP3_HUMAN 52-298
Non-standard residues in 3kn1_Golph3_xtal.cif #24
---
SO4 — sulfate ion
3kn1_Golph3_xtal.cif mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> select add #24
1934 atoms, 1950 bonds, 254 residues, 1 model selected
> color #24 #d783ffff
> color #24 #ae14ffff
> view matrix models #24,1,0,0,76.862,0,1,0,319.67,0,0,1,20.57
> view matrix models #24,1,0,0,244.68,0,1,0,293.79,0,0,1,354.95
> view matrix models #24,1,0,0,319.16,0,1,0,281,0,0,1,332.02
> view matrix models #24,1,0,0,329.65,0,1,0,285.54,0,0,1,337.19
> hide #12 models
> hide #10 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> view matrix models #24,1,0,0,323.59,0,1,0,290.3,0,0,1,325.47
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.74281,-0.61084,-0.27408,346.77,-0.66844,-0.65348,-0.35518,361.6,0.03785,0.44703,-0.89372,259.81
> view matrix models
> #24,-0.055201,0.94985,-0.30778,252.19,-0.46271,-0.29749,-0.8351,333.91,-0.88479,0.096314,0.45593,295.74
> fitmap #24 inMap #1
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map postprocess_20231221.mrc (#1)
using 1934 atoms
average map value = 0.00325, steps = 76
shifted from previous position = 1.46
rotated from previous position = 33.2 degrees
atoms outside contour = 1323, contour level = 0.0036898
Position of 3kn1_Golph3_xtal.cif (#24) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
0.23196046 0.95676416 -0.17548983 148.15479830
0.01108322 -0.18299837 -0.98305074 219.64194040
-0.97266207 0.22608391 -0.05305242 161.81679309
Axis 0.69904993 0.46087770 -0.54673662
Axis point 0.00000000 -31.84998852 207.22130057
Rotation angle (degrees) 120.13539920
Shift along axis 116.32450764
> select subtract #24
Nothing selected
> hide #11 models
> select add #24
1934 atoms, 1950 bonds, 254 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select subtract #24
Nothing selected
> hide #24 models
> show #24 models
> hide #24 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/1pzd_Cow_Cterm_COPI_gamma.cif"
1pzd_Cow_Cterm_COPI_gamma.cif title:
Structural Identification of a conserved appendage domain in the carboxyl-
terminus of the COPI gamma-subunit. [more info...]
Chain information for 1pzd_Cow_Cterm_COPI_gamma.cif #25
---
Chain | Description | UniProt
A | Coatomer gamma subunit | COPG_BOVIN 555-874
Non-standard residues in 1pzd_Cow_Cterm_COPI_gamma.cif #25
---
SO4 — sulfate ion
> color #25 #25ff00ff
> select add #25
2270 atoms, 2156 bonds, 426 residues, 1 model selected
> view matrix models
> #25,0.99785,0.051021,-0.041055,-0.040446,-0.050714,0.99868,0.008493,-0.87771,0.041434,-0.0063927,0.99912,0.71759
> show #!9 models
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.99785,0.051021,-0.041055,268.32,-0.050714,0.99868,0.008493,68.422,0.041434,-0.0063927,0.99912,-94.739
> view matrix models
> #25,0.99785,0.051021,-0.041055,443.58,-0.050714,0.99868,0.008493,42.599,0.041434,-0.0063927,0.99912,275.15
> view matrix models
> #25,0.99785,0.051021,-0.041055,342.71,-0.050714,0.99868,0.008493,278.54,0.041434,-0.0063927,0.99912,101.4
> view matrix models
> #25,0.99785,0.051021,-0.041055,306.81,-0.050714,0.99868,0.008493,413.82,0.041434,-0.0063927,0.99912,395.66
> view matrix models
> #25,0.99785,0.051021,-0.041055,370.4,-0.050714,0.99868,0.008493,389.86,0.041434,-0.0063927,0.99912,396.35
> view matrix models
> #25,0.99785,0.051021,-0.041055,369.55,-0.050714,0.99868,0.008493,392.01,0.041434,-0.0063927,0.99912,392.17
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.48233,-0.84618,0.22658,354.09,-0.57775,-0.50171,-0.64381,358.99,0.65845,0.17963,-0.73087,384.48
> select subtract #25
Nothing selected
> select add #25
2270 atoms, 2156 bonds, 426 residues, 1 model selected
> view matrix models
> #25,0.35653,-0.92737,0.11347,349.48,-0.80502,-0.36657,-0.46644,358.18,0.47416,0.074953,-0.87724,378.11
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.35653,-0.92737,0.11347,390.87,-0.80502,-0.36657,-0.46644,411.96,0.47416,0.074953,-0.87724,372.42
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.56564,-0.65159,-0.50544,389.97,-0.41843,0.30138,-0.85679,421.17,0.71061,0.69613,-0.10218,392.67
> view matrix models
> #25,-0.53046,0.19734,0.82442,393.85,-0.21141,0.911,-0.3541,437.38,-0.82092,-0.36212,-0.44153,348.7
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.53046,0.19734,0.82442,363.98,-0.21141,0.911,-0.3541,405.84,-0.82092,-0.36212,-0.44153,329.07
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.75487,-0.6524,0.067339,370.77,0.24711,0.1878,-0.95061,400.07,0.60754,0.73423,0.30298,376.45
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.75487,-0.6524,0.067339,356.56,0.24711,0.1878,-0.95061,383.71,0.60754,0.73423,0.30298,398.36
> view matrix models
> #25,0.75487,-0.6524,0.067339,359.81,0.24711,0.1878,-0.95061,386.47,0.60754,0.73423,0.30298,399.6
> view matrix models
> #25,0.75487,-0.6524,0.067339,358.31,0.24711,0.1878,-0.95061,385.62,0.60754,0.73423,0.30298,399.28
> select subtract #25
Nothing selected
> select add #25
2270 atoms, 2156 bonds, 426 residues, 1 model selected
> view matrix models
> #25,0.75487,-0.6524,0.067339,361.35,0.24711,0.1878,-0.95061,389.45,0.60754,0.73423,0.30298,396.81
> view matrix models
> #25,0.75487,-0.6524,0.067339,360.11,0.24711,0.1878,-0.95061,390.36,0.60754,0.73423,0.30298,397.06
> view matrix models
> #25,0.75487,-0.6524,0.067339,359.34,0.24711,0.1878,-0.95061,388.11,0.60754,0.73423,0.30298,396.07
> select subtract #25
Nothing selected
> hide #25 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/1r4x_human_gammaCOPI_appendage.cif"
Summary of feedback from opening /Users/becca/Desktop/Postdoc/Structure
files/COPI structures/1r4x_human_gammaCOPI_appendage.cif
---
notes | Fetching CCD CAS from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/CAS/CAS.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
1r4x_human_gammaCOPI_appendage.cif title:
Crystal Structure Analys of the Gamma-COPI Appendage domain [more info...]
Chain information for 1r4x_human_gammaCOPI_appendage.cif #26
---
Chain | Description | UniProt
A | Coatomer gamma subunit | COPG_HUMAN 608-874
Non-standard residues in 1r4x_human_gammaCOPI_appendage.cif #26
---
MG — magnesium ion
> select add #26
2431 atoms, 2223 bonds, 6 pseudobonds, 529 residues, 2 models selected
> view matrix models #26,1,0,0,-212.89,0,1,0,226.41,0,0,1,231.42
> view matrix models #26,1,0,0,256.86,0,1,0,340.17,0,0,1,111.16
> view matrix models #26,1,0,0,259.06,0,1,0,226.87,0,0,1,291.2
> view matrix models #26,1,0,0,335.89,0,1,0,395.85,0,0,1,373.68
> view matrix models #26,1,0,0,334.68,0,1,0,358.65,0,0,1,373.47
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.90568,0.26692,0.32937,328.71,0.27791,0.21291,-0.93671,376.1,-0.32016,0.93991,0.11865,363.54
> view matrix models
> #26,0.93043,0.12952,0.34283,331.25,0.3157,0.19182,-0.92927,375.77,-0.18612,0.97285,0.13758,359.97
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.93043,0.12952,0.34283,324.67,0.3157,0.19182,-0.92927,388.63,-0.18612,0.97285,0.13758,359.76
> select subtract #26
Nothing selected
> ui mousemode right "rotate selected models"
> select add #26
2431 atoms, 2223 bonds, 6 pseudobonds, 529 residues, 2 models selected
> view matrix models
> #26,0.60771,0.76591,0.20992,317.51,-0.018932,0.27822,-0.96033,393.63,-0.79393,0.57963,0.18358,380.77
> view matrix models
> #26,0.40779,0.88038,0.24214,318.79,-0.10206,0.30748,-0.94607,394.58,-0.90735,0.36108,0.21524,387.86
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.40779,0.88038,0.24214,317.48,-0.10206,0.30748,-0.94607,393.41,-0.90735,0.36108,0.21524,387.64
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.23238,0.91777,0.32203,319.75,-0.075931,0.3472,-0.93471,391.91,-0.96966,0.19276,0.15037,393.08
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.23238,0.91777,0.32203,318.06,-0.075931,0.3472,-0.93471,391.25,-0.96966,0.19276,0.15037,393.06
> view matrix models
> #26,0.23238,0.91777,0.32203,320.02,-0.075931,0.3472,-0.93471,390.45,-0.96966,0.19276,0.15037,392.61
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.18279,0.84636,0.50026,321.66,-0.36681,0.5308,-0.76401,391.24,-0.91216,-0.043845,0.40748,395.38
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.18279,0.84636,0.50026,320.13,-0.36681,0.5308,-0.76401,391.23,-0.91216,-0.043845,0.40748,395.54
> view matrix models
> #26,0.18279,0.84636,0.50026,319.95,-0.36681,0.5308,-0.76401,390.34,-0.91216,-0.043845,0.40748,396.46
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.39112,0.85498,0.34062,316.41,-0.13922,0.42081,-0.8964,388.95,-0.90975,0.30318,0.28362,389.22
> view matrix models
> #26,0.33989,0.86733,0.36362,317.05,-0.088513,0.41442,-0.90577,388.12,-0.93629,0.27568,0.21763,390.75
> view matrix models
> #26,0.33005,0.86588,0.37592,317.21,-0.14277,0.43944,-0.88685,388.54,-0.93311,0.23903,0.26866,391.24
> select subtract #26
Nothing selected
> color #26 #39ff00ff
> hide #!26 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/2hf6_human_zetaCOPI_NMR.cif"
2hf6_human_zetaCOPI_NMR.cif title:
Solution structure of human zeta-COP [more info...]
Chain information for 2hf6_human_zetaCOPI_NMR.cif
---
Chain | Description | UniProt
27.1/A 27.2/A 27.3/A 27.4/A 27.5/A 27.6/A 27.7/A 27.8/A 27.9/A 27.10/A 27.11/A 27.12/A 27.13/A 27.14/A 27.15/A 27.16/A 27.17/A 27.18/A 27.19/A 27.20/A | Coatomer subunit zeta-1 | COPZ1_HUMAN 1-149
> select add #27
48140 atoms, 48500 bonds, 2980 residues, 21 models selected
> ui mousemode right "translate selected models"
> view matrix models #27,1,0,0,307.78,0,1,0,153.43,0,0,1,-18.14
> view matrix models #27,1,0,0,441.62,0,1,0,436.79,0,0,1,179.77
> view matrix models #27,1,0,0,395.34,0,1,0,287,0,0,1,282.89
> select subtract #27
Nothing selected
> color #27 #fffb00ff models
> hide #!9 models
> show #10 models
> select add #10
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> select add #27
49560 atoms, 49941 bonds, 3157 residues, 22 models selected
> hide sel atoms
> select subtract #27
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #27
48140 atoms, 48500 bonds, 2980 residues, 21 models selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select subtract #27
Nothing selected
> hide #!27 models
> hide #10 models
> show #11 models
> show #24 models
> volume #1 level 0.003379
[Repeated 1 time(s)]
> hide #11 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v2.cxs"
——— End of log from Mon Feb 12 10:40:16 2024 ———
opened ChimeraX session
> hide #24 models
> show #24 models
> hide #24 models
> show #25 models
> hide #25 models
> close #26
> close #27
> hide #!1 models
> show #!1 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #6 models
> show #5 models
> hide #6 models
> hide #5 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #24 models
> hide #24 models
> close #25
> show #24 models
> hide #24 models
> show #24 models
> hide #24 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/5nzr_COPI_coat_leaf_2017.cif"
5nzr_COPI_coat_leaf_2017.cif title:
The structure of the COPI coat leaf [more info...]
Chain information for 5nzr_COPI_coat_leaf_2017.cif #25
---
Chain | Description | UniProt
A | Coatomer subunit alpha | COPA_MOUSE 1-1224
B | Coatomer subunit beta | COPB_MOUSE 16-968
C | Coatomer subunit beta' | COPB2_MOUSE 1-905
D | Coatomer subunit delta | COPD_MOUSE 1-511
F M R | ADP-ribosylation factor 1 | ARF1_YEAST 1-181
G K | Coatomer subunit gamma-1 | COPG1_MOUSE 1-874
L Z | Coatomer subunit zeta-1 | COPZ1_MOUSE 1-177
> hide #!25 models
> show #!25 models
> hide #!25 atoms
> show #!25 cartoons
> select add #25
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #25,1,0,0,172.93,0,1,0,-26.507,0,0,1,206.31
> view matrix models #25,1,0,0,179.54,0,1,0,116.98,0,0,1,131.95
> view matrix models #25,1,0,0,244.71,0,1,0,166.5,0,0,1,128.83
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.90934,0.39096,0.14229,191.9,0.36842,-0.91558,0.16119,334.4,0.1933,-0.094151,-0.97661,347.05
> view matrix models
> #25,0.49924,0.4639,0.73182,160.19,0.54167,-0.82631,0.15427,305.6,0.67628,0.31938,-0.66381,208.92
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.49924,0.4639,0.73182,183.77,0.54167,-0.82631,0.15427,316.9,0.67628,0.31938,-0.66381,272.8
> view matrix models
> #25,0.49924,0.4639,0.73182,129.3,0.54167,-0.82631,0.15427,311.31,0.67628,0.31938,-0.66381,282.67
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.96042,-0.17233,-0.21885,263.85,-0.20654,-0.96773,-0.14434,444.68,-0.18692,0.18383,-0.96502,428.26
> ui tool show "Fit in Map"
> fitmap #25 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 18970 atoms
average map value = 0.002473, steps = 108
shifted from previous position = 9.77
rotated from previous position = 8.8 degrees
atoms outside contour = 16052, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98864984 -0.04299359 -0.14395503 131.62784376
-0.07158428 -0.97722521 -0.19976632 331.34054902
-0.13208781 0.20780386 -0.96921121 308.56082393
Axis 0.99712807 -0.02903337 -0.06994766
Axis point 0.00000000 151.24482933 176.20665529
Rotation angle (degrees) 168.20725919
Shift along axis 100.04677794
> view matrix models
> #25,-0.025335,0.99704,0.072538,207.04,0.95599,0.04538,-0.28986,219.77,-0.29229,0.062003,-0.95432,454.07
> fitmap #25 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 18970 atoms
average map value = 0.002418, steps = 84
shifted from previous position = 12
rotated from previous position = 4.08 degrees
atoms outside contour = 16464, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.06293060 0.99182167 0.11103830 99.85964341
0.96516350 0.08879327 -0.24612022 105.71410249
-0.25396683 0.09168162 -0.96285790 328.58360677
Axis 0.67825476 0.73287482 -0.05352555
Axis point 29.96063731 0.00000000 167.00415032
Rotation angle (degrees) 165.58030383
Shift along axis 127.61786286
> select subtract #25
Nothing selected
> select #25/F
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #25/M
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #25/R
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel hot pink
> select #25/A
3251 atoms, 3250 bonds, 813 residues, 1 model selected
> color sel blue
> select #25/B
3198 atoms, 3193 bonds, 4 pseudobonds, 800 residues, 2 models selected
> color sel dark green
> select #25/C
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> color sel dark cyan
> select #25/D
706 atoms, 704 bonds, 1 pseudobond, 177 residues, 2 models selected
> color sel sienna
> select #25/L
555 atoms, 554 bonds, 139 residues, 1 model selected
> color sel yellow
> select #25/Z
555 atoms, 554 bonds, 139 residues, 1 model selected
> color sel yellow
> select add #25
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> select subtract #25
Nothing selected
> select add #25
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> show #3 models
> view matrix models
> #25,0.01455,-0.060029,-0.99809,456.44,0.66933,-0.74097,0.054323,313.78,-0.74282,-0.66884,0.029398,470.18
> select subtract #25
Nothing selected
> select add #25
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> view matrix models
> #25,0.67758,0.73257,-0.065061,182,0.23949,-0.13614,0.96131,184.56,0.69537,-0.66694,-0.26769,346.41
> fitmap #25 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 18970 atoms
average map value = 0.002096, steps = 188
shifted from previous position = 3.5
rotated from previous position = 9.88 degrees
atoms outside contour = 16648, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.67668396 0.73273835 -0.07206466 69.55834155
0.36327897 -0.24714017 0.89830402 75.35116448
0.64041174 -0.63404750 -0.43342422 254.15816540
Axis -0.88585237 -0.41188259 -0.21358446
Axis point 0.00000000 93.91308587 113.87349788
Rotation angle (degrees) 120.12844703
Shift along axis -146.93848782
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.67568,0.73393,-0.069377,237.36,0.35858,-0.24497,0.90078,57.103,0.64411,-0.63352,-0.42869,411.75
> view matrix models
> #25,0.67568,0.73393,-0.069377,166.37,0.35858,-0.24497,0.90078,2.138,0.64411,-0.63352,-0.42869,474.72
> view matrix models
> #25,0.67568,0.73393,-0.069377,205.85,0.35858,-0.24497,0.90078,-26.501,0.64411,-0.63352,-0.42869,507.68
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.25988,0.36598,-0.8936,390.27,-0.5621,0.80979,0.16818,34.201,0.78518,0.45858,0.41616,265.23
> select subtract #25
Nothing selected
> select #25/D
706 atoms, 704 bonds, 1 pseudobond, 177 residues, 2 models selected
> select #25/A
3251 atoms, 3250 bonds, 813 residues, 1 model selected
> select #25/B
3198 atoms, 3193 bonds, 4 pseudobonds, 800 residues, 2 models selected
> select #25/C
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> color sel cyan
> select #25/D
706 atoms, 704 bonds, 1 pseudobond, 177 residues, 2 models selected
> select #25/G
3190 atoms, 3188 bonds, 1 pseudobond, 798 residues, 2 models selected
> color sel lime green
> select #25/K
2239 atoms, 2237 bonds, 1 pseudobond, 560 residues, 2 models selected
> color sel lime green
> hide #3 models
> show #3 models
> select add #25
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> select subtract #25
Nothing selected
> select add #25
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> view matrix models
> #25,0.28613,0.38156,-0.87894,383.85,-0.48279,0.84976,0.21173,15.732,0.82767,0.36376,0.42736,270.51
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.28613,0.38156,-0.87894,307.95,-0.48279,0.84976,0.21173,128.43,0.82767,0.36376,0.42736,63.058
> view matrix models
> #25,0.28613,0.38156,-0.87894,346.74,-0.48279,0.84976,0.21173,263.05,0.82767,0.36376,0.42736,171.48
> ui mousemode right "rotate selected models"
> view matrix models
> #25,0.28084,0.80046,-0.52952,257.34,-0.67529,0.55685,0.48363,287.48,0.68199,0.22176,0.69693,173.16
> view matrix models
> #25,0.059471,0.97884,0.19578,176.74,-0.86514,-0.047299,0.49929,378.08,0.49799,-0.19907,0.84403,226.23
> view matrix models
> #25,-0.25415,0.43249,-0.86507,398.41,-0.83663,-0.54707,-0.027707,495.03,-0.48524,0.71671,0.50088,265.28
> hide #3 models
> show #7 models
> view matrix models
> #25,0.044164,0.83121,-0.5542,282.53,-0.87692,-0.2335,-0.4201,507.62,-0.4786,0.50455,0.7186,264.55
> view matrix models
> #25,-0.31708,0.78054,-0.53872,326.39,-0.88489,-0.44785,-0.12805,500.16,-0.34121,0.43611,0.8327,244.4
> fitmap #25 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 18970 atoms
average map value = 0.004218, steps = 352
shifted from previous position = 12.1
rotated from previous position = 32.7 degrees
atoms outside contour = 9666, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.53574835 0.84388736 -0.02877183 165.88776143
-0.84419525 -0.53602985 -0.00252343 370.77841388
-0.01755205 0.02293712 0.99958281 112.96642618
Axis 0.01508047 -0.00664556 -0.99986420
Axis point 185.48326612 138.95820238 0.00000000
Rotation angle (degrees) 122.41838510
Shift along axis -112.91345026
> hide #7 models
> select subtract #25
Nothing selected
> select #25/C
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> fitmap sel inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 72
shifted from previous position = 0.567
rotated from previous position = 4.82 degrees
atoms outside contour = 1172, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47520712 0.87648107 -0.07719527 158.57604863
-0.87870795 -0.47726261 -0.00962971 369.82561667
-0.04528268 0.06325599 0.99696948 112.94642006
Axis 0.04148324 -0.01816320 -0.99897409
Axis point 191.06280682 135.30791259 0.00000000
Rotation angle (degrees) 118.53856222
Shift along axis -112.96951683
> fitmap sel inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.058
rotated from previous position = 0.0401 degrees
atoms outside contour = 1176, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47544517 0.87640361 -0.07660664 158.52057680
-0.87858084 -0.47749115 -0.00989406 369.90681967
-0.04525018 0.06260104 0.99701229 112.97990255
Axis 0.04126634 -0.01784902 -0.99898874
Axis point 191.02675926 135.40435673 0.00000000
Rotation angle (degrees) 118.55238261
Shift along axis -112.92655935
> select #25/A
3251 atoms, 3250 bonds, 813 residues, 1 model selected
> fitmap sel inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 3251 atoms
average map value = 0.003303, steps = 64
shifted from previous position = 5.19
rotated from previous position = 4.65 degrees
atoms outside contour = 2052, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.51473956 0.84718223 -0.13162612 174.81436834
-0.85624995 -0.51574917 0.02896220 363.08006962
-0.04334980 0.12761285 0.99087625 110.56112471
Axis 0.05773878 -0.05166684 -0.99699387
Axis point 191.22843747 127.46029174 0.00000000
Rotation angle (degrees) 121.31925569
Shift along axis -118.89439414
> select #25/C
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> fitmap sel inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 76
shifted from previous position = 5.71
rotated from previous position = 4.63 degrees
atoms outside contour = 1172, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47516299 0.87650032 -0.07724834 158.57912193
-0.87873512 -0.47721455 -0.00953158 369.80308546
-0.04521847 0.06335177 0.99696631 112.92997824
Axis 0.04148076 -0.01822945 -0.99897299
Axis point 191.06132364 135.28926761 0.00000000
Rotation angle (degrees) 118.53565898
Shift along axis -112.97732216
> fitmap sel inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 64
shifted from previous position = 0.00374
rotated from previous position = 0.00725 degrees
atoms outside contour = 1171, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47511100 0.87651900 -0.07735611 158.58195988
-0.87875891 -0.47716993 -0.00957243 369.80985864
-0.04530242 0.06342940 0.99695757 112.93294602
Axis 0.04154706 -0.01824251 -0.99897000
Axis point 191.07470904 135.28593923 0.00000000
Rotation angle (degrees) 118.53279373
Shift along axis -112.97426862
> select #25/K
2239 atoms, 2237 bonds, 1 pseudobond, 560 residues, 2 models selected
> fitmap sel inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 2239 atoms
average map value = 0.005453, steps = 88
shifted from previous position = 2.86
rotated from previous position = 5.24 degrees
atoms outside contour = 1101, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.52861290 0.84867362 -0.01792962 162.26120912
-0.84874757 -0.52807480 0.02765050 368.46631966
0.01399807 0.02983414 0.99945683 106.78996296
Axis 0.00128621 -0.01880619 -0.99982232
Axis point 182.93199093 138.12732719 0.00000000
Rotation angle (degrees) 121.91195324
Shift along axis -113.49173322
> select #25/K
2239 atoms, 2237 bonds, 1 pseudobond, 560 residues, 2 models selected
> select #25/G
3190 atoms, 3188 bonds, 1 pseudobond, 798 residues, 2 models selected
> fitmap sel inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 3190 atoms
average map value = 0.005086, steps = 80
shifted from previous position = 6.04
rotated from previous position = 3.82 degrees
atoms outside contour = 1594, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.56555988 0.82461095 -0.01260167 168.08525898
-0.82433303 -0.56569752 -0.02147934 374.09170490
-0.02484084 -0.00175988 0.99968986 117.01268500
Axis 0.01195766 0.00742169 -0.99990096
Axis point 183.47113140 142.86489612 0.00000000
Rotation angle (degrees) 124.45673518
Shift along axis -112.21479764
> select #25/F
635 atoms, 634 bonds, 159 residues, 1 model selected
> fitmap sel inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#25) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.002828, steps = 88
shifted from previous position = 12.4
rotated from previous position = 12 degrees
atoms outside contour = 508, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif (#25) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.39510325 0.91706351 -0.05373946 147.27708502
-0.91853641 -0.39351912 0.03786221 369.07307876
0.01357455 0.06432113 0.99783692 104.46501204
Axis 0.01440314 -0.03664296 -0.99922462
Axis point 194.55872287 133.56188379 0.00000000
Rotation angle (degrees) 113.29046977
Shift along axis -115.78668960
> select add #25
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> select subtract #25
Nothing selected
> split #25 chains
Split 5nzr_COPI_coat_leaf_2017.cif (#25) into 11 models
Chain information for 5nzr_COPI_coat_leaf_2017.cif A #25.1
---
Chain | Description
A | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif B #25.2
---
Chain | Description
B | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif C #25.3
---
Chain | Description
C | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif D #25.4
---
Chain | Description
D | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif F #25.5
---
Chain | Description
F | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif G #25.6
---
Chain | Description
G | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif K #25.7
---
Chain | Description
K | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif L #25.8
---
Chain | Description
L | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif M #25.9
---
Chain | Description
M | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif R #25.10
---
Chain | Description
R | No description available
Chain information for 5nzr_COPI_coat_leaf_2017.cif Z #25.11
---
Chain | Description
Z | No description available
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v3.cxs"
> hide #!25 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif"
Summary of feedback from opening /Users/becca/Desktop/Postdoc/Structure
files/COPI structures/3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif
---
note | Fetching CCD GNP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GNP/GNP.cif
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif title:
Crystal Structure of Arf1 Bound to the gamma/zeta-COP Core Complex [more
info...]
Chain information for 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif #26
---
Chain | Description | UniProt
A D | ADP-ribosylation factor 1 | ARF1_YEAST 18-181
B E | Coatomer subunit gamma | COPG_BOVIN 1-355
C F | Coatomer subunit zeta-1 | COPZ1_BOVIN 1-153
Non-standard residues in 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif #26
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> hide #!26 models
> show #!26 models
> hide #!26 atoms
> show #!26 cartoons
> select add #26
8970 atoms, 9117 bonds, 11 pseudobonds, 1126 residues, 3 models selected
> view matrix models
> #26,0.5277,0.75349,-0.39216,69.779,-0.81002,0.58537,0.034737,-10.163,0.25573,0.29932,0.91924,16.02
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.5277,0.75349,-0.39216,490.52,-0.81002,0.58537,0.034737,254.15,0.25573,0.29932,0.91924,-22.305
> view matrix models
> #26,0.5277,0.75349,-0.39216,219.19,-0.81002,0.58537,0.034737,382.39,0.25573,0.29932,0.91924,134.56
> view matrix models
> #26,0.5277,0.75349,-0.39216,320.35,-0.81002,0.58537,0.034737,463.15,0.25573,0.29932,0.91924,332.64
> view matrix models
> #26,0.5277,0.75349,-0.39216,388.13,-0.81002,0.58537,0.034737,370.75,0.25573,0.29932,0.91924,351.92
> select subtract #26
Nothing selected
> select #26/A
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> color sel hot pink
> hide #!1 models
> select #26/D
1306 atoms, 1331 bonds, 4 pseudobonds, 161 residues, 2 models selected
> color sel hot pink
> select #26/C
1128 atoms, 1146 bonds, 140 residues, 1 model selected
> color sel yellow
> select #26/F
1128 atoms, 1146 bonds, 140 residues, 1 model selected
> color sel yellow
> select #26/B
2069 atoms, 2100 bonds, 2 pseudobonds, 264 residues, 2 models selected
> color sel lime green
> select #26/E
2033 atoms, 2063 bonds, 2 pseudobonds, 260 residues, 2 models selected
> color sel lime green
> select add #26
8970 atoms, 9117 bonds, 11 pseudobonds, 1126 residues, 3 models selected
> select subtract #26
Nothing selected
> show #!1 models
> show #10 models
> hide #!26 models
> hide #10 models
> show #10 models
> show #!26 models
> select add #26
8970 atoms, 9117 bonds, 11 pseudobonds, 1126 residues, 3 models selected
> view matrix models
> #26,0.5277,0.75349,-0.39216,405.68,-0.81002,0.58537,0.034737,423.29,0.25573,0.29932,0.91924,314.52
> view matrix models
> #26,0.5277,0.75349,-0.39216,390.94,-0.81002,0.58537,0.034737,414.92,0.25573,0.29932,0.91924,300.71
> view matrix models
> #26,0.5277,0.75349,-0.39216,387.65,-0.81002,0.58537,0.034737,411.98,0.25573,0.29932,0.91924,309.59
> split #26 chains
Split 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif (#26) into 6 models
Chain information for 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A #26.1
---
Chain | Description
A | No description available
Chain information for 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B #26.2
---
Chain | Description
B | No description available
Chain information for 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C #26.3
---
Chain | Description
C | No description available
Chain information for 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif D #26.4
---
Chain | Description
D | No description available
Chain information for 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif E #26.5
---
Chain | Description
E | No description available
Chain information for 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif F #26.6
---
Chain | Description
F | No description available
> hide #!26 models
> show #!26 models
> hide #!26.4 models
> close #26.4
> close #26.5
> close #26.6
> select add #26.1
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select add #26.2
3375 atoms, 3431 bonds, 5 pseudobonds, 425 residues, 4 models selected
> select add #26.3
4503 atoms, 4577 bonds, 5 pseudobonds, 565 residues, 5 models selected
> view matrix models
> #26.1,0.5277,0.75349,-0.39216,426.69,-0.81002,0.58537,0.034737,412.79,0.25573,0.29932,0.91924,272.48,#26.2,0.5277,0.75349,-0.39216,426.69,-0.81002,0.58537,0.034737,412.79,0.25573,0.29932,0.91924,272.48,#26.3,0.5277,0.75349,-0.39216,426.69,-0.81002,0.58537,0.034737,412.79,0.25573,0.29932,0.91924,272.48
> hide #!1 models
> view matrix models
> #26.1,0.5277,0.75349,-0.39216,424.99,-0.81002,0.58537,0.034737,407.1,0.25573,0.29932,0.91924,299.03,#26.2,0.5277,0.75349,-0.39216,424.99,-0.81002,0.58537,0.034737,407.1,0.25573,0.29932,0.91924,299.03,#26.3,0.5277,0.75349,-0.39216,424.99,-0.81002,0.58537,0.034737,407.1,0.25573,0.29932,0.91924,299.03
> ui mousemode right "rotate selected models"
> view matrix models
> #26.1,0.97843,-0.20567,-0.019332,362.38,0.19832,0.9614,-0.19075,417.76,0.057819,0.1828,0.98145,293.01,#26.2,0.97843,-0.20567,-0.019332,362.38,0.19832,0.9614,-0.19075,417.76,0.057819,0.1828,0.98145,293.01,#26.3,0.97843,-0.20567,-0.019332,362.38,0.19832,0.9614,-0.19075,417.76,0.057819,0.1828,0.98145,293.01
> view matrix models
> #26.1,-0.96419,0.243,0.10625,412,-0.18031,-0.30681,-0.93454,368.07,-0.1945,-0.92023,0.33964,247.68,#26.2,-0.96419,0.243,0.10625,412,-0.18031,-0.30681,-0.93454,368.07,-0.1945,-0.92023,0.33964,247.68,#26.3,-0.96419,0.243,0.10625,412,-0.18031,-0.30681,-0.93454,368.07,-0.1945,-0.92023,0.33964,247.68
> view matrix models
> #26.1,-0.46491,-0.45586,-0.75898,382.96,0.84312,0.033663,-0.53667,363.96,0.2702,-0.88941,0.36869,240.04,#26.2,-0.46491,-0.45586,-0.75898,382.96,0.84312,0.033663,-0.53667,363.96,0.2702,-0.88941,0.36869,240.04,#26.3,-0.46491,-0.45586,-0.75898,382.96,0.84312,0.033663,-0.53667,363.96,0.2702,-0.88941,0.36869,240.04
> ui mousemode right "translate selected models"
> view matrix models
> #26.1,-0.46491,-0.45586,-0.75898,317.7,0.84312,0.033663,-0.53667,369.45,0.2702,-0.88941,0.36869,225.13,#26.2,-0.46491,-0.45586,-0.75898,317.7,0.84312,0.033663,-0.53667,369.45,0.2702,-0.88941,0.36869,225.13,#26.3,-0.46491,-0.45586,-0.75898,317.7,0.84312,0.033663,-0.53667,369.45,0.2702,-0.88941,0.36869,225.13
> ui mousemode right "rotate selected models"
> view matrix models
> #26.1,0.45164,0.34272,-0.82375,352.65,-0.58768,0.80897,0.01436,423.44,0.6713,0.47761,0.56678,293.68,#26.2,0.45164,0.34272,-0.82375,352.65,-0.58768,0.80897,0.01436,423.44,0.6713,0.47761,0.56678,293.68,#26.3,0.45164,0.34272,-0.82375,352.65,-0.58768,0.80897,0.01436,423.44,0.6713,0.47761,0.56678,293.68
> view matrix models
> #26.1,0.073239,0.58986,-0.80418,373.62,0.73413,-0.57767,-0.35686,331.44,-0.67505,-0.56423,-0.47534,273.5,#26.2,0.073239,0.58986,-0.80418,373.62,0.73413,-0.57767,-0.35686,331.44,-0.67505,-0.56423,-0.47534,273.5,#26.3,0.073239,0.58986,-0.80418,373.62,0.73413,-0.57767,-0.35686,331.44,-0.67505,-0.56423,-0.47534,273.5
> show #5 models
> hide #5 models
> show #6 models
> show #!9 models
> view matrix models
> #26.1,0.037974,0.8909,-0.4526,383.45,0.91974,-0.20824,-0.33273,349.88,-0.39068,-0.40364,-0.82731,287.23,#26.2,0.037974,0.8909,-0.4526,383.45,0.91974,-0.20824,-0.33273,349.88,-0.39068,-0.40364,-0.82731,287.23,#26.3,0.037974,0.8909,-0.4526,383.45,0.91974,-0.20824,-0.33273,349.88,-0.39068,-0.40364,-0.82731,287.23
> ui mousemode right "translate selected models"
> view matrix models
> #26.1,0.037974,0.8909,-0.4526,445.91,0.91974,-0.20824,-0.33273,303.39,-0.39068,-0.40364,-0.82731,286.61,#26.2,0.037974,0.8909,-0.4526,445.91,0.91974,-0.20824,-0.33273,303.39,-0.39068,-0.40364,-0.82731,286.61,#26.3,0.037974,0.8909,-0.4526,445.91,0.91974,-0.20824,-0.33273,303.39,-0.39068,-0.40364,-0.82731,286.61
> view matrix models
> #26.1,0.037974,0.8909,-0.4526,439.11,0.91974,-0.20824,-0.33273,307.97,-0.39068,-0.40364,-0.82731,295.85,#26.2,0.037974,0.8909,-0.4526,439.11,0.91974,-0.20824,-0.33273,307.97,-0.39068,-0.40364,-0.82731,295.85,#26.3,0.037974,0.8909,-0.4526,439.11,0.91974,-0.20824,-0.33273,307.97,-0.39068,-0.40364,-0.82731,295.85
> ui mousemode right "rotate selected models"
> view matrix models
> #26.1,-0.89543,0.25326,-0.36615,416.35,0.20899,0.9653,0.1566,380.35,0.39311,0.063706,-0.91728,311.28,#26.2,-0.89543,0.25326,-0.36615,416.35,0.20899,0.9653,0.1566,380.35,0.39311,0.063706,-0.91728,311.28,#26.3,-0.89543,0.25326,-0.36615,416.35,0.20899,0.9653,0.1566,380.35,0.39311,0.063706,-0.91728,311.28
> view matrix models
> #26.1,0.047267,0.99719,-0.058155,438.2,0.62825,0.015585,0.77786,300.81,0.77658,-0.073303,-0.62575,292.69,#26.2,0.047267,0.99719,-0.058155,438.2,0.62825,0.015585,0.77786,300.81,0.77658,-0.073303,-0.62575,292.69,#26.3,0.047267,0.99719,-0.058155,438.2,0.62825,0.015585,0.77786,300.81,0.77658,-0.073303,-0.62575,292.69
> view matrix models
> #26.1,0.77259,0.19013,-0.60576,396.95,0.39113,0.60902,0.69001,341.55,0.50012,-0.77003,0.39616,229.56,#26.2,0.77259,0.19013,-0.60576,396.95,0.39113,0.60902,0.69001,341.55,0.50012,-0.77003,0.39616,229.56,#26.3,0.77259,0.19013,-0.60576,396.95,0.39113,0.60902,0.69001,341.55,0.50012,-0.77003,0.39616,229.56
> ui mousemode right "translate selected models"
> view matrix models
> #26.1,0.77259,0.19013,-0.60576,361.88,0.39113,0.60902,0.69001,352.33,0.50012,-0.77003,0.39616,257.47,#26.2,0.77259,0.19013,-0.60576,361.88,0.39113,0.60902,0.69001,352.33,0.50012,-0.77003,0.39616,257.47,#26.3,0.77259,0.19013,-0.60576,361.88,0.39113,0.60902,0.69001,352.33,0.50012,-0.77003,0.39616,257.47
> view matrix models
> #26.1,0.77259,0.19013,-0.60576,361.63,0.39113,0.60902,0.69001,346.51,0.50012,-0.77003,0.39616,264.79,#26.2,0.77259,0.19013,-0.60576,361.63,0.39113,0.60902,0.69001,346.51,0.50012,-0.77003,0.39616,264.79,#26.3,0.77259,0.19013,-0.60576,361.63,0.39113,0.60902,0.69001,346.51,0.50012,-0.77003,0.39616,264.79
> ui mousemode right "rotate selected models"
> view matrix models
> #26.1,0.4891,-0.10273,-0.86616,353.6,0.76848,-0.41898,0.48363,286.53,-0.41259,-0.90216,-0.12598,277.47,#26.2,0.4891,-0.10273,-0.86616,353.6,0.76848,-0.41898,0.48363,286.53,-0.41259,-0.90216,-0.12598,277.47,#26.3,0.4891,-0.10273,-0.86616,353.6,0.76848,-0.41898,0.48363,286.53,-0.41259,-0.90216,-0.12598,277.47
> ui mousemode right "translate selected models"
> view matrix models
> #26.1,0.4891,-0.10273,-0.86616,353.73,0.76848,-0.41898,0.48363,291.02,-0.41259,-0.90216,-0.12598,271.9,#26.2,0.4891,-0.10273,-0.86616,353.73,0.76848,-0.41898,0.48363,291.02,-0.41259,-0.90216,-0.12598,271.9,#26.3,0.4891,-0.10273,-0.86616,353.73,0.76848,-0.41898,0.48363,291.02,-0.41259,-0.90216,-0.12598,271.9
> view matrix models
> #26.1,0.4891,-0.10273,-0.86616,356.51,0.76848,-0.41898,0.48363,292.24,-0.41259,-0.90216,-0.12598,276.24,#26.2,0.4891,-0.10273,-0.86616,356.51,0.76848,-0.41898,0.48363,292.24,-0.41259,-0.90216,-0.12598,276.24,#26.3,0.4891,-0.10273,-0.86616,356.51,0.76848,-0.41898,0.48363,292.24,-0.41259,-0.90216,-0.12598,276.24
> view matrix models
> #26.1,0.4891,-0.10273,-0.86616,353.33,0.76848,-0.41898,0.48363,285.52,-0.41259,-0.90216,-0.12598,275.67,#26.2,0.4891,-0.10273,-0.86616,353.33,0.76848,-0.41898,0.48363,285.52,-0.41259,-0.90216,-0.12598,275.67,#26.3,0.4891,-0.10273,-0.86616,353.33,0.76848,-0.41898,0.48363,285.52,-0.41259,-0.90216,-0.12598,275.67
> ui mousemode right "rotate selected models"
> view matrix models
> #26.1,0.798,-0.3484,-0.49174,326.24,0.6025,0.4796,0.63795,335.26,0.013581,-0.80536,0.59263,259.36,#26.2,0.798,-0.3484,-0.49174,326.24,0.6025,0.4796,0.63795,335.26,0.013581,-0.80536,0.59263,259.36,#26.3,0.798,-0.3484,-0.49174,326.24,0.6025,0.4796,0.63795,335.26,0.013581,-0.80536,0.59263,259.36
> view matrix models
> #26.1,0.80191,-0.25129,-0.54202,332.98,0.5903,0.47312,0.65399,334.61,0.092098,-0.8444,0.52773,257.47,#26.2,0.80191,-0.25129,-0.54202,332.98,0.5903,0.47312,0.65399,334.61,0.092098,-0.8444,0.52773,257.47,#26.3,0.80191,-0.25129,-0.54202,332.98,0.5903,0.47312,0.65399,334.61,0.092098,-0.8444,0.52773,257.47
> ui mousemode right "translate selected models"
> view matrix models
> #26.1,0.80191,-0.25129,-0.54202,341.59,0.5903,0.47312,0.65399,350.85,0.092098,-0.8444,0.52773,258.32,#26.2,0.80191,-0.25129,-0.54202,341.59,0.5903,0.47312,0.65399,350.85,0.092098,-0.8444,0.52773,258.32,#26.3,0.80191,-0.25129,-0.54202,341.59,0.5903,0.47312,0.65399,350.85,0.092098,-0.8444,0.52773,258.32
> hide #!9 models
> view matrix models
> #26.1,0.80191,-0.25129,-0.54202,337.98,0.5903,0.47312,0.65399,350.92,0.092098,-0.8444,0.52773,260.48,#26.2,0.80191,-0.25129,-0.54202,337.98,0.5903,0.47312,0.65399,350.92,0.092098,-0.8444,0.52773,260.48,#26.3,0.80191,-0.25129,-0.54202,337.98,0.5903,0.47312,0.65399,350.92,0.092098,-0.8444,0.52773,260.48
> ui mousemode right "rotate selected models"
> view matrix models
> #26.1,0.84276,-0.097083,-0.52947,346.34,0.52714,-0.050334,0.84828,316.45,-0.109,-0.994,0.0087571,265.17,#26.2,0.84276,-0.097083,-0.52947,346.34,0.52714,-0.050334,0.84828,316.45,-0.109,-0.994,0.0087571,265.17,#26.3,0.84276,-0.097083,-0.52947,346.34,0.52714,-0.050334,0.84828,316.45,-0.109,-0.994,0.0087571,265.17
> view matrix models
> #26.1,0.8967,-0.046603,-0.44017,347.14,0.44234,0.13053,0.8873,327.01,0.016103,-0.99035,0.13766,260.95,#26.2,0.8967,-0.046603,-0.44017,347.14,0.44234,0.13053,0.8873,327.01,0.016103,-0.99035,0.13766,260.95,#26.3,0.8967,-0.046603,-0.44017,347.14,0.44234,0.13053,0.8873,327.01,0.016103,-0.99035,0.13766,260.95
> view matrix models
> #26.1,0.86269,-0.096518,-0.49643,345.79,0.48048,-0.14987,0.86411,310.91,-0.1578,-0.98398,-0.082914,267.9,#26.2,0.86269,-0.096518,-0.49643,345.79,0.48048,-0.14987,0.86411,310.91,-0.1578,-0.98398,-0.082914,267.9,#26.3,0.86269,-0.096518,-0.49643,345.79,0.48048,-0.14987,0.86411,310.91,-0.1578,-0.98398,-0.082914,267.9
> view matrix models
> #26.1,0.73916,-0.64204,-0.20354,307.63,0.51086,0.3375,0.79064,340.63,-0.43893,-0.68839,0.57746,277.07,#26.2,0.73916,-0.64204,-0.20354,307.63,0.51086,0.3375,0.79064,340.63,-0.43893,-0.68839,0.57746,277.07,#26.3,0.73916,-0.64204,-0.20354,307.63,0.51086,0.3375,0.79064,340.63,-0.43893,-0.68839,0.57746,277.07
> view matrix models
> #26.1,-0.2209,-0.8407,-0.4944,314.38,0.26146,-0.53941,0.80042,293.31,-0.9396,0.047549,0.33896,330.4,#26.2,-0.2209,-0.8407,-0.4944,314.38,0.26146,-0.53941,0.80042,293.31,-0.9396,0.047549,0.33896,330.4,#26.3,-0.2209,-0.8407,-0.4944,314.38,0.26146,-0.53941,0.80042,293.31,-0.9396,0.047549,0.33896,330.4
> view matrix models
> #26.1,-0.8552,0.18934,-0.48247,384.81,-0.34938,0.47698,0.80649,362.59,0.38283,0.85828,-0.34176,373.24,#26.2,-0.8552,0.18934,-0.48247,384.81,-0.34938,0.47698,0.80649,362.59,0.38283,0.85828,-0.34176,373.24,#26.3,-0.8552,0.18934,-0.48247,384.81,-0.34938,0.47698,0.80649,362.59,0.38283,0.85828,-0.34176,373.24
> hide #6 models
> show #!9 models
> view matrix models
> #26.1,-0.8404,0.022284,-0.5415,377.04,-0.17118,0.93709,0.30424,396.95,0.51422,0.34838,-0.78372,349.53,#26.2,-0.8404,0.022284,-0.5415,377.04,-0.17118,0.93709,0.30424,396.95,0.51422,0.34838,-0.78372,349.53,#26.3,-0.8404,0.022284,-0.5415,377.04,-0.17118,0.93709,0.30424,396.95,0.51422,0.34838,-0.78372,349.53
> hide #!9 models
> view matrix models
> #26.1,-0.070909,-0.96249,0.26188,290.22,0.48549,0.19605,0.85198,331.32,-0.87136,0.18756,0.45338,338.1,#26.2,-0.070909,-0.96249,0.26188,290.22,0.48549,0.19605,0.85198,331.32,-0.87136,0.18756,0.45338,338.1,#26.3,-0.070909,-0.96249,0.26188,290.22,0.48549,0.19605,0.85198,331.32,-0.87136,0.18756,0.45338,338.1
> view matrix models
> #26.1,-0.86751,-0.49671,-0.026518,337.31,0.059229,-0.15608,0.98597,317.29,-0.49387,0.85377,0.16482,376.34,#26.2,-0.86751,-0.49671,-0.026518,337.31,0.059229,-0.15608,0.98597,317.29,-0.49387,0.85377,0.16482,376.34,#26.3,-0.86751,-0.49671,-0.026518,337.31,0.059229,-0.15608,0.98597,317.29,-0.49387,0.85377,0.16482,376.34
> show #!9 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> view matrix models
> #26.1,-0.222,-0.0027303,-0.97504,379.79,0.81238,0.5525,-0.18651,374.81,0.53922,-0.83351,-0.12043,265.27,#26.2,-0.222,-0.0027303,-0.97504,379.79,0.81238,0.5525,-0.18651,374.81,0.53922,-0.83351,-0.12043,265.27,#26.3,-0.222,-0.0027303,-0.97504,379.79,0.81238,0.5525,-0.18651,374.81,0.53922,-0.83351,-0.12043,265.27
> view matrix models
> #26.1,-0.27127,0.10151,-0.95713,386.11,0.76006,0.63271,-0.14832,379.45,0.59053,-0.76771,-0.24879,270.51,#26.2,-0.27127,0.10151,-0.95713,386.11,0.76006,0.63271,-0.14832,379.45,0.59053,-0.76771,-0.24879,270.51,#26.3,-0.27127,0.10151,-0.95713,386.11,0.76006,0.63271,-0.14832,379.45,0.59053,-0.76771,-0.24879,270.51
> view matrix models
> #26.1,-0.26905,0.12773,-0.95462,387.49,0.75503,0.64332,-0.12672,379.73,0.59794,-0.75486,-0.26953,271.48,#26.2,-0.26905,0.12773,-0.95462,387.49,0.75503,0.64332,-0.12672,379.73,0.59794,-0.75486,-0.26953,271.48,#26.3,-0.26905,0.12773,-0.95462,387.49,0.75503,0.64332,-0.12672,379.73,0.59794,-0.75486,-0.26953,271.48
> ui mousemode right "translate selected models"
> view matrix models
> #26.1,-0.26905,0.12773,-0.95462,390.61,0.75503,0.64332,-0.12672,378.77,0.59794,-0.75486,-0.26953,284.76,#26.2,-0.26905,0.12773,-0.95462,390.61,0.75503,0.64332,-0.12672,378.77,0.59794,-0.75486,-0.26953,284.76,#26.3,-0.26905,0.12773,-0.95462,390.61,0.75503,0.64332,-0.12672,378.77,0.59794,-0.75486,-0.26953,284.76
> ui mousemode right "rotate selected models"
> view matrix models
> #26.1,-0.35988,0.15638,-0.9198,392.91,0.64052,0.75824,-0.1217,386.9,0.6784,-0.63294,-0.37304,292.66,#26.2,-0.35988,0.15638,-0.9198,392.91,0.64052,0.75824,-0.1217,386.9,0.6784,-0.63294,-0.37304,292.66,#26.3,-0.35988,0.15638,-0.9198,392.91,0.64052,0.75824,-0.1217,386.9,0.6784,-0.63294,-0.37304,292.66
> ui mousemode right "translate selected models"
> view matrix models
> #26.1,-0.35988,0.15638,-0.9198,394.51,0.64052,0.75824,-0.1217,387.2,0.6784,-0.63294,-0.37304,294.27,#26.2,-0.35988,0.15638,-0.9198,394.51,0.64052,0.75824,-0.1217,387.2,0.6784,-0.63294,-0.37304,294.27,#26.3,-0.35988,0.15638,-0.9198,394.51,0.64052,0.75824,-0.1217,387.2,0.6784,-0.63294,-0.37304,294.27
> view matrix models
> #26.1,-0.35988,0.15638,-0.9198,391.94,0.64052,0.75824,-0.1217,388.3,0.6784,-0.63294,-0.37304,294.67,#26.2,-0.35988,0.15638,-0.9198,391.94,0.64052,0.75824,-0.1217,388.3,0.6784,-0.63294,-0.37304,294.67,#26.3,-0.35988,0.15638,-0.9198,391.94,0.64052,0.75824,-0.1217,388.3,0.6784,-0.63294,-0.37304,294.67
> show #6 models
> hide #6 models
> view matrix models
> #26.1,-0.35988,0.15638,-0.9198,392.75,0.64052,0.75824,-0.1217,388.07,0.6784,-0.63294,-0.37304,294.25,#26.2,-0.35988,0.15638,-0.9198,392.75,0.64052,0.75824,-0.1217,388.07,0.6784,-0.63294,-0.37304,294.25,#26.3,-0.35988,0.15638,-0.9198,392.75,0.64052,0.75824,-0.1217,388.07,0.6784,-0.63294,-0.37304,294.25
> ui mousemode right "rotate selected models"
> view matrix models
> #26.1,-0.40865,0.25097,-0.87751,397.72,0.68395,0.72082,-0.11235,385.23,0.60433,-0.64609,-0.46621,296.48,#26.2,-0.40865,0.25097,-0.87751,397.72,0.68395,0.72082,-0.11235,385.23,0.60433,-0.64609,-0.46621,296.48,#26.3,-0.40865,0.25097,-0.87751,397.72,0.68395,0.72082,-0.11235,385.23,0.60433,-0.64609,-0.46621,296.48
> hide #10 models
> show #10 models
> view matrix models
> #26.1,-0.30992,0.28191,-0.90801,398.61,0.71685,0.69665,-0.028386,381.7,0.62456,-0.65971,-0.41799,294.45,#26.2,-0.30992,0.28191,-0.90801,398.61,0.71685,0.69665,-0.028386,381.7,0.62456,-0.65971,-0.41799,294.45,#26.3,-0.30992,0.28191,-0.90801,398.61,0.71685,0.69665,-0.028386,381.7,0.62456,-0.65971,-0.41799,294.45
> ui mousemode right "translate selected models"
> view matrix models
> #26.1,-0.30992,0.28191,-0.90801,400.27,0.71685,0.69665,-0.028386,381.49,0.62456,-0.65971,-0.41799,294.35,#26.2,-0.30992,0.28191,-0.90801,400.27,0.71685,0.69665,-0.028386,381.49,0.62456,-0.65971,-0.41799,294.35,#26.3,-0.30992,0.28191,-0.90801,400.27,0.71685,0.69665,-0.028386,381.49,0.62456,-0.65971,-0.41799,294.35
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> view matrix models
> #26.1,-0.30992,0.28191,-0.90801,399.38,0.71685,0.69665,-0.028386,381.71,0.62456,-0.65971,-0.41799,294.46,#26.2,-0.30992,0.28191,-0.90801,399.38,0.71685,0.69665,-0.028386,381.71,0.62456,-0.65971,-0.41799,294.46,#26.3,-0.30992,0.28191,-0.90801,399.38,0.71685,0.69665,-0.028386,381.71,0.62456,-0.65971,-0.41799,294.46
> select subtract #26.2
2434 atoms, 2477 bonds, 3 pseudobonds, 301 residues, 3 models selected
> select add #26.2
4503 atoms, 4577 bonds, 5 pseudobonds, 565 residues, 5 models selected
> select subtract #26.2
2434 atoms, 2477 bonds, 3 pseudobonds, 301 residues, 3 models selected
> select add #26.2
4503 atoms, 4577 bonds, 5 pseudobonds, 565 residues, 5 models selected
> select subtract #26.2
2434 atoms, 2477 bonds, 3 pseudobonds, 301 residues, 3 models selected
> hide #26.3 models
> select subtract #26.3
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> hide #!26.1 models
> select add #26
4503 atoms, 4577 bonds, 5 pseudobonds, 565 residues, 6 models selected
> select subtract #26.1
3197 atoms, 3246 bonds, 2 pseudobonds, 404 residues, 4 models selected
> select subtract #26.3
2069 atoms, 2100 bonds, 2 pseudobonds, 264 residues, 3 models selected
> select subtract #26.2
1 model selected
> select add #26.2
2069 atoms, 2100 bonds, 2 pseudobonds, 264 residues, 3 models selected
> select subtract #26.2
1 model selected
> select add #26.2
2069 atoms, 2100 bonds, 2 pseudobonds, 264 residues, 3 models selected
> select add #26.1
3375 atoms, 3431 bonds, 5 pseudobonds, 425 residues, 5 models selected
> select add #26.3
4503 atoms, 4577 bonds, 5 pseudobonds, 565 residues, 6 models selected
> view matrix models #26,1,0,0,4.2091,0,1,0,1.5586,0,0,1,0.98728
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.99292,0.046255,-0.1094,26.419,-0.057538,0.99308,-0.10234,57.876,0.10391,0.10791,0.98872,-69.757
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.99292,0.046255,-0.1094,25.7,-0.057538,0.99308,-0.10234,57.766,0.10391,0.10791,0.98872,-69.773
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.9943,0.090076,-0.05699,-7.6676,-0.096073,0.98893,-0.11311,76.212,0.04617,0.11794,0.99195,-54.31
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.9943,0.090076,-0.05699,-8.0235,-0.096073,0.98893,-0.11311,76.44,0.04617,0.11794,0.99195,-53.214
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.98874,0.14081,0.050686,-59.702,-0.13797,0.98886,-0.055852,72.11,-0.057986,0.048231,0.99715,6.0638
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.98874,0.14081,0.050686,-59.111,-0.13797,0.98886,-0.055852,72.269,-0.057986,0.048231,0.99715,5.6766
> show #26.3 models
> hide #26.3 models
> show #26.3 models
> hide #26.3 models
> select subtract #26.3
3375 atoms, 3431 bonds, 5 pseudobonds, 425 residues, 5 models selected
> select subtract #26.1
2069 atoms, 2100 bonds, 2 pseudobonds, 264 residues, 3 models selected
> select add #26
4503 atoms, 4577 bonds, 5 pseudobonds, 565 residues, 6 models selected
> select subtract #26
Nothing selected
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!1 models
> hide #!9 models
> hide #10 models
> show #!26.2 models
> fitmap #26.2 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) to map
postprocess_20231221.mrc (#1) using 2069 atoms
average map value = 0.005974, steps = 84
shifted from previous position = 3.66
rotated from previous position = 6.23 degrees
atoms outside contour = 720, contour level = 0.0033794
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.25151266 0.19854926 -0.94726953 280.15790271
0.70120494 0.71200202 -0.03694244 273.62980535
0.66712293 -0.67352156 -0.31830125 179.25904604
Axis -0.35234390 -0.89355952 0.27821783
Axis point -6.15326635 0.00000000 194.77142939
Rotation angle (degrees) 115.39814881
Shift along axis -293.34338391
> hide #!26.2 models
> show #26.3 models
> fitmap #26.3 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
postprocess_20231221.mrc (#1) using 1128 atoms
average map value = 0.004508, steps = 72
shifted from previous position = 4.99
rotated from previous position = 7.06 degrees
atoms outside contour = 422, contour level = 0.0033794
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.24642181 0.18243493 -0.95183705 278.78686774
0.71472521 0.69751812 -0.05134514 272.65638016
0.65455645 -0.69295451 -0.30227453 177.98352930
Axis -0.35451301 -0.88759210 0.29411016
Axis point -9.04055568 0.00000000 197.28184806
Rotation angle (degrees) 115.18795785
Shift along axis -288.49445780
> hide #26.3 models
> show #!26.1 models
> fitmap #26.1 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#26.1) to map
postprocess_20231221.mrc (#1) using 1306 atoms
average map value = 0.004381, steps = 88
shifted from previous position = 4.09
rotated from previous position = 9.86 degrees
atoms outside contour = 492, contour level = 0.0033794
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#26.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.18671356 0.19708855 -0.96244176 280.99462623
0.67999636 0.73299000 0.01818230 273.70447792
0.70904371 -0.65106201 -0.27087867 179.37002260
Axis -0.35901311 -0.89666089 0.25905373
Axis point -12.36298520 0.00000000 195.35880618
Rotation angle (degrees) 111.24158265
Shift along axis -299.83438256
> hide #!26.1 models
> hide #!26 models
> show #!26.1 models
> show #!26.2 models
> show #26.3 models
> hide #!1 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #!26 models
> show #!25 models
> hide #25.11 models
> hide #25.10 models
> hide #25.9 models
> hide #25.8 models
> hide #!25.7 models
> hide #!25.6 models
> hide #25.5 models
> hide #!25.4 models
> hide #25.3 models
> hide #!25.2 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v4.cxs"
> show #3 models
> show #!1 models
> hide #3 models
> fitmap #25.1 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
postprocess_20231221.mrc (#1) using 3251 atoms
average map value = 0.003304, steps = 76
shifted from previous position = 6.61
rotated from previous position = 8.15 degrees
atoms outside contour = 2052, contour level = 0.0033794
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.51570328 0.84654128 -0.13197720 175.00196838
-0.85566106 -0.51671538 0.02914378 363.06707979
-0.04352323 0.12795729 0.99082423 110.61591954
Axis 0.05787500 -0.05180742 -0.99697867
Axis point 191.18696526 127.45480887 0.00000000
Rotation angle (degrees) 121.38574275
Shift along axis -118.96304353
> volume #1 level 0.003071
> hide #25.1 models
> show #25.1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> select add #25.1
3251 atoms, 3250 bonds, 813 residues, 1 model selected
> select subtract #25.1
Nothing selected
> select add #25.1
3251 atoms, 3250 bonds, 813 residues, 1 model selected
> select subtract #25.1
Nothing selected
> show #!1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> select add #25.1
3251 atoms, 3250 bonds, 813 residues, 1 model selected
> view matrix models
> #25.1,-0.51709,0.8453,-0.13446,287.41,-0.8545,-0.5189,0.023964,478.85,-0.049517,0.12729,0.99063,221.57
> view matrix models
> #25.1,-0.51709,0.8453,-0.13446,289.02,-0.8545,-0.5189,0.023964,478.87,-0.049517,0.12729,0.99063,223.3
> view matrix models
> #25.1,-0.51709,0.8453,-0.13446,289.82,-0.8545,-0.5189,0.023964,480.94,-0.049517,0.12729,0.99063,224.61
> fitmap #25.1 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
postprocess_20231221.mrc (#1) using 3251 atoms
average map value = 0.003304, steps = 72
shifted from previous position = 5.72
rotated from previous position = 0.0289 degrees
atoms outside contour = 1774, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.51531842 0.84673508 -0.13223699 174.97340097
-0.85588796 -0.51634064 0.02912268 363.05334011
-0.04362014 0.12818750 0.99079021 110.60727657
Axis 0.05800716 -0.05188938 -0.99696673
Axis point 191.22444071 127.42113577 0.00000000
Rotation angle (degrees) 121.36139660
Shift along axis -118.96067676
> view matrix models
> #25.1,-0.51671,0.8455,-0.13472,290.27,-0.85472,-0.51853,0.023944,478.36,-0.049614,0.12752,0.99059,225.17
> view matrix models
> #25.1,-0.51671,0.8455,-0.13472,288.94,-0.85472,-0.51853,0.023944,479.27,-0.049614,0.12752,0.99059,223.88
> ui mousemode right "rotate selected models"
> view matrix models
> #25.1,-0.45653,0.83292,-0.31278,302.89,-0.87051,-0.49081,-0.036415,486.46,-0.18385,0.25565,0.94913,237.18
> view matrix models
> #25.1,-0.49779,0.82837,-0.25692,301.69,-0.85509,-0.51829,-0.014326,483.69,-0.14502,0.21256,0.96633,233.09
> view matrix models
> #25.1,-0.54342,0.83542,-0.082221,286.71,-0.83935,-0.53919,0.069007,473.48,0.013318,0.10651,0.99422,217.18
> fitmap #25.1 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
postprocess_20231221.mrc (#1) using 3251 atoms
average map value = 0.003303, steps = 60
shifted from previous position = 3.59
rotated from previous position = 4.18 degrees
atoms outside contour = 1781, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.51505629 0.84701325 -0.13147459 174.85233957
-0.85604854 -0.51609939 0.02867597 363.09628018
-0.04356503 0.12731837 0.99090469 110.58957119
Axis 0.05774709 -0.05146389 -0.99700388
Axis point 191.21569735 127.49165061 0.00000000
Rotation angle (degrees) 121.34066991
Shift along axis -118.84736446
> select add #25
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 16 models selected
> select subtract #25
Nothing selected
> hide #25.1 models
> hide #3 models
> show #4 models
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map postprocess_20231221.mrc (#1) using
7501 atoms
average map value = 0.002923, steps = 104
shifted from previous position = 0.0401
rotated from previous position = 0.0432 degrees
atoms outside contour = 4902, contour level = 0.0030713
Position of CopB_Q9JIF7.pdb (#4) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04178861 -0.73263752 0.67933495 172.38956196
-0.03794698 0.68060212 0.73166985 204.58398347
-0.99840560 0.00479676 -0.05624279 236.24298737
Axis -0.37162091 0.85776110 0.35516727
Axis point 209.21418723 0.00000000 -39.77416060
Rotation angle (degrees) 102.04703741
Shift along axis 195.32639425
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map postprocess_20231221.mrc (#1) using
7501 atoms
average map value = 0.002923, steps = 64
shifted from previous position = 0.021
rotated from previous position = 0.0638 degrees
atoms outside contour = 4911, contour level = 0.0030713
Position of CopB_Q9JIF7.pdb (#4) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04153332 -0.73322783 0.67871344 172.38830087
-0.03864426 0.67997019 0.73222071 204.57471491
-0.99838950 0.00418318 -0.05657646 236.22842183
Axis -0.37224512 0.85750164 0.35514012
Axis point 209.31973663 0.00000000 -39.80649837
Rotation angle (degrees) 102.06784558
Shift along axis 195.14664218
> show #!25.2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004743, steps = 2000
shifted from previous position = 2.46
rotated from previous position = 6.13 degrees
atoms outside contour = 1278, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49442736 0.86623346 -0.07198031 164.49609954
-0.86875419 -0.49517333 0.00833736 369.63869235
-0.02842063 0.06665542 0.99737120 110.41166003
Axis 0.03358341 -0.02508456 -0.99912107
Axis point 190.62534040 134.54688866 0.00000000
Rotation angle (degrees) 119.74328500
Shift along axis -114.06249956
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!25.2 models
> show #!25.2 models
> select add #25.2
3198 atoms, 3193 bonds, 4 pseudobonds, 800 residues, 2 models selected
> view matrix models
> #25.2,-0.46567,0.88192,-0.073296,271.78,-0.88478,-0.4623,0.058711,474.61,0.017894,0.09219,0.99558,214.64
> view matrix models
> #25.2,-0.55363,0.8313,-0.04925,284.93,-0.82948,-0.55573,-0.055934,489.52,-0.073868,0.0098851,0.99722,233.82
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004821, steps = 244
shifted from previous position = 0.916
rotated from previous position = 5.51 degrees
atoms outside contour = 1143, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49480240 0.86519279 -0.08131428 165.41453083
-0.86827537 -0.49605252 0.00545632 369.30583029
-0.03561538 0.07330299 0.99667357 111.45220029
Axis 0.03909576 -0.02633339 -0.99888842
Axis point 191.15498632 133.89450699 0.00000000
Rotation angle (degrees) 119.80770683
Shift along axis -114.58638176
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004764, steps = 2000
shifted from previous position = 0.361
rotated from previous position = 0.941 degrees
atoms outside contour = 1209, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50397347 0.85977352 -0.08246348 167.59629738
-0.86244191 -0.50611966 -0.00606848 370.88262237
-0.04695391 0.06806161 0.99657560 113.48239203
Axis 0.04299451 -0.02059510 -0.99886301
Axis point 191.78983766 134.87081926 0.00000000
Rotation angle (degrees) 120.44817291
Shift along axis -113.78600849
> view matrix models
> #25.2,-0.52732,0.84847,-0.04497,279.39,-0.84721,-0.52908,-0.047938,487.91,-0.064467,0.01282,0.99784,232.87
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004716, steps = 2000
shifted from previous position = 1.33
rotated from previous position = 3.97 degrees
atoms outside contour = 1306, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49998814 0.86167462 -0.08676811 167.17452842
-0.86494971 -0.50185844 0.00029869 370.68848982
-0.04328793 0.07519939 0.99622848 113.29837933
Axis 0.04332538 -0.02515057 -0.99874439
Axis point 191.95191307 134.34120970 0.00000000
Rotation angle (degrees) 120.18601978
Shift along axis -115.23624630
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.00482, steps = 1460
shifted from previous position = 1.17
rotated from previous position = 0.568 degrees
atoms outside contour = 1142, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49481135 0.86517107 -0.08149067 165.44107902
-0.86826309 -0.49607509 0.00535787 369.30747054
-0.03579002 0.07340647 0.99665970 111.47256480
Axis 0.03921271 -0.02633480 -0.99888380
Axis point 191.17291252 133.88464128 0.00000000
Rotation angle (degrees) 119.80920530
Shift along axis -114.58638455
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.00482, steps = 284
shifted from previous position = 0.0185
rotated from previous position = 0.0285 degrees
atoms outside contour = 1142, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49470936 0.86523406 -0.08144115 165.39792504
-0.86833929 -0.49593640 0.00582651 369.24411712
-0.03534834 0.07360098 0.99666111 111.39932371
Axis 0.03905162 -0.02655866 -0.99888418
Axis point 191.13185436 133.85100747 0.00000000
Rotation angle (degrees) 119.80121255
Shift along axis -114.62259411
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004746, steps = 2000
shifted from previous position = 0.694
rotated from previous position = 0.66 degrees
atoms outside contour = 1128, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49256507 0.86546488 -0.09137930 166.00008670
-0.86954869 -0.49372383 0.01103833 368.07811210
-0.03556285 0.08489585 0.99575497 110.89448300
Axis 0.04250837 -0.03212492 -0.99857951
Axis point 191.35857281 132.53582797 0.00000000
Rotation angle (degrees) 119.68735605
Shift along axis -115.50504323
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004821, steps = 780
shifted from previous position = 0.714
rotated from previous position = 0.668 degrees
atoms outside contour = 1143, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49491778 0.86510217 -0.08157577 165.47325028
-0.86820239 -0.49618068 0.00541596 369.31835657
-0.03579097 0.07350473 0.99665242 111.47245341
Axis 0.03923870 -0.02638520 -0.99888145
Axis point 191.17660800 133.88399063 0.00000000
Rotation angle (degrees) 119.81644617
Shift along axis -114.59935024
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004821, steps = 64
shifted from previous position = 0.0131
rotated from previous position = 0.0221 degrees
atoms outside contour = 1139, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49481708 0.86518268 -0.08133249 165.41686729
-0.86827439 -0.49605177 0.00567551 369.28671394
-0.03543477 0.07342726 0.99667086 111.44218595
Axis 0.03904127 -0.02644811 -0.99888752
Axis point 191.14217122 133.87985316 0.00000000
Rotation angle (degrees) 119.80825626
Shift along axis -114.62705853
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004764, steps = 2000
shifted from previous position = 0.359
rotated from previous position = 1.01 degrees
atoms outside contour = 1207, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50510844 0.85913549 -0.08216852 167.75724459
-0.86177597 -0.50725145 -0.00617524 370.89827941
-0.04698546 0.06769169 0.99659931 113.55791641
Axis 0.04287471 -0.02042136 -0.99887173
Axis point 191.71488637 134.92029494 0.00000000
Rotation angle (degrees) 120.52273971
Shift along axis -113.81149688
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004769, steps = 2000
shifted from previous position = 0.932
rotated from previous position = 2.1 degrees
atoms outside contour = 1231, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.48810056 0.86985764 -0.07145288 162.94544324
-0.87262846 -0.48793578 0.02093378 367.84554135
-0.01665501 0.07256960 0.99722427 108.46520732
Axis 0.02960580 -0.03141878 -0.99906774
Axis point 189.80852921 133.47148642 0.00000000
Rotation angle (degrees) 119.30154973
Shift along axis -115.09721800
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004649, steps = 2000
shifted from previous position = 1.27
rotated from previous position = 1.18 degrees
atoms outside contour = 1118, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49420295 0.86552472 -0.08142722 165.10368776
-0.86860495 -0.49547861 0.00513516 368.74739200
-0.03590084 0.07326590 0.99666605 110.61360921
Axis 0.03924436 -0.02622390 -0.99888547
Axis point 190.92237643 133.68971650 0.00000000
Rotation angle (degrees) 119.76922245
Shift along axis -113.68093322
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004761, steps = 2000
shifted from previous position = 1.18
rotated from previous position = 0.58 degrees
atoms outside contour = 1134, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49092819 0.86696017 -0.08584618 164.92126958
-0.87065608 -0.49171552 0.01318449 367.99085791
-0.03078148 0.08121514 0.99622115 110.40135658
Axis 0.03910214 -0.03164967 -0.99873386
Axis point 190.88331822 132.82886345 0.00000000
Rotation angle (degrees) 119.55186916
Shift along axis -115.45958874
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004749, steps = 2000
shifted from previous position = 0.2
rotated from previous position = 0.26 degrees
atoms outside contour = 1125, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49206589 0.86591460 -0.08979457 165.67929543
-0.86988864 -0.49310893 0.01171904 368.04099763
-0.03413081 0.08387782 0.99589135 110.75434375
Axis 0.04151365 -0.03202390 -0.99862460
Axis point 191.21549454 132.61304680 0.00000000
Rotation angle (degrees) 119.64612847
Shift along axis -115.51016963
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004821, steps = 1348
shifted from previous position = 0.679
rotated from previous position = 0.63 degrees
atoms outside contour = 1142, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49459935 0.86532014 -0.08119434 165.36859381
-0.86839978 -0.49583294 0.00561293 369.28123388
-0.03540185 0.07328530 0.99668248 111.41325860
Axis 0.03898977 -0.02638357 -0.99889124
Axis point 191.14669718 133.88281268 0.00000000
Rotation angle (degrees) 119.79346036
Shift along axis -114.58500103
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004768, steps = 2000
shifted from previous position = 0.809
rotated from previous position = 1.18 degrees
atoms outside contour = 1233, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.48800487 0.86993760 -0.07113230 162.89402781
-0.87268732 -0.48782476 0.02106729 367.83006280
-0.01637287 0.07235719 0.99724438 108.42625211
Axis 0.02940531 -0.03139445 -0.99907443
Axis point 189.78296479 133.48069498 0.00000000
Rotation angle (degrees) 119.29409879
Shift along axis -115.08376766
> view matrix models
> #25.2,-0.53208,0.84559,-0.043089,279.75,-0.84349,-0.53381,-0.059738,489.8,-0.073515,0.004559,0.99728,234.33
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004631, steps = 2000
shifted from previous position = 1.18
rotated from previous position = 5.05 degrees
atoms outside contour = 1147, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.48815171 0.86762043 -0.09456580 165.62279976
-0.87118662 -0.49090427 -0.00684532 370.03919003
-0.05236190 0.07904290 0.99549507 112.85429778
Axis 0.04932028 -0.02423508 -0.99848894
Axis point 192.95003348 133.60578009 0.00000000
Rotation angle (degrees) 119.45767326
Shift along axis -113.48313585
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004719, steps = 2000
shifted from previous position = 1.54
rotated from previous position = 1.34 degrees
atoms outside contour = 1179, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50656202 0.85664740 -0.09772482 169.61094538
-0.86000131 -0.51010794 -0.01369808 371.28799353
-0.06158463 0.07710455 0.99511919 115.79424995
Axis 0.05280977 -0.02101872 -0.99838336
Axis point 192.99506333 134.36543524 0.00000000
Rotation angle (degrees) 120.71549142
Shift along axis -114.45393709
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004768, steps = 2000
shifted from previous position = 1.41
rotated from previous position = 1.12 degrees
atoms outside contour = 1211, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50197269 0.86100337 -0.08183276 167.17027116
-0.86368653 -0.50400525 -0.00492678 370.78555390
-0.04548612 0.06820474 0.99663389 113.17870968
Axis 0.04235525 -0.02105072 -0.99888082
Axis point 191.78578620 134.80515999 0.00000000
Rotation angle (degrees) 120.30958336
Shift along axis -113.77680632
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.00482, steps = 1560
shifted from previous position = 0.399
rotated from previous position = 0.787 degrees
atoms outside contour = 1141, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49484515 0.86513945 -0.08162107 165.45679030
-0.86824047 -0.49611484 0.00534265 369.29931336
-0.03587129 0.07351050 0.99664911 111.47595487
Axis 0.03928252 -0.02636384 -0.99888029
Axis point 191.17583080 133.87458033 0.00000000
Rotation angle (degrees) 119.81198347
Shift along axis -114.58772451
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004821, steps = 512
shifted from previous position = 0.0301
rotated from previous position = 0.0216 degrees
atoms outside contour = 1144, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49493164 0.86512442 -0.08125513 165.42697493
-0.86819945 -0.49618631 0.00537170 369.32678383
-0.03567049 0.07320428 0.99667885 111.47713848
Axis 0.03909097 -0.02626979 -0.99889028
Axis point 191.15121103 133.91325672 0.00000000
Rotation angle (degrees) 119.81621672
Shift along axis -114.58886669
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004735, steps = 2000
shifted from previous position = 0.966
rotated from previous position = 1.37 degrees
atoms outside contour = 1148, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50248574 0.85925464 -0.09586205 168.60347666
-0.86269476 -0.50562413 -0.01009856 370.75051195
-0.05714740 0.07762530 0.99534340 114.76512812
Axis 0.05086571 -0.02244826 -0.99845318
Axis point 192.76925102 134.08584606 0.00000000
Rotation angle (degrees) 120.42321792
Shift along axis -114.33417459
> select subtract #25.2
Nothing selected
> hide #!25.2 models
> show #25.3 models
> hide #4 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> select add #7
7214 atoms, 7373 bonds, 905 residues, 1 model selected
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 2.07
rotated from previous position = 7.06 degrees
atoms outside contour = 978, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47545733 0.87640103 -0.07656081 158.51716871
-0.87857427 -0.47750275 -0.00991786 369.90335293
-0.04525002 0.06254884 0.99701558 112.99556207
Axis 0.04125043 -0.01782314 -0.99898986
Axis point 191.02269376 135.40608677 0.00000000
Rotation angle (degrees) 118.55305011
Shift along axis -112.93535652
> view matrix models
> #7,-0.36432,-0.067161,-0.92885,297.27,0.22543,-0.97409,-0.017987,296.83,-0.90358,-0.21594,0.37002,346.7
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 64
shifted from previous position = 0.00767
rotated from previous position = 0.0173 degrees
atoms outside contour = 979, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47532870 0.87644996 -0.07679897 158.52680230
-0.87864353 -0.47737760 -0.00980606 369.88315964
-0.04525663 0.06281782 0.99699837 112.96036915
Axis 0.04133688 -0.01795363 -0.99898395
Axis point 191.03872860 135.37544611 0.00000000
Rotation angle (degrees) 118.54533465
Shift along axis -112.93333754
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.0552
rotated from previous position = 0.0291 degrees
atoms outside contour = 979, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47523174 0.87646484 -0.07722804 158.59065575
-0.87869684 -0.47728443 -0.00956120 369.81255513
-0.04523979 0.06331625 0.99696760 112.93527431
Axis 0.04147916 -0.01820653 -0.99897347
Axis point 191.06092423 135.29625759 0.00000000
Rotation angle (degrees) 118.54013797
Shift along axis -112.97414056
> view matrix models
> #7,-0.18466,-0.061928,-0.98085,300.57,-0.28631,-0.95134,0.11397,287.8,-0.94018,0.30187,0.15794,351.03
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.0165
rotated from previous position = 0.00533 degrees
atoms outside contour = 978, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47530223 0.87643103 -0.07717786 158.59298727
-0.87865977 -0.47735271 -0.00955947 369.82530316
-0.04521928 0.06326945 0.99697150 112.92595021
Axis 0.04145327 -0.01819041 -0.99897484
Axis point 191.05511213 135.30825161 0.00000000
Rotation angle (degrees) 118.54453621
Shift along axis -112.96325958
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.0466
rotated from previous position = 0.0305 degrees
atoms outside contour = 977, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47532057 0.87645827 -0.07675451 158.51183318
-0.87864577 -0.47737198 -0.00987840 369.89939667
-0.04529846 0.06274462 0.99700108 112.97741102
Axis 0.04133618 -0.01790442 -0.99898486
Axis point 191.03910614 135.39019927 0.00000000
Rotation angle (degrees) 118.54479799
Shift along axis -112.93328385
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 76
shifted from previous position = 0.0517
rotated from previous position = 0.0235 degrees
atoms outside contour = 976, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47523483 0.87647428 -0.07710170 158.56597258
-0.87869259 -0.47728974 -0.00968672 369.83604006
-0.04529001 0.06314522 0.99697617 112.95918118
Axis 0.04145326 -0.01810604 -0.99897638
Axis point 191.05770751 135.32190842 0.00000000
Rotation angle (degrees) 118.54013231
Shift along axis -112.96674420
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.0425
rotated from previous position = 0.0182 degrees
atoms outside contour = 978, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47534774 0.87643769 -0.07682111 158.53698924
-0.87863438 -0.47739524 -0.00976706 369.87784034
-0.04523426 0.06285491 0.99699705 112.95396532
Axis 0.04133628 -0.01797917 -0.99898351
Axis point 191.03855454 135.36953188 0.00000000
Rotation angle (degrees) 118.54657438
Shift along axis -112.93591686
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.00591
rotated from previous position = 0.012 degrees
atoms outside contour = 979, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47542699 0.87640826 -0.07666634 158.52781577
-0.87859017 -0.47747440 -0.00987431 369.89735913
-0.04526014 0.06266377 0.99700790 112.98110921
Axis 0.04129042 -0.01787716 -0.99898724
Axis point 191.03030121 135.39393921 0.00000000
Rotation angle (degrees) 118.55138644
Shift along axis -112.93372065
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 64
shifted from previous position = 0.0208
rotated from previous position = 0.0226 degrees
atoms outside contour = 975, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47526491 0.87649565 -0.07667224 158.48228974
-0.87866184 -0.47733488 -0.01023597 369.94394497
-0.04557011 0.06250417 0.99700380 113.06380899
Axis 0.04140162 -0.01770244 -0.99898575
Axis point 191.05651983 135.42671950 0.00000000
Rotation angle (degrees) 118.54168418
Shift along axis -112.93662236
> view matrix models
> #7,-0.28866,-0.11227,-0.95083,298.71,-0.30709,-0.92977,0.20301,285.33,-0.90684,0.3506,0.23392,349.46
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.0526
rotated from previous position = 0.0308 degrees
atoms outside contour = 974, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47495325 0.87662798 -0.07708953 158.50383441
-0.87881880 -0.47704477 -0.01028609 369.91372761
-0.04579223 0.06286231 0.99697111 113.09251968
Axis 0.04162666 -0.01781040 -0.99897448
Axis point 191.10946912 135.37243598 0.00000000
Rotation angle (degrees) 118.52312738
Shift along axis -112.96686564
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 44
shifted from previous position = 0.0526
rotated from previous position = 0.0368 degrees
atoms outside contour = 979, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47535997 0.87643990 -0.07672018 158.52214584
-0.87862059 -0.47741625 -0.00997899 369.90795329
-0.04537344 0.06266432 0.99700272 113.00354608
Axis 0.04134878 -0.01784265 -0.99898544
Axis point 191.04424832 135.39684200 0.00000000
Rotation angle (degrees) 118.54747320
Shift along axis -112.93433985
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 76
shifted from previous position = 0.0415
rotated from previous position = 0.0284 degrees
atoms outside contour = 976, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47524069 0.87647169 -0.07709506 158.56622957
-0.87868942 -0.47729551 -0.00968985 369.83672080
-0.04529000 0.06313760 0.99697665 112.95987184
Axis 0.04145084 -0.01810233 -0.99897654
Axis point 191.05723336 135.32281988 0.00000000
Rotation angle (degrees) 118.54049592
Shift along axis -112.96646428
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.0426
rotated from previous position = 0.0168 degrees
atoms outside contour = 977, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47534798 0.87643644 -0.07683393 158.53933827
-0.87863466 -0.47739506 -0.00975115 369.87593931
-0.04522640 0.06287377 0.99699621 112.95017722
Axis 0.04133797 -0.01799095 -0.99898323
Axis point 191.03875226 135.36720668 0.00000000
Rotation angle (degrees) 118.54660343
Shift along axis -112.93605809
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.0467
rotated from previous position = 0.0239 degrees
atoms outside contour = 978, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47519240 0.87648884 -0.07719767 158.57300363
-0.87871531 -0.47724879 -0.00964283 369.82620699
-0.04529432 0.06325257 0.99696917 112.94962485
Axis 0.04148840 -0.01815778 -0.99897398
Axis point 191.06401223 135.30831728 0.00000000
Rotation angle (degrees) 118.53764154
Shift along axis -112.97001914
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.0506
rotated from previous position = 0.0261 degrees
atoms outside contour = 979, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47531070 0.87646150 -0.07677865 158.52036171
-0.87865558 -0.47735621 -0.00976759 369.87910847
-0.04521168 0.06281934 0.99700031 112.95253245
Axis 0.04131532 -0.01796741 -0.99898459
Axis point 191.03531248 135.37407238 0.00000000
Rotation angle (degrees) 118.54398695
Shift along axis -112.93428991
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.0542
rotated from previous position = 0.0257 degrees
atoms outside contour = 978, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47525371 0.87645634 -0.07718930 158.58846566
-0.87868413 -0.47730708 -0.00959885 369.82029855
-0.04525597 0.06326312 0.99697024 112.94328927
Axis 0.04147089 -0.01817551 -0.99897438
Axis point 191.05980700 135.30412830 0.00000000
Rotation angle (degrees) 118.54150687
Shift along axis -112.97232105
> select subtract #7
Nothing selected
> select add #7
7214 atoms, 7373 bonds, 905 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
7214 atoms, 7373 bonds, 905 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #25.3
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.052
rotated from previous position = 0.0219 degrees
atoms outside contour = 978, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47531155 0.87645449 -0.07685344 158.53312907
-0.87865324 -0.47736051 -0.00976832 369.87749105
-0.04524829 0.06288453 0.99699454 112.95097096
Axis 0.04135298 -0.01798921 -0.99898264
Axis point 191.04202451 135.36723140 0.00000000
Rotation angle (degrees) 118.54434302
Shift along axis -112.93404570
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 64
shifted from previous position = 0.00761
rotated from previous position = 0.0171 degrees
atoms outside contour = 978, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47544691 0.87640134 -0.07662189 158.52466536
-0.87858021 -0.47749262 -0.00987876 369.90162500
-0.04524415 0.06262165 0.99701127 112.97927090
Axis 0.04126942 -0.01786116 -0.99898840
Axis point 191.02673411 135.39983726 0.00000000
Rotation angle (degrees) 118.55252039
Shift along axis -112.92963021
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.0558
rotated from previous position = 0.0355 degrees
atoms outside contour = 975, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47526835 0.87645184 -0.07715024 158.58396185
-0.87867573 -0.47732192 -0.00962940 369.82656908
-0.04526520 0.06321349 0.99697297 112.95017554
Axis 0.04146038 -0.01814817 -0.99897532
Axis point 191.05789318 135.31134266 0.00000000
Rotation angle (degrees) 118.54237935
Shift along axis -112.97116325
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.00488
rotated from previous position = 0.0013 degrees
atoms outside contour = 977, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47525820 0.87645883 -0.07713326 158.57888826
-0.87868203 -0.47731049 -0.00962170 369.82738709
-0.04524954 0.06320282 0.99697436 112.94459965
Axis 0.04144962 -0.01814730 -0.99897578
Axis point 191.05650349 135.31307075 0.00000000
Rotation angle (degrees) 118.54163027
Shift along axis -112.96725292
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.00445
rotated from previous position = 0.00633 degrees
atoms outside contour = 975, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47527033 0.87645853 -0.07706200 158.56801263
-0.87867344 -0.47732463 -0.00970424 369.83968258
-0.04528895 0.06310019 0.99697907 112.96447076
Axis 0.04143847 -0.01808443 -0.99897738
Axis point 191.05491510 135.32697136 0.00000000
Rotation angle (degrees) 118.54233328
Shift along axis -112.96647383
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.0403
rotated from previous position = 0.0183 degrees
atoms outside contour = 979, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47533984 0.87644582 -0.07677719 158.52777202
-0.87863714 -0.47738898 -0.00982497 369.88348376
-0.04526364 0.06278909 0.99699986 112.96898440
Axis 0.04133156 -0.01793736 -0.99898446
Axis point 191.03816673 135.37698554 0.00000000
Rotation angle (degrees) 118.54602065
Shift along axis -112.93679257
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.00627
rotated from previous position = 0.0148 degrees
atoms outside contour = 977, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47538762 0.87643915 -0.07655734 158.50235918
-0.87861097 -0.47743459 -0.00994791 369.90367199
-0.04526986 0.06253500 0.99701555 112.99656841
Axis 0.04125790 -0.01780910 -0.99898980
Axis point 191.02610562 135.40690521 0.00000000
Rotation angle (degrees) 118.54855456
Shift along axis -112.93059754
> fitmap #7 inMap #1
Fit molecule CopBprime_O55029.pdb (#7) to map postprocess_20231221.mrc (#1)
using 7214 atoms
average map value = 0.00312, steps = 96
shifted from previous position = 3.54
rotated from previous position = 19.3 degrees
atoms outside contour = 3686, contour level = 0.0030713
Position of CopBprime_O55029.pdb (#7) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.16312220 -0.17485605 -0.97098739 188.46974228
-0.01374495 -0.98367120 0.17944926 177.44362101
-0.98651012 0.04261833 0.15805523 238.56001859
Axis -0.64559811 0.07323964 0.76015725
Axis point 189.52310479 85.45609714 0.00000000
Rotation angle (degrees) 173.91681678
Shift along axis 72.66332588
> fitmap #7 inMap #1
Fit molecule CopBprime_O55029.pdb (#7) to map postprocess_20231221.mrc (#1)
using 7214 atoms
average map value = 0.003119, steps = 28
shifted from previous position = 0.059
rotated from previous position = 0.0701 degrees
atoms outside contour = 3678, contour level = 0.0030713
Position of CopBprime_O55029.pdb (#7) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
-0.16270247 -0.17502716 -0.97102698 188.49518175
-0.01484005 -0.98359506 0.17977910 177.40834426
-0.98656357 0.04366059 0.15743593 238.52181597
Axis -0.64577505 0.07370887 0.75996157
Axis point 189.60735220 85.32080770 0.00000000
Rotation angle (degrees) 173.95027220
Shift along axis 72.61849739
> hide #!1 models
> select subtract #25.3
Nothing selected
> select add #25.3
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> select subtract #25.3
Nothing selected
> hide #25.3 models
> hide #7 models
> show #8 models
> show #!25.4 models
> select add #25.4
706 atoms, 704 bonds, 1 pseudobond, 177 residues, 2 models selected
> fitmap #25.4 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif D (#25.4) to map
postprocess_20231221.mrc (#1) using 706 atoms
average map value = 0.005751, steps = 84
shifted from previous position = 5.75
rotated from previous position = 7.61 degrees
atoms outside contour = 156, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif D (#25.4) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49064014 0.86626986 -0.09406793 165.85506336
-0.87120858 -0.48971430 0.03428547 365.69516018
-0.01636594 0.09877461 0.99497523 106.56737989
Axis 0.03705399 -0.04464579 -0.99831546
Axis point 190.16165110 130.77700867 0.00000000
Rotation angle (degrees) 119.51751550
Shift along axis -116.56901947
> hide #!25.4 models
> select subtract #25.4
Nothing selected
> show #25.5 models
> hide #8 models
> show #6 models
> hide #6 models
> show #5 models
> select add #25.5
635 atoms, 634 bonds, 159 residues, 1 model selected
> view matrix models
> #25.5,-0.81618,0.4547,-0.35651,366.16,-0.56125,-0.47727,0.67617,389.42,0.13731,0.75197,0.64474,185.92
> ui mousemode right "translate selected models"
> view matrix models
> #25.5,-0.81618,0.4547,-0.35651,379.31,-0.56125,-0.47727,0.67617,385.17,0.13731,0.75197,0.64474,180.27
> fitmap #25.5 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif F (#25.5) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.002979, steps = 308
shifted from previous position = 6.54
rotated from previous position = 59.7 degrees
atoms outside contour = 415, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif F (#25.5) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.71654810 0.43382071 0.54622193 191.36896955
-0.32335676 -0.90043574 0.29095682 282.02334066
0.61806085 0.03186001 0.78548438 23.37614478
Axis -0.32246089 -0.08940766 -0.94235091
Axis point 121.98149155 122.51853562 0.00000000
Rotation angle (degrees) 156.31242445
Shift along axis -108.95258872
> view matrix models
> #25.5,-0.7187,0.43216,0.54472,305.35,-0.32546,-0.90136,0.28569,390.65,0.61445,0.028044,0.78845,135.72
> fitmap #25.5 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif F (#25.5) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.00298, steps = 148
shifted from previous position = 4.55
rotated from previous position = 0.283 degrees
atoms outside contour = 416, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif F (#25.5) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.71339898 0.43568499 0.54885379 190.53612584
-0.32599318 -0.89965518 0.29042900 282.46371120
0.62031471 0.02826916 0.78384342 23.36045444
Axis -0.32417629 -0.08836569 -0.94186052
Axis point 121.83877150 122.72602465 0.00000000
Rotation angle (degrees) 156.14974611
Shift along axis -108.72968597
> fitmap #25.5 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif F (#25.5) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.002979, steps = 128
shifted from previous position = 0.0438
rotated from previous position = 0.246 degrees
atoms outside contour = 417, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif F (#25.5) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.71633393 0.43402068 0.54634397 191.29103107
-0.32422244 -0.90037898 0.29016804 282.24449040
0.61785556 0.03072023 0.78569126 23.47204407
Axis -0.32246098 -0.08887991 -0.94240081
Axis point 122.00120769 122.61282859 0.00000000
Rotation angle (degrees) 156.27837564
Shift along axis -108.88983065
> view matrix models
> #25.5,-0.71848,0.43236,0.54484,303.98,-0.32632,-0.9013,0.2849,391.85,0.61424,0.026905,0.78866,136.39
> fitmap #25.5 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif F (#25.5) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.002979, steps = 136
shifted from previous position = 3.4
rotated from previous position = 0.196 degrees
atoms outside contour = 416, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif F (#25.5) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.71397866 0.43506650 0.54859057 190.69622708
-0.32491193 -0.89991822 0.29082543 282.26969342
0.62021505 0.02939952 0.78388070 23.29855258
Axis -0.32399963 -0.08876820 -0.94188346
Axis point 121.82842948 122.65232790 0.00000000
Rotation angle (degrees) 156.20687582
Shift along axis -108.78660015
> fitmap #5 inMap #1
Fit molecule hArf1_P84078 (#5) to map postprocess_20231221.mrc (#1) using 1457
atoms
average map value = 0.002587, steps = 48
shifted from previous position = 0.0368
rotated from previous position = 0.0255 degrees
atoms outside contour = 1149, contour level = 0.0030713
Position of hArf1_P84078 (#5) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.15764381 0.02404457 0.98720326 126.73261994
-0.68671661 -0.71572886 0.12709238 200.57813479
0.70962575 -0.69796421 -0.09631842 178.39050082
Axis -0.73416016 0.24699681 -0.63245666
Axis point 0.00000000 138.26266793 -15.48832808
Rotation angle (degrees) 145.81235297
Shift along axis -156.32414243
> fitmap #5 inMap #1
Fit molecule hArf1_P84078 (#5) to map postprocess_20231221.mrc (#1) using 1457
atoms
average map value = 0.002587, steps = 44
shifted from previous position = 0.00981
rotated from previous position = 0.0462 degrees
atoms outside contour = 1150, contour level = 0.0030713
Position of hArf1_P84078 (#5) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.15689280 0.02422660 0.98731844 126.72229531
-0.68692000 -0.71560036 0.12671632 200.57644266
0.70959535 -0.69808966 -0.09563081 178.39181938
Axis -0.73387458 0.24710529 -0.63274566
Axis point 0.00000000 138.27844137 -15.55661388
Rotation angle (degrees) 145.80903401
Shift along axis -156.31142131
> fitmap #25.5 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif F (#25.5) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.002979, steps = 248
shifted from previous position = 0.0207
rotated from previous position = 0.177 degrees
atoms outside contour = 418, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif F (#25.5) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.71390883 0.43627272 0.54772281 190.65990615
-0.32756532 -0.89940270 0.28944038 282.77508578
0.61889832 0.02721904 0.78499935 23.55080874
Axis -0.32344066 -0.08779246 -0.94216698
Axis point 121.99487683 122.81354587 0.00000000
Rotation angle (degrees) 156.08616419
Shift along axis -108.68147988
> fitmap #25.5 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif F (#25.5) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.002979, steps = 100
shifted from previous position = 0.026
rotated from previous position = 0.173 degrees
atoms outside contour = 417, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif F (#25.5) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.71499486 0.43483737 0.54744753 190.94416222
-0.32495537 -0.90001607 0.29047386 282.30441960
0.61902047 0.02979130 0.78480961 23.38220887
Axis -0.32324665 -0.08875052 -0.94214380
Axis point 121.92660031 122.64481230 0.00000000
Rotation angle (degrees) 156.22002669
Shift along axis -108.80612902
> fitmap #25.5 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif F (#25.5) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.002979, steps = 296
shifted from previous position = 0.019
rotated from previous position = 0.062 degrees
atoms outside contour = 417, contour level = 0.0030713
Position of 5nzr_COPI_coat_leaf_2017.cif F (#25.5) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.71427567 0.43543346 0.54791236 190.76898317
-0.32523139 -0.89973120 0.29104691 282.28959226
0.61970541 0.02968943 0.78427274 23.32706989
Axis -0.32365836 -0.08890667 -0.94198772
Axis point 121.88785716 122.63494813 0.00000000
Rotation angle (degrees) 156.18685604
Shift along axis -108.81521620
> show #!1 models
> hide #5 models
> select subtract #25.5
Nothing selected
> hide #25.5 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v5.cxs"
> show #25.5 models
> hide #25.5 models
> select add #25.5
635 atoms, 634 bonds, 159 residues, 1 model selected
> select subtract #25.5
Nothing selected
> select add #25.5
635 atoms, 634 bonds, 159 residues, 1 model selected
> select subtract #25.5
Nothing selected
> show #25.5 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #25.5 models
> hide #!1 models
> show #!1 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> show #5 models
> hide #5 models
> hide #6 models
> show #6 models
> show #5 models
> hide #6 models
> hide #5 models
> show #6 models
> show #5 models
> hide #5 models
> hide #6 models
> show #4 models
> volume #1 level 0.003994
> volume #1 level 0.00261
> select add #4
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.05188,-0.63754,0.76867,284,-0.29607,0.74492,0.59786,318.34,-0.95376,-0.19656,-0.2274,349.89
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map postprocess_20231221.mrc (#1) using
7501 atoms
average map value = 0.002923, steps = 168
shifted from previous position = 1.37
rotated from previous position = 17.4 degrees
atoms outside contour = 4241, contour level = 0.0026099
Position of CopB_Q9JIF7.pdb (#4) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04176347 -0.73290883 0.67904378 172.38294327
-0.03836890 0.68031190 0.73191772 204.58729961
-0.99839052 0.00451326 -0.05653309 236.22237826
Axis -0.37191513 0.85765654 0.35511180
Axis point 209.24883276 0.00000000 -39.77291852
Rotation angle (degrees) 102.06330668
Shift along axis 195.23916518
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map postprocess_20231221.mrc (#1) using
7501 atoms
average map value = 0.002923, steps = 84
shifted from previous position = 0.0295
rotated from previous position = 0.0281 degrees
atoms outside contour = 4239, contour level = 0.0026099
Position of CopB_Q9JIF7.pdb (#4) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04186364 -0.73313873 0.67878939 172.36289881
-0.03871970 0.68006509 0.73212858 204.56813767
-0.99837279 0.00436704 -0.05685691 236.22572632
Axis -0.37212500 0.85758032 0.35507603
Axis point 209.25927852 0.00000000 -39.73446400
Rotation angle (degrees) 102.08295835
Shift along axis 195.17115835
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map postprocess_20231221.mrc (#1) using
7501 atoms
average map value = 0.002923, steps = 64
shifted from previous position = 0.0254
rotated from previous position = 0.0438 degrees
atoms outside contour = 4237, contour level = 0.0026099
Position of CopB_Q9JIF7.pdb (#4) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04160064 -0.73285881 0.67910776 172.35253082
-0.03812474 0.68036549 0.73188066 204.56244996
-0.99840668 0.00455589 -0.05624369 236.24744801
Axis -0.37185384 0.85765014 0.35519144
Axis point 209.24263523 0.00000000 -39.78121436
Rotation angle (degrees) 102.04848903
Shift along axis 195.26613509
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map postprocess_20231221.mrc (#1) using
7501 atoms
average map value = 0.002923, steps = 88
shifted from previous position = 0.0061
rotated from previous position = 0.0174 degrees
atoms outside contour = 4239, contour level = 0.0026099
Position of CopB_Q9JIF7.pdb (#4) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
-0.04184488 -0.73286543 0.67908561 172.35866702
-0.03830325 0.68035797 0.73187833 204.56322632
-0.99838964 0.00461417 -0.05654063 236.24556931
Axis -0.37184514 0.85768149 0.35512484
Axis point 209.22469544 0.00000000 -39.73577931
Rotation angle (degrees) 102.06456279
Shift along axis 195.25603077
> select subtract #4
Nothing selected
> show #!25.2 models
> hide #4 models
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004719, steps = 2000
shifted from previous position = 0.362
rotated from previous position = 0.363 degrees
atoms outside contour = 834, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50636564 0.85675765 -0.09777602 169.57780713
-0.86012716 -0.50990038 -0.01352292 371.25526671
-0.06144189 0.07725227 0.99511656 115.74602408
Axis 0.05278650 -0.02112859 -0.99838228
Axis point 192.99162836 134.33980830 0.00000000
Rotation angle (degrees) 120.70211983
Shift along axis -114.45145959
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.00482, steps = 536
shifted from previous position = 1.23
rotated from previous position = 1.72 degrees
atoms outside contour = 799, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49464042 0.86526798 -0.08149953 165.39425343
-0.86837674 -0.49587111 0.00580183 369.24428351
-0.03539312 0.07364212 0.99665649 111.40460245
Axis 0.03908787 -0.02656536 -0.99888259
Axis point 191.14127299 133.84616419 0.00000000
Rotation angle (degrees) 119.79693397
Shift along axis -114.62431386
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004821, steps = 980
shifted from previous position = 0.0229
rotated from previous position = 0.0197 degrees
atoms outside contour = 800, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49468130 0.86527653 -0.08115991 165.37085423
-0.86836176 -0.49589685 0.00584550 369.25692230
-0.03518897 0.07336782 0.99668395 111.40497384
Axis 0.03890517 -0.02648764 -0.99889178
Axis point 191.12185163 133.87138068 0.00000000
Rotation angle (degrees) 119.79822657
Shift along axis -114.62847805
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004749, steps = 2000
shifted from previous position = 0.642
rotated from previous position = 0.636 degrees
atoms outside contour = 800, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49149695 0.86624681 -0.08970622 165.57569659
-0.87021696 -0.49252729 0.01180287 368.01917561
-0.03395856 0.08386495 0.99589833 110.70394502
Axis 0.04144232 -0.03206003 -0.99862640
Axis point 191.23240381 132.59584765 0.00000000
Rotation angle (degrees) 119.60797979
Shift along axis -115.48874741
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004719, steps = 2000
shifted from previous position = 0.813
rotated from previous position = 1.91 degrees
atoms outside contour = 835, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50634022 0.85677189 -0.09778293 169.57700834
-0.86013886 -0.50987927 -0.01357418 371.26630152
-0.06148747 0.07723375 0.99511518 115.75480340
Axis 0.05280471 -0.02110577 -0.99838179
Axis point 192.99968517 134.34467403 0.00000000
Rotation angle (degrees) 120.70061558
Shift along axis -114.44888593
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004725, steps = 2000
shifted from previous position = 0.191
rotated from previous position = 0.172 degrees
atoms outside contour = 847, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50743553 0.85643414 -0.09502485 169.28322407
-0.85961565 -0.51077340 -0.01309400 371.31505890
-0.05975031 0.07504049 0.99538877 115.80005830
Axis 0.05128053 -0.02052428 -0.99847337
Axis point 192.66583518 134.59673048 0.00000000
Rotation angle (degrees) 120.75780048
Shift along axis -114.56331573
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004741, steps = 2000
shifted from previous position = 1.14
rotated from previous position = 0.899 degrees
atoms outside contour = 953, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50305498 0.85978935 -0.08773792 167.88037321
-0.86307723 -0.50507115 -0.00090608 370.78933379
-0.04509293 0.07526879 0.99614317 113.45485580
Axis 0.04415738 -0.02472063 -0.99871869
Axis point 191.95152599 134.39625416 0.00000000
Rotation angle (degrees) 120.39719134
Shift along axis -115.06247320
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004765, steps = 2000
shifted from previous position = 1.01
rotated from previous position = 0.423 degrees
atoms outside contour = 866, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50359516 0.86000616 -0.08234871 167.51856402
-0.86267696 -0.50572126 -0.00587080 370.87795232
-0.04669441 0.06808383 0.99658628 113.43225743
Axis 0.04288124 -0.02067349 -0.99886626
Axis point 191.79511786 134.86449404 0.00000000
Rotation angle (degrees) 120.42201089
Shift along axis -113.78759381
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004745, steps = 2000
shifted from previous position = 0.934
rotated from previous position = 1.35 degrees
atoms outside contour = 798, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49260004 0.86554228 -0.09045301 165.87029937
-0.86955802 -0.49370059 0.01133828 368.05758140
-0.03484294 0.08423937 0.99583617 110.84105115
Axis 0.04195695 -0.03200540 -0.99860666
Axis point 191.26189535 132.58842921 0.00000000
Rotation angle (degrees) 119.68506517
Shift along axis -115.50703149
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004715, steps = 2000
shifted from previous position = 0.551
rotated from previous position = 1.08 degrees
atoms outside contour = 806, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49691031 0.86175197 -0.10229205 168.08104532
-0.86621925 -0.49966190 -0.00147959 369.47644931
-0.05238647 0.08787212 0.99475330 113.38812739
Axis 0.05161856 -0.02883050 -0.99825063
Axis point 192.72913075 132.83692567 0.00000000
Rotation angle (degrees) 120.06018753
Shift along axis -115.16585742
> fitmap #25.2 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
postprocess_20231221.mrc (#1) using 3198 atoms
average map value = 0.004723, steps = 2000
shifted from previous position = 1.52
rotated from previous position = 0.873 degrees
atoms outside contour = 968, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50092577 0.86104342 -0.08762183 167.41226756
-0.86432877 -0.50292643 -0.00087810 370.87113815
-0.04482342 0.07529420 0.99615342 113.44095535
Axis 0.04409183 -0.02477358 -0.99872027
Axis point 192.03852716 134.42788571 0.00000000
Rotation angle (degrees) 120.25500255
Shift along axis -115.10207321
> hide #!25.2 models
> show #25.3 models
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 44
shifted from previous position = 0.054
rotated from previous position = 0.0481 degrees
atoms outside contour = 737, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47518849 0.87648454 -0.07727061 158.58564377
-0.87871888 -0.47724366 -0.00957144 369.81381560
-0.04526613 0.06335090 0.99696421 112.93537532
Axis 0.04150368 -0.01821532 -0.99897230
Axis point 191.06573654 135.29446658 0.00000000
Rotation angle (degrees) 118.53750854
Shift along axis -112.97369921
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 64
shifted from previous position = 0.0507
rotated from previous position = 0.0272 degrees
atoms outside contour = 732, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47532486 0.87644646 -0.07686258 158.53837832
-0.87864630 -0.47737353 -0.00975648 369.87524863
-0.04524320 0.06289752 0.99699395 112.94969031
Axis 0.04135398 -0.01799746 -0.99898245
Axis point 191.04184026 135.36488118 0.00000000
Rotation angle (degrees) 118.54522094
Shift along axis -112.93537940
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.0187
rotated from previous position = 0.014 degrees
atoms outside contour = 734, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47527994 0.87646538 -0.07692468 158.52367551
-0.87865859 -0.47734607 -0.00999032 369.89893637
-0.04547587 0.06284233 0.99698685 113.00413809
Axis 0.04145483 -0.01790001 -0.99898002
Axis point 191.05652571 135.38051906 0.00000000
Rotation angle (degrees) 118.54309199
Shift along axis -112.93849955
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 44
shifted from previous position = 0.0384
rotated from previous position = 0.0184 degrees
atoms outside contour = 734, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47533018 0.87642335 -0.07709296 158.58640517
-0.87863936 -0.47738704 -0.00972003 369.84429471
-0.04532204 0.06311669 0.99697652 112.96267918
Axis 0.04145844 -0.01808392 -0.99897656
Axis point 191.05786763 135.32713922 0.00000000
Rotation angle (degrees) 118.54640344
Shift along axis -112.96055642
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 64
shifted from previous position = 0.0441
rotated from previous position = 0.0294 degrees
atoms outside contour = 730, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47515651 0.87654065 -0.07682952 158.48449319
-0.87872211 -0.47722632 -0.01012294 369.92210555
-0.04553824 0.06270182 0.99699285 113.05181481
Axis 0.04144714 -0.01780898 -0.99898197
Axis point 191.06480286 135.40078755 0.00000000
Rotation angle (degrees) 118.53496621
Shift along axis -112.95592957
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 40
shifted from previous position = 0.0416
rotated from previous position = 0.0456 degrees
atoms outside contour = 732, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47560906 0.87630331 -0.07673663 158.57882732
-0.87850696 -0.47763542 -0.00948209 369.84754069
-0.04496132 0.06290389 0.99700630 112.89946853
Axis 0.04120824 -0.01808920 -0.99898682
Axis point 191.00310529 135.35610620 0.00000000
Rotation angle (degrees) 118.56262877
Shift along axis -112.94057261
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 76
shifted from previous position = 0.0448
rotated from previous position = 0.0311 degrees
atoms outside contour = 734, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47526730 0.87645852 -0.07708070 158.57002802
-0.87867486 -0.47732212 -0.00969911 369.83916504
-0.04529319 0.06311920 0.99697767 112.96112486
Axis 0.04144632 -0.01809263 -0.99897691
Axis point 191.05622279 135.32528255 0.00000000
Rotation angle (degrees) 118.54219836
Shift along axis -112.96477632
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 64
shifted from previous position = 0.0132
rotated from previous position = 0.0162 degrees
atoms outside contour = 735, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47517741 0.87648910 -0.07728691 158.58719798
-0.87872597 -0.47723124 -0.00953915 369.80660124
-0.04524469 0.06338123 0.99696325 112.92983269
Axis 0.04150227 -0.01823667 -0.99897196
Axis point 191.06507637 135.28853304 0.00000000
Rotation angle (degrees) 118.53677364
Shift along axis -112.97604896
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.00626
rotated from previous position = 0.0138 degrees
atoms outside contour = 734, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47524832 0.87646522 -0.07712165 158.57460902
-0.87868451 -0.47730450 -0.00969196 369.83142480
-0.04530518 0.06315951 0.99697457 112.96672946
Axis 0.04146476 -0.01810893 -0.99897585
Axis point 191.05927194 135.31724824 0.00000000
Rotation angle (degrees) 118.54110551
Shift along axis -112.97302762
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 60
shifted from previous position = 0.0518
rotated from previous position = 0.0162 degrees
atoms outside contour = 732, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47535329 0.87643098 -0.07686337 158.54627710
-0.87863301 -0.47739898 -0.00970769 369.87016193
-0.04520261 0.06292011 0.99699437 112.94058206
Axis 0.04133975 -0.01802130 -0.99898261
Axis point 191.03866438 135.36087099 0.00000000
Rotation angle (degrees) 118.54696470
Shift along axis -112.93695699
> hide #25.3 models
> show #!25.4 models
> fitmap #25.4 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif D (#25.4) to map
postprocess_20231221.mrc (#1) using 706 atoms
average map value = 0.005749, steps = 44
shifted from previous position = 0.0483
rotated from previous position = 0.0777 degrees
atoms outside contour = 92, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif D (#25.4) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49175644 0.86568701 -0.09360338 166.01477332
-0.87058599 -0.49079828 0.03459883 365.70599887
-0.01598862 0.09850399 0.99500820 106.55878534
Axis 0.03674439 -0.04462718 -0.99832773
Axis point 190.07626131 130.81897209 0.00000000
Rotation angle (degrees) 119.58889033
Shift along axis -116.60090709
> fitmap #25.4 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif D (#25.4) to map
postprocess_20231221.mrc (#1) using 706 atoms
average map value = 0.005749, steps = 44
shifted from previous position = 0.00111
rotated from previous position = 0.00328 degrees
atoms outside contour = 92, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif D (#25.4) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.49177182 0.86567510 -0.09363271 166.02076157
-0.87057630 -0.49081850 0.03455563 365.70949473
-0.01604272 0.09850790 0.99500694 106.56690226
Axis 0.03677193 -0.04461348 -0.99832733
Axis point 190.07986149 130.81979432 0.00000000
Rotation angle (degrees) 119.59010474
Shift along axis -116.59931997
> hide #!25.4 models
> show #8 models
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003728, steps = 56
shifted from previous position = 0.0299
rotated from previous position = 0.0476 degrees
atoms outside contour = 697, contour level = 0.0026099
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23860010 0.93122280 0.27548884 -92.93313357
-0.88661028 0.09314362 0.45304137 105.82589483
0.39622242 -0.35234695 0.84785578 472.48356496
Axis -0.40432771 -0.06061167 -0.91260360
Axis point -102.22586219 189.90213751 0.00000000
Rotation angle (degrees) 84.84791292
Shift along axis -400.02904637
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003728, steps = 44
shifted from previous position = 0.0631
rotated from previous position = 0.119 degrees
atoms outside contour = 699, contour level = 0.0026099
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23980372 0.93133895 0.27404734 -92.97708941
-0.88584969 0.09442385 0.45426257 105.58989849
0.39719582 -0.35169860 0.84766950 472.32860191
Axis -0.40465765 -0.06183049 -0.91237557
Axis point -102.68373743 189.74615125 0.00000000
Rotation angle (degrees) 84.78182200
Shift along axis -399.84586167
> hide #8 models
> show #!9 models
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 48
shifted from previous position = 0.0589
rotated from previous position = 0.0374 degrees
atoms outside contour = 3625, contour level = 0.0026099
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48869765 -0.51171806 -0.70662524 223.57914699
0.54907211 -0.44902694 0.70490752 282.28473714
-0.67800769 -0.73247486 0.06153171 258.72752902
Axis -0.80450694 -0.01601733 0.59372723
Axis point 0.00000000 245.02451097 103.92196750
Rotation angle (degrees) 116.70511792
Shift along axis -30.77884326
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 44
shifted from previous position = 0.0104
rotated from previous position = 0.00895 degrees
atoms outside contour = 3621, contour level = 0.0026099
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48883282 -0.51165712 -0.70657587 223.57062704
0.54903299 -0.44898430 0.70496515 282.29045776
-0.67794192 -0.73254357 0.06143838 258.72873284
Axis -0.80455852 -0.01602612 0.59365711
Axis point 0.00000000 245.03043827 103.90366345
Rotation angle (degrees) 116.70240841
Shift along axis -30.80352213
> hide #!9 models
> show #!25.6 models
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 40
shifted from previous position = 0.0495
rotated from previous position = 0.0484 degrees
atoms outside contour = 3619, contour level = 0.0026099
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48948640 -0.51114897 -0.70649118 223.51703606
0.54884026 -0.44899469 0.70510860 282.30192656
-0.67762633 -0.73289187 0.06076234 258.73320035
Axis -0.80484119 -0.01615551 0.59327031
Axis point 0.00000000 245.01224896 103.84167427
Rotation angle (degrees) 116.70346172
Shift along axis -30.95772135
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 44
shifted from previous position = 0.0542
rotated from previous position = 0.0567 degrees
atoms outside contour = 3613, contour level = 0.0026099
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48878646 -0.51166535 -0.70660198 223.57207532
0.54926427 -0.44877614 0.70491754 282.27235203
-0.67778799 -0.73266537 0.06168380 258.74790944
Axis -0.80450784 -0.01612504 0.59372311
Axis point 0.00000000 245.04686971 103.90184910
Rotation angle (degrees) 116.68935055
Shift along axis -30.79252770
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 48
shifted from previous position = 0.014
rotated from previous position = 0.0161 degrees
atoms outside contour = 3623, contour level = 0.0026099
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48880777 -0.51161079 -0.70662675 223.57376434
0.54909324 -0.44899243 0.70491305 282.28181295
-0.67791119 -0.73257094 0.06145103 258.72889521
Axis -0.80454933 -0.01607189 0.59366832
Axis point 0.00000000 245.02207305 103.91147262
Rotation angle (degrees) 116.70306678
Shift along axis -30.81377494
> fitmap #9 inMap #1
Fit molecule CopG_Q9QZE5 (#9) to map postprocess_20231221.mrc (#1) using 6673
atoms
average map value = 0.003524, steps = 40
shifted from previous position = 0.0168
rotated from previous position = 0.00674 degrees
atoms outside contour = 3620, contour level = 0.0026099
Position of CopG_Q9QZE5 (#9) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.48884254 -0.51164875 -0.70657521 223.56186580
0.54899521 -0.44902301 0.70496992 282.29147811
-0.67796550 -0.73252570 0.06139116 258.73202214
Axis -0.80456844 -0.01601289 0.59364401
Axis point 0.00000000 245.02601416 103.90513276
Rotation angle (degrees) 116.70485206
Shift along axis -30.79641215
> hide #!25.6 models
> show #!25.7 models
> fitmap #25.7 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif K (#25.7) to map
postprocess_20231221.mrc (#1) using 2239 atoms
average map value = 0.005453, steps = 68
shifted from previous position = 5.09
rotated from previous position = 3.83 degrees
atoms outside contour = 897, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif K (#25.7) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.52809778 0.84897184 -0.01896147 162.25143821
-0.84908305 -0.52756007 0.02717232 368.47098555
0.01306522 0.03044950 0.99945091 106.79493761
Axis 0.00192961 -0.01885742 -0.99982032
Axis point 183.03405856 138.07720643 0.00000000
Rotation angle (degrees) 121.87740335
Shift along axis -113.41107829
> fitmap #25.7 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif K (#25.7) to map
postprocess_20231221.mrc (#1) using 2239 atoms
average map value = 0.005454, steps = 44
shifted from previous position = 0.0759
rotated from previous position = 0.124 degrees
atoms outside contour = 905, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif K (#25.7) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.52840627 0.84882470 -0.01683532 162.07563992
-0.84887694 -0.52790507 0.02691033 368.52314419
0.01395470 0.02851070 0.99949607 107.05091473
Axis 0.00094251 -0.01813331 -0.99983513
Axis point 182.88564640 138.23925690 0.00000000
Rotation angle (degrees) 121.89792835
Shift along axis -113.56305017
> hide #!25.7 models
> show #25.8 models
> fitmap #25.8 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif L (#25.8) to map
postprocess_20231221.mrc (#1) using 555 atoms
average map value = 0.009445, steps = 72
shifted from previous position = 4.8
rotated from previous position = 5.37 degrees
atoms outside contour = 61, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif L (#25.8) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.50953081 0.86016443 -0.02225986 156.84466949
-0.86007521 -0.50837107 0.04277251 364.92411960
0.02547512 0.04093906 0.99883682 103.35018694
Axis -0.00106540 -0.02773834 -0.99961465
Axis point 181.51446483 136.34374262 0.00000000
Rotation angle (degrees) 120.63269672
Shift along axis -113.59985176
> hide #25.8 models
> show #25.9 models
> fitmap #25.9 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif M (#25.9) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.005017, steps = 64
shifted from previous position = 2.67
rotated from previous position = 5.57 degrees
atoms outside contour = 32, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif M (#25.9) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.54245973 0.83717279 0.06985093 157.30691966
-0.83809913 -0.54501467 0.02342739 368.53850958
0.05768256 -0.04583358 0.99728230 115.07742252
Axis -0.04130675 0.00725713 -0.99912016
Axis point 176.58181683 143.30451871 0.00000000
Rotation angle (degrees) 123.03122791
Shift along axis -118.79947888
> hide #25.9 models
> show #25.10 models
> fitmap #25.10 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.005793, steps = 60
shifted from previous position = 1.15
rotated from previous position = 1.46 degrees
atoms outside contour = 78, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.56117641 0.82769249 -0.00248451 165.77495010
-0.82682250 -0.56071939 -0.04425285 376.49759487
-0.03802086 -0.02277941 0.99901727 120.78977355
Axis 0.01297461 0.02147165 -0.99968526
Axis point 184.09818845 145.22408755 0.00000000
Rotation angle (degrees) 124.15539123
Shift along axis -110.51686734
> fitmap #25.10 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
postprocess_20231221.mrc (#1) using 635 atoms
average map value = 0.005793, steps = 44
shifted from previous position = 0.013
rotated from previous position = 0.0303 degrees
atoms outside contour = 78, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.56102005 0.82779773 -0.00272041 165.76483812
-0.82693876 -0.56058191 -0.04382006 376.44606227
-0.03779916 -0.02233431 0.99903573 120.69649921
Axis 0.01298038 0.02119244 -0.99969115
Axis point 184.09340805 145.17307910 0.00000000
Rotation angle (degrees) 124.14458036
Shift along axis -110.52971987
> hide #25.10 models
> show #25.11 models
> fitmap #25.11 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) to map
postprocess_20231221.mrc (#1) using 555 atoms
average map value = 0.006618, steps = 56
shifted from previous position = 0.987
rotated from previous position = 4.56 degrees
atoms outside contour = 13, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.51534999 0.85618388 -0.03692622 163.83052471
-0.85697829 -0.51478944 0.02408388 365.15179210
0.00161100 0.04405659 0.99902773 110.02746277
Axis 0.01165465 -0.02248757 -0.99967919
Axis point 185.07392398 134.62747847 0.00000000
Rotation angle (degrees) 121.03461621
Shift along axis -116.29415434
> fitmap #25.11 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) to map
postprocess_20231221.mrc (#1) using 555 atoms
average map value = 0.006619, steps = 56
shifted from previous position = 0.0125
rotated from previous position = 0.0228 degrees
atoms outside contour = 13, contour level = 0.0026099
Position of 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.51510414 0.85634315 -0.03666222 163.77587716
-0.85712590 -0.51454655 0.02402157 365.14477906
0.00170628 0.04379774 0.99903895 110.05636752
Axis 0.01153794 -0.02238519 -0.99968284
Axis point 185.07618372 134.63281353 0.00000000
Rotation angle (degrees) 121.01790200
Shift along axis -116.30566190
> hide #25.11 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> fitmap #26.1 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#26.1) to map
postprocess_20231221.mrc (#1) using 1306 atoms
average map value = 0.00438, steps = 48
shifted from previous position = 0.0519
rotated from previous position = 0.127 degrees
atoms outside contour = 335, contour level = 0.0026099
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#26.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.18847588 0.19690185 -0.96213642 281.01818938
0.68066320 0.73240949 0.01655086 273.62397864
0.70793675 -0.65177142 -0.27206537 179.30959236
Axis -0.35878329 -0.89656497 0.25970329
Axis point -12.14308848 0.00000000 195.36315833
Rotation angle (degrees) 111.35010673
Shift along axis -299.57901651
> hide #!26.2 models
> show #!26.2 models
> fitmap #26.2 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) to map
postprocess_20231221.mrc (#1) using 2069 atoms
average map value = 0.005973, steps = 40
shifted from previous position = 0.0411
rotated from previous position = 0.0333 degrees
atoms outside contour = 595, contour level = 0.0026099
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.25112743 0.19896442 -0.94728463 280.14955795
0.70125958 0.71197797 -0.03636418 273.60673566
0.66721061 -0.67342447 -0.31832291 179.23078798
Axis -0.35257877 -0.89353670 0.27799349
Axis point -6.18676783 0.00000000 194.69723932
Rotation angle (degrees) 115.38738201
Shift along axis -293.42745438
> fitmap #26.3 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
postprocess_20231221.mrc (#1) using 1128 atoms
average map value = 0.004508, steps = 44
shifted from previous position = 0.0401
rotated from previous position = 0.0984 degrees
atoms outside contour = 321, contour level = 0.0026099
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.24788043 0.18304448 -0.95134116 278.85298200
0.71427199 0.69794712 -0.05182019 272.73112847
0.65450043 -0.69236155 -0.30375098 178.06704899
Axis -0.35415396 -0.88786639 0.29371456
Axis point -8.77830869 0.00000000 197.19185440
Rotation angle (degrees) 115.26732127
Shift along axis -288.60480618
> fitmap #26.3 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
postprocess_20231221.mrc (#1) using 1128 atoms
average map value = 0.004508, steps = 64
shifted from previous position = 0.012
rotated from previous position = 0.0352 degrees
atoms outside contour = 318, contour level = 0.0026099
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.24796808 0.18246169 -0.95143027 278.83442524
0.71425394 0.69792925 -0.05230738 272.75307943
0.65448693 -0.69253338 -0.30338816 178.04496522
Axis -0.35395583 -0.88784859 0.29400706
Axis point -8.79177732 0.00000000 197.26697225
Rotation angle (degrees) 115.25917032
Shift along axis -288.51202928
> hide #!26 models
> hide #!26.1 models
> hide #!26.2 models
> hide #26.3 models
> hide #!25 models
> show #24 models
> fitmap #24 inMap #1
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map postprocess_20231221.mrc (#1)
using 1934 atoms
average map value = 0.003249, steps = 28
shifted from previous position = 0.0375
rotated from previous position = 0.0176 degrees
atoms outside contour = 520, contour level = 0.0026099
Position of 3kn1_Golph3_xtal.cif (#24) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
0.23176072 0.95684027 -0.17533874 148.11891218
0.01096390 -0.18280423 -0.98308820 219.61211962
-0.97271104 0.22591883 -0.05285755 161.82170270
Axis 0.69893176 0.46096409 -0.54681487
Axis point 0.00000000 -31.89182107 207.24160583
Rotation angle (degrees) 120.12912994
Shift along axis 116.27179801
> fitmap #24 inMap #1
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map postprocess_20231221.mrc (#1)
using 1934 atoms
average map value = 0.00325, steps = 28
shifted from previous position = 0.0392
rotated from previous position = 0.0284 degrees
atoms outside contour = 520, contour level = 0.0026099
Position of 3kn1_Golph3_xtal.cif (#24) relative to postprocess_20231221.mrc
(#1) coordinates:
Matrix rotation and translation
0.23211744 0.95670781 -0.17558947 148.15930491
0.01108837 -0.18311074 -0.98302976 219.64929055
-0.97262456 0.22623135 -0.05311152 161.80787421
Axis 0.69912644 0.46080066 -0.54670373
Axis point 0.00000000 -31.82049284 207.20523321
Rotation angle (degrees) 120.13587974
Shift along axis 116.33565695
> show #11 models
> hide #24 models
> fitmap #11 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#11) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 48
shifted from previous position = 0.0446
rotated from previous position = 0.0524 degrees
atoms outside contour = 802, contour level = 0.0026099
Position of Golph3_ Q9CRA5.pdb (#11) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66114170 -0.23531581 0.71240306 198.02073230
-0.68852537 -0.56749706 0.45153062 233.21090068
0.29803435 -0.78903330 -0.53721687 191.32348518
Axis -0.89621076 0.29934910 -0.32740859
Axis point 0.00000000 180.07923499 -4.24272432
Rotation angle (degrees) 136.20214329
Shift along axis -170.29778917
> fitmap #11 inMap #1
Fit molecule Golph3_ Q9CRA5.pdb (#11) to map postprocess_20231221.mrc (#1)
using 2367 atoms
average map value = 0.0031, steps = 40
shifted from previous position = 0.0266
rotated from previous position = 0.0483 degrees
atoms outside contour = 804, contour level = 0.0026099
Position of Golph3_ Q9CRA5.pdb (#11) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.66078286 -0.23607293 0.71248549 198.03562590
-0.68900494 -0.56730843 0.45103584 233.22569948
0.29772167 -0.78894278 -0.53752310 191.33298066
Axis -0.89610969 0.29974217 -0.32732561
Axis point 0.00000000 180.13836515 -4.22165558
Rotation angle (degrees) 136.22186734
Shift along axis -170.18225266
> hide #11 models
> volume #1 level 0.003696
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v6.cxs"
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/3mkq_yeast_alpha_betaprimeCOPI.cif"
3mkq_yeast_alpha_betaprimeCOPI.cif title:
Crystal structure of yeast alpha/betaprime-COP subcomplex of the COPI
vesicular coat [more info...]
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif #27
---
Chain | Description | UniProt
A C E | Coatomer beta'-subunit | A6ZU46_YEAS7 1-814
B D F | Coatomer subunit alpha | COPA_YEAST 642-818
3mkq_yeast_alpha_betaprimeCOPI.cif mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
4| software_defined_assembly
> select add #27
23730 atoms, 23992 bonds, 2 pseudobonds, 3231 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #27,1,0,0,392.67,0,1,0,238.34,0,0,1,282.33
> view matrix models #27,1,0,0,417.09,0,1,0,317.03,0,0,1,269.19
> view matrix models #27,1,0,0,396.35,0,1,0,248.96,0,0,1,148.11
> view matrix models #27,1,0,0,352.36,0,1,0,262.58,0,0,1,140.07
> select subtract #27
Nothing selected
> select add #27
23730 atoms, 23992 bonds, 2 pseudobonds, 3231 residues, 2 models selected
> select subtract #27
Nothing selected
> hide #!27 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/3mkr_yeast_alpha_epsilonCOPI.cif"
3mkr_yeast_alpha_epsilonCOPI.cif title:
Crystal structure of yeast alpha/epsilon-COP subcomplex of the COPI vesicular
coat [more info...]
Chain information for 3mkr_yeast_alpha_epsilonCOPI.cif #28
---
Chain | Description | UniProt
A | Coatomer subunit epsilon | COPE_BOVIN 17-307
B | Coatomer subunit alpha | COPA_BOVIN 905-1224
> select add #28
4908 atoms, 4974 bonds, 645 residues, 1 model selected
> view matrix models #28,1,0,0,338.36,0,1,0,298.71,0,0,1,206.93
> view matrix models #28,1,0,0,261.35,0,1,0,284.84,0,0,1,295.86
> select subtract #28
Nothing selected
> hide #28 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/1pzd_Cow_Cterm_COPI_gamma.cif"
1pzd_Cow_Cterm_COPI_gamma.cif title:
Structural Identification of a conserved appendage domain in the carboxyl-
terminus of the COPI gamma-subunit. [more info...]
Chain information for 1pzd_Cow_Cterm_COPI_gamma.cif #29
---
Chain | Description | UniProt
A | Coatomer gamma subunit | COPG_BOVIN 555-874
Non-standard residues in 1pzd_Cow_Cterm_COPI_gamma.cif #29
---
SO4 — sulfate ion
> select add #29
2270 atoms, 2156 bonds, 426 residues, 1 model selected
> view matrix models #29,1,0,0,234.68,0,1,0,350.63,0,0,1,60.953
> view matrix models #29,1,0,0,415.01,0,1,0,436.04,0,0,1,263.89
> view matrix models #29,1,0,0,353.18,0,1,0,323.73,0,0,1,357.15
> select subtract #29
Nothing selected
> hide #29 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/4j87_yeast_alphaCOPI.cif"
4j87_yeast_alphaCOPI.cif title:
Crystal structure of alpha-COP [more info...]
Chain information for 4j87_yeast_alphaCOPI.cif #30
---
Chain | Description | UniProt
A | coatomer subunit alpha | COPA_SCHPO 1-327
> select add #30
2737 atoms, 2622 bonds, 1 pseudobond, 505 residues, 2 models selected
> view matrix models #30,1,0,0,419.29,0,1,0,126.53,0,0,1,226.78
> view matrix models #30,1,0,0,249.55,0,1,0,194.59,0,0,1,357.2
> view matrix models #30,1,0,0,295.54,0,1,0,289.31,0,0,1,436.41
> view matrix models #30,1,0,0,332.12,0,1,0,305.75,0,0,1,378.14
> select subtract #30
Nothing selected
> hide #!30 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/5mc7_human_zeta1COPI.cif"
5mc7_human_zeta1COPI.cif title:
Crystal structure of Truncated Human Coatomer Protein Complex, subunit Z1
(CopZ1) [more info...]
Chain information for 5mc7_human_zeta1COPI.cif #31
---
Chain | Description | UniProt
A B | Coatomer subunit zeta-1 | COPZ1_HUMAN 7-150
5mc7_human_zeta1COPI.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select add #31
2340 atoms, 2256 bonds, 394 residues, 1 model selected
> view matrix models #31,1,0,0,330.02,0,1,0,82.452,0,0,1,370.35
> view matrix models #31,1,0,0,244.56,0,1,0,227.11,0,0,1,313.43
> view matrix models #31,1,0,0,289.31,0,1,0,324.83,0,0,1,331.93
> select subtract #31
Nothing selected
> hide #31 models
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/5mu7_Thermophila_beta_deltaCOPI.cif"
5mu7_Thermophila_beta_deltaCOPI.cif title:
Crystal Structure of the beta/delta-COPI Core Complex [more info...]
Chain information for 5mu7_Thermophila_beta_deltaCOPI.cif #32
---
Chain | Description | UniProt
A | Coatomer subunit beta | G0S6G7_CHATD 19-391
B | Coatomer subunit delta-like protein | G0S6I4_CHATD 1-175
> select add #32
4213 atoms, 4232 bonds, 565 residues, 1 model selected
> view matrix models #32,1,0,0,355.8,0,1,0,175.3,0,0,1,23.729
> view matrix models #32,1,0,0,206.13,0,1,0,267.92,0,0,1,311.94
> view matrix models #32,1,0,0,310.15,0,1,0,268.59,0,0,1,354.79
> select subtract #32
Nothing selected
> hide #32 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v7.cxs"
> show #!26 models
> show #!26.1 models
> show #!26.2 models
> show #26.3 models
> hide #!26 models
> show #!27 models
> split #27 chains
Split 3mkq_yeast_alpha_betaprimeCOPI.cif (#27) into 6 models
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif A #27.1
---
Chain | Description
A | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif B #27.2
---
Chain | Description
B | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif C #27.3
---
Chain | Description
C | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif D #27.4
---
Chain | Description
D | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif E #27.5
---
Chain | Description
E | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif F #27.6
---
Chain | Description
F | No description available
> close #27.5
> close #27.6
> close #27.3
> close #27.4
> hide #27.2 models
> hide #27.1 models
> show #27.1 models
> show #27.2 models
> select #27.1/A
6538 atoms, 6591 bonds, 911 residues, 1 model selected
> color sel blue
> hide #27.1 models
> select subtract #27.1
Nothing selected
> hide #27.2 models
> show #27.2 models
> select add #27.2
1407 atoms, 1415 bonds, 194 residues, 1 model selected
> color sel cyan
> show #27.1 models
> select add #27.1
7945 atoms, 8006 bonds, 1105 residues, 2 models selected
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> select subtract #27
Nothing selected
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> show #3 models
> show #7 models
> undo
[Repeated 9 time(s)]
> hide #!27 models
> show #!27 models
> hide #!27 models
> close #27
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/3mkq_yeast_alpha_betaprimeCOPI.cif"
3mkq_yeast_alpha_betaprimeCOPI.cif title:
Crystal structure of yeast alpha/betaprime-COP subcomplex of the COPI
vesicular coat [more info...]
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif #27
---
Chain | Description | UniProt
A C E | Coatomer beta'-subunit | A6ZU46_YEAS7 1-814
B D F | Coatomer subunit alpha | COPA_YEAST 642-818
3mkq_yeast_alpha_betaprimeCOPI.cif mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
4| software_defined_assembly
> split #27 chains
Split 3mkq_yeast_alpha_betaprimeCOPI.cif (#27) into 6 models
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif A #27.1
---
Chain | Description
A | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif B #27.2
---
Chain | Description
B | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif C #27.3
---
Chain | Description
C | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif D #27.4
---
Chain | Description
D | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif E #27.5
---
Chain | Description
E | No description available
Chain information for 3mkq_yeast_alpha_betaprimeCOPI.cif F #27.6
---
Chain | Description
F | No description available
> select add #27
23730 atoms, 23992 bonds, 2 pseudobonds, 3231 residues, 9 models selected
> view matrix models #27,1,0,0,-33.471,0,1,0,18.268,0,0,1,-43.011
> view matrix models #27,1,0,0,-66.467,0,1,0,47.118,0,0,1,-97.087
> hide sel atoms
> show sel cartoons
> view matrix models #27,1,0,0,-110.34,0,1,0,105.95,0,0,1,6.2245
> view matrix models #27,1,0,0,-112.27,0,1,0,152.59,0,0,1,154.38
> view matrix models #27,1,0,0,-43.946,0,1,0,169.44,0,0,1,304.3
> view matrix models #27,1,0,0,5.3436,0,1,0,169.99,0,0,1,376.48
> view matrix models #27,1,0,0,199.46,0,1,0,49.048,0,0,1,271.6
> view matrix models #27,1,0,0,220.77,0,1,0,261.81,0,0,1,312.16
> view matrix models #27,1,0,0,264.54,0,1,0,181.16,0,0,1,203.66
> view matrix models #27,1,0,0,359.57,0,1,0,289.43,0,0,1,185.26
> view matrix models #27,1,0,0,351.51,0,1,0,278.44,0,0,1,154.94
> view matrix models #27,1,0,0,348.56,0,1,0,271.19,0,0,1,154.23
> view matrix models #27,1,0,0,310.53,0,1,0,384.31,0,0,1,171.03
> view matrix models #27,1,0,0,352.37,0,1,0,269.74,0,0,1,153.79
> hide #27.1 models
> show #27.1 models
> hide #!1 models
> select subtract #27
Nothing selected
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
> show #3 models
> show #7 models
> close #27.3
> close #27.4
> close #27.5
> close #27.6
> select add #27.1
6538 atoms, 6591 bonds, 911 residues, 1 model selected
> color sel blue
> select subtract #27.1
Nothing selected
> select add #27.2
1407 atoms, 1415 bonds, 194 residues, 1 model selected
> color sel cyan\
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel cyan
> select add #27.1
7945 atoms, 8006 bonds, 1105 residues, 2 models selected
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> select subtract #27
Nothing selected
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> view matrix models #27,1,0,0,224.88,0,1,0,278.4,0,0,1,185.4
> ui mousemode right "rotate selected models"
> view matrix models
> #27,-0.8019,-0.39029,-0.45235,357.11,0.26435,-0.91078,0.31718,431.22,-0.53579,0.13477,0.83353,205.04
> view matrix models
> #27,-0.3088,-0.50226,0.8077,151.67,0.82975,-0.55736,-0.029367,446.47,0.46493,0.66112,0.58886,180.55
> view matrix models
> #27,-0.39879,-0.41722,0.81663,141.04,0.67815,-0.73363,-0.043649,469.43,0.61732,0.53639,0.5755,196.08
> ui mousemode right "translate selected models"
> view matrix models
> #27,-0.39879,-0.41722,0.81663,160.04,0.67815,-0.73363,-0.043649,420.23,0.61732,0.53639,0.5755,168.81
> view matrix models
> #27,-0.39879,-0.41722,0.81663,167.07,0.67815,-0.73363,-0.043649,415.41,0.61732,0.53639,0.5755,172.38
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.087653,0.44658,0.89044,55.324,0.95808,-0.28254,0.047392,348.03,0.27275,0.84896,-0.45263,313.8
> view matrix models
> #27,-0.00017276,0.96234,0.27185,106.34,0.92638,0.10253,-0.36236,376.65,-0.37658,0.25178,-0.89151,459.02
> view matrix models
> #27,-0.56985,0.14592,0.80869,109.58,0.79912,-0.13098,0.58673,242.14,0.19153,0.98059,-0.04197,229.92
> ui mousemode right "translate selected models"
> view matrix models
> #27,-0.56985,0.14592,0.80869,109.79,0.79912,-0.13098,0.58673,242.97,0.19153,0.98059,-0.04197,231.59
> view matrix models
> #27,-0.56985,0.14592,0.80869,90.528,0.79912,-0.13098,0.58673,243.4,0.19153,0.98059,-0.04197,255.5
> ui mousemode right "rotate selected models"
> view matrix models
> #27,-0.39522,0.80772,-0.43749,229.61,0.20082,-0.38877,-0.89918,529.2,-0.89637,-0.44323,-0.0085523,416.21
> view matrix models
> #27,0.32357,0.9258,0.19545,103.01,0.85876,-0.2006,-0.47148,430.34,-0.39729,0.3204,-0.85995,473.27
> select subtract #27
Nothing selected
> select add #27.1
6538 atoms, 6591 bonds, 911 residues, 1 model selected
> color sel cyan
> select subtract #27.1
Nothing selected
> select add #27.2
1407 atoms, 1415 bonds, 194 residues, 1 model selected
> color sel blue
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> select subtract #27
Nothing selected
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> view matrix models
> #27,0.67294,-0.17512,-0.71866,377.06,-0.41892,0.71051,-0.5654,354.34,0.60964,0.68154,0.40477,212.27
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.67294,-0.17512,-0.71866,420.58,-0.41892,0.71051,-0.5654,312.06,0.60964,0.68154,0.40477,205.11
> view matrix models
> #27,0.67294,-0.17512,-0.71866,426.42,-0.41892,0.71051,-0.5654,314.25,0.60964,0.68154,0.40477,204.16
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.27365,-0.79674,-0.53882,467.55,-0.36388,0.43281,-0.82478,388.29,0.89034,0.42177,-0.17148,328.22
> view matrix models
> #27,0.0094825,-0.88128,-0.47249,467.78,-0.48973,0.40787,-0.77059,382.87,0.87182,0.2387,-0.42772,392.01
> view matrix models
> #27,0.04732,-0.84816,-0.52763,473.19,-0.51437,0.43211,-0.74075,375.35,0.85626,0.30645,-0.41582,382.68
> ui mousemode right zoom
> select subtract #27
Nothing selected
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> select subtract #27
Nothing selected
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> select subtract #27
Nothing selected
> ui mousemode right "rotate selected models"
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> view matrix models
> #27,0.46289,-0.51191,-0.72366,466.08,-0.47119,0.5494,-0.69003,353.49,0.75081,0.66039,0.013104,271.83
> view matrix models
> #27,0.53247,-0.48857,-0.69121,457.42,-0.40665,0.56853,-0.71513,355.11,0.74236,0.66187,0.10405,256.29
> ui mousemode right "translate selected models"
> view matrix models
> #27,0.53247,-0.48857,-0.69121,452.1,-0.40665,0.56853,-0.71513,360.23,0.74236,0.66187,0.10405,262.33
> view matrix models
> #27,0.53247,-0.48857,-0.69121,451.55,-0.40665,0.56853,-0.71513,361.48,0.74236,0.66187,0.10405,258.38
> select subtract #27
Nothing selected
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> show #!1 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> view matrix models
> #27,0.53247,-0.48857,-0.69121,450.51,-0.40665,0.56853,-0.71513,359.29,0.74236,0.66187,0.10405,264.47
> ui mousemode right "rotate selected models"
> view matrix models
> #27,0.29764,-0.72075,-0.62605,466.91,-0.60733,0.36301,-0.70666,382.11,0.73659,0.59055,-0.32968,346.04
> select subtract #27.2
6538 atoms, 6591 bonds, 911 residues, 2 models selected
> select add #27.2
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> select subtract #27.2
6538 atoms, 6591 bonds, 911 residues, 2 models selected
> select add #27.2
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
postprocess_20231221.mrc (#1) using 6538 atoms
average map value = 0.003372, steps = 64
shifted from previous position = 3.67
rotated from previous position = 5.26 degrees
atoms outside contour = 3801, contour level = 0.0036964
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99563534 -0.01884854 0.09140567 -126.42192730
0.01701031 0.99963793 0.02084829 -116.29768557
-0.09176553 -0.01920246 0.99559548 -103.45651657
Axis -0.20980309 0.95952970 0.18784414
Axis point -989.11740259 0.00000000 1575.71651882
Rotation angle (degrees) 5.47712995
Shift along axis -104.50107148
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
postprocess_20231221.mrc (#1) using 6538 atoms
average map value = 0.003372, steps = 24
shifted from previous position = 0.00833
rotated from previous position = 0.0572 degrees
atoms outside contour = 3796, contour level = 0.0036964
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99554749 -0.01869817 0.09238819 -126.60260018
0.01684025 0.99964080 0.02084884 -116.29480603
-0.09274484 -0.01920017 0.99550477 -103.42435891
Axis -0.20780890 0.96063031 0.18440409
Axis point -982.92709826 0.00000000 1557.96731563
Rotation angle (degrees) 5.52961189
Shift along axis -104.47904405
> fitmap #27.2 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
postprocess_20231221.mrc (#1) using 1407 atoms
average map value = 0.002636, steps = 76
shifted from previous position = 8.09
rotated from previous position = 17.7 degrees
atoms outside contour = 1160, contour level = 0.0036964
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99552776 0.00840910 -0.09409449 -103.09535974
0.01959858 0.95597622 0.29278894 -159.42111449
0.09241419 -0.29332364 0.95153605 -62.53786473
Axis -0.95275953 -0.30318054 0.01818914
Axis point 0.00000000 -280.34050268 351.75735188
Rotation angle (degrees) 17.91386203
Shift along axis 145.42095540
> hide #7 models
> select subtract #27.1
1407 atoms, 1415 bonds, 194 residues, 2 models selected
> hide #27.1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select subtract #27.2
1 model selected
> hide #27.2 models
> hide #!27 models
> select add #27
7945 atoms, 8006 bonds, 1105 residues, 3 models selected
> select subtract #27
Nothing selected
> show #28 models
> select add #28
4908 atoms, 4974 bonds, 645 residues, 1 model selected
> split #28 chains
Split 3mkr_yeast_alpha_epsilonCOPI.cif (#28) into 2 models
Chain information for 3mkr_yeast_alpha_epsilonCOPI.cif A #28.1
---
Chain | Description
A | No description available
Chain information for 3mkr_yeast_alpha_epsilonCOPI.cif B #28.2
---
Chain | Description
B | No description available
> select add #28.1
2342 atoms, 2367 bonds, 309 residues, 1 model selected
> select subtract #28.1
Nothing selected
> select add #28.2
2566 atoms, 2607 bonds, 336 residues, 1 model selected
> select subtract #28.2
Nothing selected
> hide #!1 models
> show #3 models
> select add #28.2
2566 atoms, 2607 bonds, 336 residues, 1 model selected
> select subtract #28.2
Nothing selected
> select add #28.2
2566 atoms, 2607 bonds, 336 residues, 1 model selected
> color sel blue
> select subtract #28.2
Nothing selected
> select add #28.1
2342 atoms, 2367 bonds, 309 residues, 1 model selected
> color sel orange
> select subtract #28.1
Nothing selected
> select add #28
4908 atoms, 4974 bonds, 645 residues, 3 models selected
> view matrix models
> #28,0.27094,-0.90598,-0.32525,650.32,-0.93818,-0.32415,0.12139,703.67,-0.21541,0.27225,-0.93781,646.09
> view matrix models
> #28,-0.72497,0.43806,-0.53153,610.37,-0.03694,0.74585,0.66509,-131.96,0.68779,0.5018,-0.52454,131.15
> ui mousemode right "translate selected models"
> view matrix models
> #28,-0.72497,0.43806,-0.53153,578.74,-0.03694,0.74585,0.66509,-102.29,0.68779,0.5018,-0.52454,169.61
> view matrix models
> #28,-0.72497,0.43806,-0.53153,572.54,-0.03694,0.74585,0.66509,-78.73,0.68779,0.5018,-0.52454,174.16
> ui mousemode right "rotate selected models"
> view matrix models
> #28,-0.61624,-0.35726,-0.70186,854.63,-0.52069,0.85344,0.022757,266.96,0.59087,0.37948,-0.71195,310.55
> view matrix models
> #28,-0.10838,-0.97616,-0.18805,713.55,-0.8857,0.18071,-0.42764,761.8,0.45142,0.12021,-0.88418,500.47
> view matrix models
> #28,0.1959,-0.68831,-0.69846,693.59,-0.74299,0.36067,-0.56381,702.29,0.63999,0.6294,-0.44075,119.75
> show #!1 models
> view matrix models
> #28,0.92946,0.13561,-0.3431,60.309,-0.11667,-0.77422,-0.62207,886.84,-0.34999,0.61822,-0.70378,538.85
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.92946,0.13561,-0.3431,41.654,-0.11667,-0.77422,-0.62207,861.16,-0.34999,0.61822,-0.70378,548.17
> view matrix models
> #28,0.92946,0.13561,-0.3431,43.224,-0.11667,-0.77422,-0.62207,848.66,-0.34999,0.61822,-0.70378,541.05
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.21767,0.93544,-0.27852,-4.1958,0.67225,-0.35057,-0.65206,458.24,-0.7076,-0.045302,-0.70516,877.28
> view matrix models
> #28,-0.20838,0.7607,-0.61474,309.65,0.79983,-0.22921,-0.55474,342.94,-0.5629,-0.60729,-0.56067,964.53
> hide #3 models
> show #3 models
> view matrix models
> #28,-0.37026,0.81787,-0.44045,284.72,0.91574,0.40097,-0.025257,-83.166,0.15595,-0.41269,-0.89742,778.5
> hide #!28 models
> hide #3 models
> show #!28 models
> view matrix models
> #28,0.54646,0.46329,-0.69767,183.82,0.3112,-0.88573,-0.34443,645.8,-0.77752,-0.028895,-0.62819,870.21
> hide #!28 models
> show #3 models
> hide #3 models
> show #!28 models
> show #3 models
> view matrix models
> #28,0.57422,0.45144,-0.68299,173.42,0.22738,-0.88935,-0.39667,692.76,-0.78649,0.072481,-0.61334,835.01
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.57422,0.45144,-0.68299,173.55,0.22738,-0.88935,-0.39667,708.24,-0.78649,0.072481,-0.61334,843.23
> view matrix models
> #28,0.57422,0.45144,-0.68299,175.76,0.22738,-0.88935,-0.39667,708.31,-0.78649,0.072481,-0.61334,839.12
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.56852,0.45387,-0.68614,177.95,0.22624,-0.88814,-0.40003,709.44,-0.79095,0.072191,-0.60761,838.73
> view matrix models
> #28,0.56184,0.42352,-0.71061,198.48,0.20667,-0.90363,-0.37516,712.5,-0.80101,0.063921,-0.59523,840.54
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.56184,0.42352,-0.71061,195.64,0.20667,-0.90363,-0.37516,706.04,-0.80101,0.063921,-0.59523,844.64
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.56647,0.33017,-0.75505,239.72,-0.052948,-0.89975,-0.43318,810.82,-0.82238,0.28536,-0.4922,744.22
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.56647,0.33017,-0.75505,238.7,-0.052948,-0.89975,-0.43318,806.34,-0.82238,0.28536,-0.4922,747.27
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.56476,0.24152,-0.78912,279.86,-0.40724,-0.75012,-0.52104,904.9,-0.71778,0.61562,-0.32528,547.7
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.56476,0.24152,-0.78912,279.03,-0.40724,-0.75012,-0.52104,904.01,-0.71778,0.61562,-0.32528,548.96
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.46944,0.26357,-0.84271,321.72,-0.35954,-0.81464,-0.45508,886.75,-0.80645,0.51661,-0.28766,597.77
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.46944,0.26357,-0.84271,323.88,-0.35954,-0.81464,-0.45508,888.31,-0.80645,0.51661,-0.28766,598.15
> view matrix models
> #28,0.46944,0.26357,-0.84271,322.26,-0.35954,-0.81464,-0.45508,888.45,-0.80645,0.51661,-0.28766,598.93
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.58942,0.23895,-0.77168,266.27,-0.34892,-0.78624,-0.50997,894.47,-0.72859,0.56984,-0.38005,587.44
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.58942,0.23895,-0.77168,266.89,-0.34892,-0.78624,-0.50997,895.27,-0.72859,0.56984,-0.38005,586.64
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!1 models
> show #!1 models
> select subtract #28
Nothing selected
> ui mousemode right zoom
> hide #!28 models
> show #29 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v8.cxs"
> select add #29
2270 atoms, 2156 bonds, 426 residues, 1 model selected
> color sel lime green
> select subtract #29
Nothing selected
> hide #29 models
> show #29 models
> select add #29
2270 atoms, 2156 bonds, 426 residues, 1 model selected
> show #!9 models
> hide #!1 models
> ui mousemode right "translate selected models"
> view matrix models #29,1,0,0,375.34,0,1,0,388.97,0,0,1,396.79
> view matrix models #29,1,0,0,428.18,0,1,0,380.13,0,0,1,342.71
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.83833,-0.49981,0.21772,422.81,0.32688,0.14123,-0.93445,366.32,0.4363,0.85455,0.28178,350.68
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.83833,-0.49981,0.21772,371.69,0.32688,0.14123,-0.93445,391.6,0.4363,0.85455,0.28178,399.82
> ui mousemode right zoom
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.8548,-0.37766,0.35593,374.92,0.47797,0.30579,-0.82343,397.49,0.20214,0.87399,0.4419,397.51
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.8548,-0.37766,0.35593,375,0.47797,0.30579,-0.82343,394.09,0.20214,0.87399,0.4419,399.97
> view matrix models
> #29,0.8548,-0.37766,0.35593,371.98,0.47797,0.30579,-0.82343,396.12,0.20214,0.87399,0.4419,403.61
> view matrix models
> #29,0.8548,-0.37766,0.35593,370.55,0.47797,0.30579,-0.82343,397.11,0.20214,0.87399,0.4419,403.75
> view matrix models
> #29,0.8548,-0.37766,0.35593,370.1,0.47797,0.30579,-0.82343,396.07,0.20214,0.87399,0.4419,400.61
> view matrix models
> #29,0.8548,-0.37766,0.35593,368.66,0.47797,0.30579,-0.82343,395.18,0.20214,0.87399,0.4419,399.13
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.79685,-0.40594,0.44748,368.4,0.54533,0.16442,-0.82194,395.08,0.26008,0.89899,0.35239,399.38
> view matrix models
> #29,0.93787,0.087344,0.33582,374.61,0.28212,0.37149,-0.88453,391.34,-0.20201,0.92432,0.32377,390.45
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.93787,0.087344,0.33582,374.66,0.28212,0.37149,-0.88453,390.76,-0.20201,0.92432,0.32377,389.31
> view matrix models
> #29,0.93787,0.087344,0.33582,372.22,0.28212,0.37149,-0.88453,390.66,-0.20201,0.92432,0.32377,390.82
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.92879,0.017925,0.37018,371.78,0.33922,0.3612,-0.8686,391.85,-0.14928,0.93232,0.3294,391.98
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.92879,0.017925,0.37018,372.65,0.33922,0.3612,-0.8686,391.75,-0.14928,0.93232,0.3294,391.71
> view matrix models
> #29,0.92879,0.017925,0.37018,373.04,0.33922,0.3612,-0.8686,392.19,-0.14928,0.93232,0.3294,390.82
> view matrix models
> #29,0.92879,0.017925,0.37018,372.95,0.33922,0.3612,-0.8686,392.11,-0.14928,0.93232,0.3294,390.88
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.93952,-0.036326,0.34055,372.25,0.32812,0.3804,-0.86466,392.14,-0.098138,0.92411,0.36932,392.27
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.93952,-0.036326,0.34055,372.49,0.32812,0.3804,-0.86466,391.54,-0.098138,0.92411,0.36932,392.82
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.93561,-0.042104,0.35051,372.48,0.33743,0.39859,-0.8528,392.04,-0.1038,0.91616,0.38713,392.85
> view matrix models
> #29,0.93508,-0.066989,0.34804,372.19,0.34797,0.36016,-0.86557,391.71,-0.067366,0.93048,0.36009,393.36
> select subtract #29
Nothing selected
> hide #29 models
> show #!1 models
> show #29 models
> hide #29 models
> show #29 models
> select add #29
2270 atoms, 2156 bonds, 426 residues, 1 model selected
> view matrix models
> #29,0.9287,-0.093321,0.3589,371.94,0.3671,0.36847,-0.85409,392.3,-0.052542,0.92494,0.37646,393.79
> view matrix models
> #29,0.93478,0.008194,0.35514,373.02,0.33418,0.31874,-0.88698,390.77,-0.12047,0.94781,0.29522,391.71
> select subtract #29
Nothing selected
> hide #29 models
> show #!30 models
> select add #30
2737 atoms, 2622 bonds, 1 pseudobond, 505 residues, 2 models selected
> color sel blue
> hide #!9 models
> show #3 models
> hide #!1 models
> view matrix models
> #30,0.79132,0.085843,0.60535,342.1,-0.0093616,0.99168,-0.12839,302.91,-0.61133,0.09593,0.78554,365.41
> view matrix models
> #30,-0.24899,0.12054,-0.96098,295.64,0.86303,0.4779,-0.16366,319.44,0.43952,-0.8701,-0.22302,369.25
> view matrix models
> #30,-0.27578,0.087921,-0.95719,295.96,0.90872,0.34843,-0.22981,320.5,0.31331,-0.9332,-0.17599,369.99
> ui mousemode right "translate selected models"
> view matrix models
> #30,-0.27578,0.087921,-0.95719,263.02,0.90872,0.34843,-0.22981,367.61,0.31331,-0.9332,-0.17599,317.21
> view matrix models
> #30,-0.27578,0.087921,-0.95719,256.75,0.90872,0.34843,-0.22981,369.1,0.31331,-0.9332,-0.17599,313.93
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.75135,-0.36095,0.55244,308.4,-0.54131,0.14169,0.8288,380.85,-0.37743,-0.92176,-0.088924,308.45
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.75135,-0.36095,0.55244,300.71,-0.54131,0.14169,0.8288,377.79,-0.37743,-0.92176,-0.088924,307.47
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.75135,-0.36095,0.55244,301.05,-0.54131,0.14169,0.8288,377.4,-0.37743,-0.92176,-0.088924,306.34
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.75135,-0.36095,0.55244,306.04,-0.54131,0.14169,0.8288,377.36,-0.37743,-0.92176,-0.088924,307.64
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.73746,-0.38813,0.55273,306.33,-0.52055,0.1948,0.83131,376.79,-0.43033,-0.90078,-0.05838,307.43
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.73746,-0.38813,0.55273,302.77,-0.52055,0.1948,0.83131,374.28,-0.43033,-0.90078,-0.05838,306.95
> view matrix models
> #30,0.73746,-0.38813,0.55273,303.4,-0.52055,0.1948,0.83131,375.49,-0.43033,-0.90078,-0.05838,305.83
> view matrix models
> #30,0.73746,-0.38813,0.55273,304.24,-0.52055,0.1948,0.83131,376.71,-0.43033,-0.90078,-0.05838,305.94
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.81542,-0.39068,0.42716,302.29,-0.40454,0.14323,0.90323,380.36,-0.41406,-0.90932,-0.04125,306.63
> view matrix models
> #30,0.82816,-0.48879,0.27428,300.57,-0.36661,-0.10223,0.92474,385.14,-0.42396,-0.86639,-0.26386,300.86
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.82816,-0.48879,0.27428,298.77,-0.36661,-0.10223,0.92474,382.56,-0.42396,-0.86639,-0.26386,300.43
> view matrix models
> #30,0.82816,-0.48879,0.27428,298.1,-0.36661,-0.10223,0.92474,384.39,-0.42396,-0.86639,-0.26386,299.48
> view matrix models
> #30,0.82816,-0.48879,0.27428,298.04,-0.36661,-0.10223,0.92474,383.35,-0.42396,-0.86639,-0.26386,300.87
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.78042,-0.47085,0.4114,300.32,-0.45137,0.031056,0.8918,379.61,-0.43268,-0.88167,-0.18829,302.71
> view matrix models
> #30,0.8048,-0.42303,0.41633,299.92,-0.45528,0.010045,0.89029,379.87,-0.3808,-0.90606,-0.18451,303.73
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.8048,-0.42303,0.41633,300.4,-0.45528,0.010045,0.89029,380.98,-0.3808,-0.90606,-0.18451,304.23
> view matrix models
> #30,0.8048,-0.42303,0.41633,300.6,-0.45528,0.010045,0.89029,380.37,-0.3808,-0.90606,-0.18451,303.94
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.83865,-0.45123,0.30505,298.92,-0.36787,-0.056235,0.92818,383.18,-0.40166,-0.89064,-0.21315,302.83
> view matrix models
> #30,0.79527,-0.52538,0.30252,299.59,-0.39715,-0.074472,0.91473,382.87,-0.45805,-0.8476,-0.26788,300.33
> ui mousemode right "translate selected models"
> view matrix models
> #30,0.79527,-0.52538,0.30252,299.35,-0.39715,-0.074472,0.91473,382.32,-0.45805,-0.8476,-0.26788,299.81
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.72405,-0.51886,0.45446,301.89,-0.54275,-0.021995,0.83961,378.28,-0.42564,-0.85458,-0.29753,299.59
> show #!1 models
> hide #!1 models
> hide #3 models
> show #!1 models
> fitmap #30 inMap #1
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map postprocess_20231221.mrc
(#1) using 2737 atoms
average map value = 0.003386, steps = 52
shifted from previous position = 1.93
rotated from previous position = 9.04 degrees
atoms outside contour = 1731, contour level = 0.0036964
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.80232827 -0.50188592 0.32307875 187.68257184
-0.41022520 -0.07048171 0.90925663 269.80500093
-0.43357196 -0.86205734 -0.26243572 189.57183217
Axis -0.91857179 0.39238555 0.04753362
Axis point 0.00000000 254.75327857 -21.62954113
Rotation angle (degrees) 105.38445736
Shift along axis -57.52129884
> hide #!1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> fitmap #3 inMap #1
Fit molecule CopA_F8WHL2.pdb (#3) to map postprocess_20231221.mrc (#1) using
9810 atoms
average map value = 0.001845, steps = 48
shifted from previous position = 0.0635
rotated from previous position = 0.06 degrees
atoms outside contour = 8390, contour level = 0.0036964
Position of CopA_F8WHL2.pdb (#3) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.89969968 0.40483834 0.16323723 162.22508583
-0.20999045 0.72925801 -0.65121943 244.63047450
-0.38268065 0.55162366 0.74112539 239.09252445
Axis 0.82555696 0.37468421 -0.42198038
Axis point 0.00000000 -323.15021497 438.25527850
Rotation angle (degrees) 46.76112549
Shift along axis 124.69286920
> hide #3 models
> hide #!30 models
> show #!30 models
> show #!1 models
> fitmap #30 inMap #1
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map postprocess_20231221.mrc
(#1) using 2737 atoms
average map value = 0.003385, steps = 28
shifted from previous position = 0.0431
rotated from previous position = 0.0812 degrees
atoms outside contour = 1725, contour level = 0.0036964
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.80295655 -0.50066555 0.32341119 187.67454501
-0.41013749 -0.07039394 0.90930300 269.81751356
-0.43249050 -0.86277384 -0.26186499 189.64270915
Axis -0.91879892 0.39192525 0.04693763
Axis point 0.00000000 254.75671482 -21.74749759
Rotation angle (degrees) 105.34622736
Shift along axis -57.78549428
> fitmap #30 inMap #1
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map postprocess_20231221.mrc
(#1) using 2737 atoms
average map value = 0.003386, steps = 28
shifted from previous position = 0.0564
rotated from previous position = 0.0807 degrees
atoms outside contour = 1733, contour level = 0.0036964
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.80231444 -0.50188366 0.32311660 187.68914075
-0.41022632 -0.07040021 0.90926244 269.80159975
-0.43359649 -0.86206531 -0.26236899 189.56128331
Axis -0.91856133 0.39241037 0.04753095
Axis point 0.00000000 254.75820348 -21.64414576
Rotation angle (degrees) 105.38046415
Shift along axis -57.52101283
> hide #!1 models
> hide #!30 models
> show #!30 models
> select subtract #30
Nothing selected
> select add #30
2737 atoms, 2622 bonds, 1 pseudobond, 505 residues, 2 models selected
> select subtract #30
Nothing selected
> hide #!30 models
> show #31 models
> select add #31
2340 atoms, 2256 bonds, 394 residues, 1 model selected
> split #31 chains
Split 5mc7_human_zeta1COPI.cif (#31) into 2 models
Chain information for 5mc7_human_zeta1COPI.cif A #31.1
---
Chain | Description
A | No description available
Chain information for 5mc7_human_zeta1COPI.cif B #31.2
---
Chain | Description
B | No description available
> hide #31.2 models
> show #31.2 models
> hide #31.2 models
> show #31.2 models
> close #31.2
> select add #31.1
1187 atoms, 1128 bonds, 214 residues, 1 model selected
> color sel yellow
> select add #31
1187 atoms, 1128 bonds, 214 residues, 2 models selected
> select subtract #31
Nothing selected
> select add #31
1187 atoms, 1128 bonds, 214 residues, 2 models selected
> show #!1 models
> show #10 models
> view matrix models
> #31,0.77045,-0.26029,0.58195,-46.985,0.36195,0.93005,-0.063212,-65.34,-0.52479,0.25934,0.81077,140.57
> view matrix models
> #31,0.72521,-0.27949,0.62925,-43.367,0.34932,0.9369,0.013553,-90.273,-0.59334,0.20998,0.77708,189.06
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.72521,-0.27949,0.62925,-16.885,0.34932,0.9369,0.013553,-51.066,-0.59334,0.20998,0.77708,176.45
> view matrix models
> #31,0.72521,-0.27949,0.62925,-6.5132,0.34932,0.9369,0.013553,-57.31,-0.59334,0.20998,0.77708,174.64
> hide #!1 models
> view matrix models
> #31,0.72521,-0.27949,0.62925,-7.6962,0.34932,0.9369,0.013553,-59.076,-0.59334,0.20998,0.77708,174.86
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #31,-0.095195,0.87129,-0.48146,251.77,0.83505,-0.19338,-0.51506,343.26,-0.54187,-0.45107,-0.70916,887.8
> ui mousemode right "translate selected models"
> view matrix models
> #31,-0.095195,0.87129,-0.48146,244.89,0.83505,-0.19338,-0.51506,340.66,-0.54187,-0.45107,-0.70916,889.02
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.0027708,0.40312,-0.91514,517.14,0.90915,0.3801,0.17018,-105.02,0.41645,-0.83248,-0.36544,603.02
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.0027708,0.40312,-0.91514,517.9,0.90915,0.3801,0.17018,-105.01,0.41645,-0.83248,-0.36544,601.65
> view matrix models
> #31,0.0027708,0.40312,-0.91514,517.09,0.90915,0.3801,0.17018,-105.49,0.41645,-0.83248,-0.36544,602.57
> ui mousemode right "rotate selected models"
> view matrix models
> #31,-0.28237,0.90449,-0.31965,234.95,-0.86547,-0.096463,0.49159,477.04,0.4138,0.41545,0.81004,-208.33
> view matrix models
> #31,0.41595,0.56615,-0.71166,268.31,-0.82648,0.5618,-0.036124,433.89,0.37936,0.6032,0.7016,-221.35
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.41595,0.56615,-0.71166,277.82,-0.82648,0.5618,-0.036124,434.95,0.37936,0.6032,0.7016,-219.83
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.45932,0.67175,-0.58119,185.25,-0.76826,0.62885,0.11967,341.62,0.44587,0.39154,0.80492,-207.01
> view matrix models
> #31,0.49942,0.66357,-0.55701,167.37,-0.76647,0.63812,0.072971,354.22,0.40386,0.39049,0.82729,-201.65
> select add #10
2607 atoms, 2569 bonds, 391 residues, 3 models selected
> select subtract #10
1187 atoms, 1128 bonds, 214 residues, 2 models selected
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.003717, steps = 72
shifted from previous position = 1.37
rotated from previous position = 11.3 degrees
atoms outside contour = 668, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98920702 -0.11431776 -0.09165649 177.62995202
0.10191685 0.98624349 -0.13014121 214.61813191
0.10527306 0.11939526 0.98724989 218.15252352
Axis 0.64906227 -0.51222791 0.56244176
Axis point 0.00000000 -982.87079504 2257.03819953
Rotation angle (degrees) 11.08286238
Shift along axis 128.05759337
> show #!1 models
> view matrix models
> #31,0.35297,0.7657,-0.53769,171.74,0.58437,0.26839,0.76582,-173.96,0.7307,-0.58453,-0.35272,425.29
> undo
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.003717, steps = 60
shifted from previous position = 0.0413
rotated from previous position = 0.0922 degrees
atoms outside contour = 665, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98923110 -0.11511984 -0.09038398 177.64670787
0.10292017 0.98620208 -0.12966451 214.58254620
0.10406382 0.11896584 0.98742992 218.18063668
Axis 0.64810713 -0.50686895 0.56836698
Axis point 0.00000000 -971.46735600 2267.93030426
Rotation angle (degrees) 11.05858996
Shift along axis 130.37553701
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.003716, steps = 44
shifted from previous position = 0.0381
rotated from previous position = 0.0919 degrees
atoms outside contour = 667, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98918508 -0.11442244 -0.09176266 177.64700501
0.10202250 0.98624996 -0.13000930 214.61097362
0.10537690 0.11924140 0.98725741 218.13649995
Axis 0.64825051 -0.51271998 0.56292938
Axis point 0.00000000 -984.03286467 2259.28865913
Rotation angle (degrees) 11.08404793
Shift along axis 127.91987227
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.003717, steps = 44
shifted from previous position = 0.0469
rotated from previous position = 0.075 degrees
atoms outside contour = 668, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98923236 -0.11489400 -0.09065705 177.64035366
0.10267391 0.98624230 -0.12955380 214.56846478
0.10429477 0.11885070 0.98741942 218.18379972
Axis 0.64778617 -0.50839292 0.56737088
Axis point 0.00000000 -976.04731314 2269.13723907
Rotation angle (degrees) 11.05396135
Shift along axis 129.77901020
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.003716, steps = 44
shifted from previous position = 0.0412
rotated from previous position = 0.0284 degrees
atoms outside contour = 667, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98924764 -0.11453745 -0.09094107 177.63369995
0.10226801 0.98626419 -0.12970815 214.61188083
0.10454836 0.11901312 0.98737304 218.16491755
Axis 0.64853243 -0.50973217 0.56531302
Axis point 0.00000000 -979.31739909 2265.77471243
Rotation angle (degrees) 11.05533860
Shift along axis 129.13810349
> ui mousemode right zoom
> hide #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.49942,0.66357,-0.55701,166.95,-0.76647,0.63812,0.072971,353.77,0.40386,0.39049,0.82729,-201
> ui mousemode right "rotate selected models"
> view matrix models
> #31,-0.0050664,0.88664,-0.46243,214.32,-0.99768,0.026918,0.062541,626.7,0.067899,0.46167,0.88445,-142.2
> ui mousemode right "translate selected models"
> view matrix models
> #31,-0.0050664,0.88664,-0.46243,215.66,-0.99768,0.026918,0.062541,624.93,0.067899,0.46167,0.88445,-143.47
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.003637, steps = 68
shifted from previous position = 1.88
rotated from previous position = 18.3 degrees
atoms outside contour = 677, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.97473504 0.20185998 -0.09562508 177.00592570
-0.21326145 0.96834748 -0.12970238 220.13806386
0.06641659 0.14681860 0.98693117 218.77322994
Axis 0.52725961 -0.30897485 -0.79153764
Axis point 987.15896034 -1139.52275349 0.00000000
Rotation angle (degrees) 15.20210867
Shift along axis -147.85629610
> ui mousemode right "translate selected models"
> view matrix models
> #31,-0.0050664,0.88664,-0.46243,213.12,-0.99768,0.026918,0.062541,623.69,0.067899,0.46167,0.88445,-140.94
> ui mousemode right "rotate selected models"
> view matrix models
> #31,0.5719,0.73327,-0.36777,56.314,-0.66712,0.67662,0.31167,225.21,0.47738,0.067104,0.87613,-132.67
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.5719,0.73327,-0.36777,57.865,-0.66712,0.67662,0.31167,226.72,0.47738,0.067104,0.87613,-134.9
> view matrix models
> #31,0.5719,0.73327,-0.36777,58.366,-0.66712,0.67662,0.31167,224.23,0.47738,0.067104,0.87613,-135.91
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.004243, steps = 44
shifted from previous position = 2.92
rotated from previous position = 8.79 degrees
atoms outside contour = 535, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.97561013 0.21805111 -0.02527050 173.84988966
-0.21797583 0.97593735 0.00572980 216.59416419
0.02591181 -0.00008169 0.99966423 218.26571160
Axis -0.01323624 -0.11657272 -0.99309396
Axis point 937.80314794 -677.56254760 0.00000000
Rotation angle (degrees) 12.68140254
Shift along axis -244.30844807
> view matrix models
> #31,0.5719,0.73327,-0.36777,58.257,-0.66712,0.67662,0.31167,224.66,0.47738,0.067104,0.87613,-136.13
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.004243, steps = 56
shifted from previous position = 0.493
rotated from previous position = 0.00302 degrees
atoms outside contour = 536, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.97560056 0.21809656 -0.02524739 174.30252276
-0.21802102 0.97592719 0.00574050 216.39994082
0.02589160 -0.00009597 0.99966475 218.28650928
Axis -0.01329055 -0.11645144 -0.99310746
Axis point 937.10166342 -679.47384917 0.00000000
Rotation angle (degrees) 12.68390747
Shift along axis -244.29862027
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.004242, steps = 28
shifted from previous position = 0.0505
rotated from previous position = 0.0784 degrees
atoms outside contour = 536, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.97564166 0.21802433 -0.02426420 174.29818099
-0.21792528 0.97594255 0.00668655 216.34230322
0.02513830 -0.00123589 0.99968322 218.31938758
Axis -0.01805431 -0.11258254 -0.99347834
Axis point 940.89158557 -674.08609334 0.00000000
Rotation angle (degrees) 12.67412881
Shift along axis -244.39878296
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.004243, steps = 28
shifted from previous position = 0.0678
rotated from previous position = 0.0773 degrees
atoms outside contour = 534, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.97569828 0.21766563 -0.02519006 174.30319213
-0.21758931 0.97602339 0.00576536 216.41284502
0.02584101 -0.00014416 0.99966605 218.28451887
Axis -0.01348355 -0.11643589 -0.99310668
Axis point 938.87049799 -680.82686875 0.00000000
Rotation angle (degrees) 12.65841235
Shift along axis -244.32826222
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.004243, steps = 44
shifted from previous position = 0.0146
rotated from previous position = 0.035 degrees
atoms outside contour = 535, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.97558580 0.21813613 -0.02547497 174.30486945
-0.21806593 0.97591834 0.00553590 216.40767360
0.02606907 0.00015447 0.99966013 218.28104983
Axis -0.01225085 -0.11734027 -0.99301620
Axis point 936.10467349 -680.57464736 0.00000000
Rotation angle (degrees) 12.68759066
Shift along axis -244.28533769
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.004242, steps = 28
shifted from previous position = 0.0587
rotated from previous position = 0.111 degrees
atoms outside contour = 536, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.97564956 0.21800947 -0.02407940 174.29594873
-0.21790629 0.97594558 0.00686077 216.33753389
0.02499589 -0.00144665 0.99968651 218.32268651
Axis -0.01893437 -0.11185298 -0.99354436
Axis point 941.64347534 -673.08423480 0.00000000
Rotation angle (degrees) 12.67227216
Shift along axis -244.41145590
> fitmap #31.1 inMap #1
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
postprocess_20231221.mrc (#1) using 1187 atoms
average map value = 0.004243, steps = 28
shifted from previous position = 0.0707
rotated from previous position = 0.0881 degrees
atoms outside contour = 534, contour level = 0.0036964
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.97573383 0.21751480 -0.02511586 174.30425498
-0.21743675 0.97605700 0.00583087 216.41142752
0.02578281 -0.00022827 0.99966754 218.28714955
Axis -0.01383486 -0.11621723 -0.99312746
Axis point 939.66803661 -680.97238480 0.00000000
Rotation angle (degrees) 12.64917355
Shift along axis -244.34917355
> fitmap #10 inMap #1
Fit molecule CopZ1_P61924.pdb (#10) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 44
shifted from previous position = 0.0503
rotated from previous position = 0.0659 degrees
atoms outside contour = 724, contour level = 0.0036964
Position of CopZ1_P61924.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16464547 -0.94010508 -0.29848672 230.52921764
-0.38697262 0.21678845 -0.89624493 241.48307989
0.90727287 0.26306886 -0.32810169 218.16058628
Axis 0.65804065 -0.68440386 0.31396473
Axis point 143.59602606 0.00000000 249.37721862
Rotation angle (degrees) 118.25092460
Shift along axis 54.92037460
> fitmap #10 inMap #1
Fit molecule CopZ1_P61924.pdb (#10) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 40
shifted from previous position = 0.0453
rotated from previous position = 0.0539 degrees
atoms outside contour = 728, contour level = 0.0036964
Position of CopZ1_P61924.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16475228 -0.93984435 -0.29924787 230.50212183
-0.38665624 0.21756915 -0.89619229 241.46489641
0.90738837 0.26335578 -0.32755167 218.19248372
Axis 0.65788547 -0.68460159 0.31385885
Axis point 143.42644626 0.00000000 249.42964094
Rotation angle (degrees) 118.20418399
Shift along axis 54.81838662
> fitmap #10 inMap #1
Fit molecule CopZ1_P61924.pdb (#10) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 44
shifted from previous position = 0.0111
rotated from previous position = 0.0464 degrees
atoms outside contour = 730, contour level = 0.0036964
Position of CopZ1_P61924.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16528469 -0.93968504 -0.29945452 230.49692380
-0.38615897 0.21772757 -0.89636821 241.46057391
0.90750329 0.26379299 -0.32688077 218.20121332
Axis 0.65796097 -0.68450069 0.31392064
Axis point 143.36777827 0.00000000 249.51847068
Rotation angle (degrees) 118.15992656
Shift along axis 54.87591693
> fitmap #10 inMap #1
Fit molecule CopZ1_P61924.pdb (#10) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 44
shifted from previous position = 0.00482
rotated from previous position = 0.00886 degrees
atoms outside contour = 729, contour level = 0.0036964
Position of CopZ1_P61924.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16517051 -0.93970815 -0.29944501 230.49930068
-0.38625587 0.21772958 -0.89632597 241.46236599
0.90748285 0.26370901 -0.32700528 218.19738498
Axis 0.65793667 -0.68453289 0.31390135
Axis point 143.37628380 0.00000000 249.50094452
Rotation angle (degrees) 118.16761754
Shift along axis 54.85746595
> fitmap #10 inMap #1
Fit molecule CopZ1_P61924.pdb (#10) to map postprocess_20231221.mrc (#1) using
1420 atoms
average map value = 0.003933, steps = 36
shifted from previous position = 0.00809
rotated from previous position = 0.0184 degrees
atoms outside contour = 727, contour level = 0.0036964
Position of CopZ1_P61924.pdb (#10) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.16519231 -0.93971155 -0.29942231 230.49169125
-0.38654060 0.21761768 -0.89623039 241.46358631
0.90735763 0.26378925 -0.32728790 218.19578263
Axis 0.65800248 -0.68452651 0.31377732
Axis point 143.40144878 -0.00000000 249.45936266
Rotation angle (degrees) 118.17973038
Shift along axis 54.84076550
> hide #10 models
> hide #!31 models
> select subtract #31
Nothing selected
> show #32 models
> split #32 chains
Split 5mu7_Thermophila_beta_deltaCOPI.cif (#32) into 2 models
Chain information for 5mu7_Thermophila_beta_deltaCOPI.cif A #32.1
---
Chain | Description
A | No description available
Chain information for 5mu7_Thermophila_beta_deltaCOPI.cif B #32.2
---
Chain | Description
B | No description available
> select add #32.1
2991 atoms, 3010 bonds, 400 residues, 1 model selected
> view matrix models #32.1,1,0,0,310.44,0,1,0,269.77,0,0,1,353.04
> undo
> ui mousemode right zoom
> show #4 models
> show #!9 models
> hide #!32 models
> show #!32 models
> ui mousemode right "translate selected models"
> select add #32
4213 atoms, 4232 bonds, 565 residues, 3 models selected
> view matrix models #32,1,0,0,6.3488,0,1,0,-55.027,0,0,1,-14.936
> hide #!9 models
> show #8 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v9.cxs"
> select subtract #32.1
1222 atoms, 1222 bonds, 165 residues, 2 models selected
> color sel sienna
> select subtract #32.2
1 model selected
> select add #32.1
2991 atoms, 3010 bonds, 400 residues, 2 models selected
> color sel dark green
> select subtract #32.1
1 model selected
> select add #32
4213 atoms, 4232 bonds, 565 residues, 3 models selected
> select subtract #32
Nothing selected
> select add #32
4213 atoms, 4232 bonds, 565 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #32,0.86713,-0.47402,-0.15291,246.78,0.40908,0.50265,0.76157,-304.31,-0.28414,-0.72294,0.62978,426.28
> view matrix models
> #32,0.80472,-0.48596,-0.34097,336.09,0.44907,0.12266,0.88504,-245.39,-0.38827,-0.86533,0.31694,611.99
> ui mousemode right "translate selected models"
> view matrix models
> #32,0.80472,-0.48596,-0.34097,286.27,0.44907,0.12266,0.88504,-195.95,-0.38827,-0.86533,0.31694,603.62
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.69152,-0.70058,0.17603,670.7,-0.20042,-0.048039,-0.97853,712.99,0.69399,-0.71196,-0.10719,343.18
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.69152,-0.70058,0.17603,672.68,-0.20042,-0.048039,-0.97853,719.82,0.69399,-0.71196,-0.10719,360.23
> ui mousemode right zoom
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.28518,-0.53956,-0.79218,823.6,0.94948,-0.04611,-0.31041,106.73,0.13096,-0.84068,0.52545,368.03
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.28518,-0.53956,-0.79218,806.69,0.94948,-0.04611,-0.31041,118.41,0.13096,-0.84068,0.52545,363.68
> view matrix models
> #32,-0.28518,-0.53956,-0.79218,806.23,0.94948,-0.04611,-0.31041,118.56,0.13096,-0.84068,0.52545,363.19
> view matrix models
> #32,-0.28518,-0.53956,-0.79218,804.04,0.94948,-0.04611,-0.31041,116.36,0.13096,-0.84068,0.52545,361.62
> view matrix models
> #32,-0.28518,-0.53956,-0.79218,804.76,0.94948,-0.04611,-0.31041,115.3,0.13096,-0.84068,0.52545,362.39
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.0016578,-0.50367,-0.8639,723.67,0.9595,0.24256,-0.14326,-31.15,0.2817,-0.82915,0.48287,322.86
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.0016578,-0.50367,-0.8639,726.03,0.9595,0.24256,-0.14326,-32.307,0.2817,-0.82915,0.48287,323.95
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.1547,-0.53164,-0.83273,774.68,0.93159,0.20215,-0.30212,43.964,0.32895,-0.8225,0.46399,312.71
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.1547,-0.53164,-0.83273,776.7,0.93159,0.20215,-0.30212,41.911,0.32895,-0.8225,0.46399,314.56
> view matrix models
> #32,-0.1547,-0.53164,-0.83273,773.69,0.93159,0.20215,-0.30212,39.425,0.32895,-0.8225,0.46399,315.24
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.5662,-0.55884,-0.6059,839.99,0.80288,-0.20757,-0.55883,295.21,0.18653,-0.80288,0.56621,321.67
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.5662,-0.55884,-0.6059,839.41,0.80288,-0.20757,-0.55883,296.1,0.18653,-0.80288,0.56621,319.88
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.50172,-0.63014,-0.59262,834.98,0.83927,-0.18865,-0.50994,261.4,0.20954,-0.75322,0.62351,277.44
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.50172,-0.63014,-0.59262,835.58,0.83927,-0.18865,-0.50994,261.52,0.20954,-0.75322,0.62351,278.27
> view matrix models
> #32,-0.50172,-0.63014,-0.59262,835.95,0.83927,-0.18865,-0.50994,262.26,0.20954,-0.75322,0.62351,278.02
> ui mousemode right "rotate selected models"
> view matrix models
> #32,-0.38225,-0.59979,-0.70294,824.97,0.90132,-0.074311,-0.42672,178.3,0.20371,-0.7967,0.56902,311.9
> view matrix models
> #32,-0.38961,-0.59043,-0.70683,825.91,0.89701,-0.069323,-0.43653,181.59,0.20874,-0.80411,0.55663,316.73
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.38961,-0.59043,-0.70683,825.37,0.89701,-0.069323,-0.43653,181.63,0.20874,-0.80411,0.55663,316.62
> select subtract #32
Nothing selected
> show #!1 models
> select add #32.1
2991 atoms, 3010 bonds, 400 residues, 1 model selected
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
postprocess_20231221.mrc (#1) using 2991 atoms
average map value = 0.004241, steps = 88
shifted from previous position = 3.45
rotated from previous position = 11.7 degrees
atoms outside contour = 1593, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99523070 -0.08932351 0.03920676 204.56594606
0.08053771 0.97916422 0.18641649 155.92418488
-0.05504123 -0.18236979 0.98168820 251.08480869
Axis -0.88476167 0.22611203 0.40751705
Axis point 0.00000000 1545.72793857 -716.32216947
Rotation angle (degrees) 12.02918781
Shift along axis -43.41443344
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
postprocess_20231221.mrc (#1) using 2991 atoms
average map value = 0.004241, steps = 88
shifted from previous position = 3.45
rotated from previous position = 11.7 degrees
atoms outside contour = 1593, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99523070 -0.08932351 0.03920676 204.56594606
0.08053771 0.97916422 0.18641649 155.92418488
-0.05504123 -0.18236979 0.98168820 251.08480869
Axis -0.88476167 0.22611203 0.40751705
Axis point 0.00000000 1545.72793857 -716.32216947
Rotation angle (degrees) 12.02918781
Shift along axis -43.41443344
> select subtract #32.1
Nothing selected
> select add #32.2
1222 atoms, 1222 bonds, 165 residues, 1 model selected
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004216, steps = 52
shifted from previous position = 1.66
rotated from previous position = 10.6 degrees
atoms outside contour = 618, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98239247 0.00608297 0.18672983 201.11786552
-0.00915230 0.99983674 0.01557958 155.89204427
-0.18660457 -0.01701427 0.98228776 245.74518368
Axis -0.08690208 0.99538837 -0.04062043
Axis point 1439.71905732 0.00000000 -1000.73205923
Rotation angle (degrees) 10.80879096
Shift along axis 127.71329308
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004217, steps = 48
shifted from previous position = 0.0497
rotated from previous position = 0.0595 degrees
atoms outside contour = 616, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98236776 0.00609305 0.18685946 201.07531739
-0.00897212 0.99985366 0.01456580 155.88604759
-0.18674336 -0.01598549 0.98227867 245.68947894
Axis -0.08143698 0.99586917 -0.04015745
Axis point 1437.96863175 0.00000000 -996.61080216
Rotation angle (degrees) 10.81137091
Shift along axis 129.00087941
> select add #32
4213 atoms, 4232 bonds, 565 residues, 3 models selected
> select subtract #32
Nothing selected
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!1 models
> select add #32.2
1222 atoms, 1222 bonds, 165 residues, 1 model selected
> view matrix models
> #32.2,0.98283,0.0078888,0.18437,313.02,-0.0096897,0.99991,0.0088691,268.96,-0.18428,-0.010503,0.98282,357.09
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004217, steps = 48
shifted from previous position = 1.52
rotated from previous position = 0.00409 degrees
atoms outside contour = 616, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98236810 0.00610753 0.18685720 201.07437146
-0.00899935 0.99985245 0.01463173 155.88746910
-0.18674027 -0.01605534 0.98227812 245.69185612
Axis -0.08179732 0.99583518 -0.04026784
Axis point 1438.08129766 0.00000000 -996.81322728
Rotation angle (degrees) 10.81158760
Shift along axis 128.89739988
> view matrix models
> #32.2,0.98283,0.0079035,0.18437,313.39,-0.009717,0.99991,0.0089351,268.63,-0.18428,-0.010573,0.98282,357
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004217, steps = 48
shifted from previous position = 1.29
rotated from previous position = 0.0164 degrees
atoms outside contour = 617, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98238754 0.00633303 0.18674746 201.05607706
-0.00924431 0.99984888 0.01472270 155.89686848
-0.18662599 -0.01618975 0.98229763 245.68968712
Axis -0.08243879 0.99572992 -0.04154239
Axis point 1439.69594941 0.00000000 -997.54365442
Rotation angle (degrees) 10.80618268
Shift along axis 128.44982063
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004216, steps = 44
shifted from previous position = 0.0615
rotated from previous position = 0.102 degrees
atoms outside contour = 619, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98230680 0.00593569 0.18718472 201.13630720
-0.00917519 0.99982268 0.01644478 155.90258547
-0.18705391 -0.01787128 0.98218708 245.78808678
Axis -0.09123885 0.99501825 -0.04017650
Axis point 1436.53838089 0.00000000 -1000.60261088
Rotation angle (degrees) 10.83936585
Shift along axis 126.89956630
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004216, steps = 48
shifted from previous position = 0.0108
rotated from previous position = 0.0508 degrees
atoms outside contour = 617, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98239838 0.00615838 0.18669626 201.10767232
-0.00925467 0.99983364 0.01571762 155.89759312
-0.18656840 -0.01716878 0.98229194 245.74769396
Axis -0.08769065 0.99529959 -0.04109847
Axis point 1440.30349037 0.00000000 -1001.25410015
Rotation angle (degrees) 10.80772335
Shift along axis 127.42969183
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003729, steps = 40
shifted from previous position = 0.0262
rotated from previous position = 0.0998 degrees
atoms outside contour = 873, contour level = 0.0036964
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23865497 0.93132114 0.27510863 -92.99261701
-0.88651295 0.09329923 0.45319978 105.78305390
0.39640711 -0.35204574 0.84789457 472.37094058
Axis -0.40426058 -0.06089596 -0.91261441
Axis point -102.29713427 189.82668068 0.00000000
Rotation angle (degrees) 84.84074291
Shift along axis -399.94103851
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003728, steps = 48
shifted from previous position = 0.0483
rotated from previous position = 0.0351 degrees
atoms outside contour = 875, contour level = 0.0036964
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23841751 0.93124468 0.27557296 -92.95214680
-0.88673475 0.09302332 0.45282244 105.83055914
0.39605377 -0.35232091 0.84794539 472.46264138
Axis -0.40420083 -0.06048419 -0.91266826
Axis point -102.16592094 189.89358785 0.00000000
Rotation angle (degrees) 84.85404781
Shift along axis -400.03139873
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003728, steps = 48
shifted from previous position = 0.0228
rotated from previous position = 0.118 degrees
atoms outside contour = 877, contour level = 0.0036964
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.23978913 0.93130708 0.27416839 -92.95993950
-0.88604379 0.09452161 0.45386351 105.51737731
0.39677146 -0.35175673 0.84784410 472.35122351
Axis -0.40449126 -0.06155738 -0.91246781
Axis point -102.60506985 189.74855585 0.00000000
Rotation angle (degrees) 84.77440663
Shift along axis -399.89917828
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map postprocess_20231221.mrc (#1) using 1462
atoms
average map value = 0.003728, steps = 48
shifted from previous position = 0.00444
rotated from previous position = 0.0249 degrees
atoms outside contour = 878, contour level = 0.0036964
Position of CopD_Q5XJY5 (#8) relative to postprocess_20231221.mrc (#1)
coordinates:
Matrix rotation and translation
0.24019715 0.93124148 0.27403402 -92.90318641
-0.88593165 0.09491266 0.45400078 105.41274879
0.39677506 -0.35182511 0.84781404 472.36960966
Axis -0.40460883 -0.06162883 -0.91241086
Axis point -102.67598760 189.73986486 0.00000000
Rotation angle (degrees) 84.75228379
Shift along axis -399.90217788
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004216, steps = 48
shifted from previous position = 0.00417
rotated from previous position = 0.0207 degrees
atoms outside contour = 618, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98241385 0.00607818 0.18661745 201.11227473
-0.00911074 0.99983995 0.01539681 155.88981786
-0.18649400 -0.01682626 0.98231200 245.73446032
Axis -0.08597216 0.99547303 -0.04052452
Axis point 1440.38116124 0.00000000 -1000.87336171
Rotation angle (degrees) 10.80132904
Shift along axis 127.93578107
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004217, steps = 40
shifted from previous position = 0.0531
rotated from previous position = 0.0392 degrees
atoms outside contour = 617, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98241386 0.00649415 0.18660341 201.04872379
-0.00941781 0.99984633 0.01478552 155.90228349
-0.18647871 -0.01628290 0.98232406 245.68872568
Axis -0.08291291 0.99565165 -0.04246457
Axis point 1441.33793611 0.00000000 -998.50320932
Rotation angle (degrees) 10.79850883
Shift along axis 128.12176560
> fitmap #32.2 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
postprocess_20231221.mrc (#1) using 1222 atoms
average map value = 0.004217, steps = 40
shifted from previous position = 0.0198
rotated from previous position = 0.0275 degrees
atoms outside contour = 616, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.98235946 0.00617017 0.18690057 201.08453605
-0.00913930 0.99984529 0.01502867 155.89330045
-0.18677893 -0.01647170 0.98226387 245.71224507
Axis -0.08392998 0.99563642 -0.04079075
Axis point 1438.29185698 0.00000000 -997.75841929
Rotation angle (degrees) 10.81617490
Shift along axis 128.31323939
> select subtract #32.2
Nothing selected
> select add #32.1
2991 atoms, 3010 bonds, 400 residues, 1 model selected
> view matrix models
> #32.1,0.99551,-0.087137,0.037019,318.16,0.079076,0.9803,0.18098,267.67,-0.05206,-0.17724,0.98279,362.86
> ui mousemode right "rotate selected models"
> view matrix models
> #32.1,0.99092,-0.05475,0.1228,318,0.062046,0.99648,-0.056389,265.34,-0.11928,0.063496,0.99083,356.58
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
postprocess_20231221.mrc (#1) using 2991 atoms
average map value = 0.004241, steps = 84
shifted from previous position = 2.25
rotated from previous position = 14.6 degrees
atoms outside contour = 1592, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99530720 -0.08850785 0.03911444 204.53962622
0.07970003 0.97905488 0.18734845 155.90993657
-0.05487699 -0.18335184 0.98151445 251.09966490
Axis -0.88729237 0.22497388 0.40261520
Axis point 0.00000000 1541.01835524 -714.32479979
Rotation angle (degrees) 12.05755199
Shift along axis -45.31424535
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
postprocess_20231221.mrc (#1) using 2991 atoms
average map value = 0.00424, steps = 48
shifted from previous position = 0.0448
rotated from previous position = 0.0377 degrees
atoms outside contour = 1596, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99528348 -0.08879701 0.03906262 204.56589890
0.08002562 0.97913646 0.18678247 155.93880820
-0.05483336 -0.18277550 0.98162438 251.08241743
Axis -0.88622599 0.22516917 0.40484854
Axis point 0.00000000 1544.34030617 -716.04620285
Rotation angle (degrees) 12.03452034
Shift along axis -44.52865349
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
postprocess_20231221.mrc (#1) using 2991 atoms
average map value = 0.00424, steps = 40
shifted from previous position = 0.0342
rotated from previous position = 0.0314 degrees
atoms outside contour = 1594, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99532569 -0.08829616 0.03912245 204.54167069
0.07951145 0.97914249 0.18697037 155.91860289
-0.05481522 -0.18298573 0.98158622 251.07444595
Axis -0.88728134 0.22529470 0.40246008
Axis point 0.00000000 1543.83636390 -716.29708101
Rotation angle (degrees) 12.03313503
Shift along axis -45.31093217
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
postprocess_20231221.mrc (#1) using 2991 atoms
average map value = 0.004241, steps = 44
shifted from previous position = 0.0371
rotated from previous position = 0.0216 degrees
atoms outside contour = 1596, contour level = 0.0036964
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99529199 -0.08866635 0.03914245 204.54651877
0.07987446 0.97912152 0.18692543 155.93624436
-0.05489921 -0.18291890 0.98159399 251.10027350
Axis -0.88654561 0.22542516 0.40400542
Axis point 0.00000000 1543.58380884 -715.76424350
Rotation angle (degrees) 12.03957768
Shift along axis -44.74199257
> show #!1 models
> select subtract #32.1
Nothing selected
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> hide #32.2 models
> hide #!32 models
> show #32.1 models
> show #32.2 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #32.1 models
> show #32.1 models
> hide #!32 models
> show #!32 models
> hide #4 models
> hide #8 models
> ui mousemode right zoom
> show #!31 models
> show #!30 models
> show #29 models
> hide #29 models
> show #!28 models
> hide #!28 models
> show #!27 models
> show #27.1 models
> show #27.2 models
> show #!26 models
> show #24 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!25 models
> show #25.1 models
> show #!25.2 models
> show #25.3 models
> show #!25.4 models
> show #25.5 models
> show #!25.6 models
> show #!25.7 models
> show #25.8 models
> show #25.9 models
> show #25.10 models
> show #25.11 models
> hide #!1 models
> hide #25.9 models
> show #25.9 models
> hide #25.10 models
> show #25.10 models
> hide #25.10 models
> show #25.10 models
> hide #25.10 models
> hide #25.11 models
> show #25.11 models
> hide #25.11 models
> show #25.11 models
> hide #25.11 models
> show #25.11 models
> hide #!25.7 models
> hide #!25.6 models
> hide #25.3 models
> show #25.3 models
> hide #25.3 models
> show #25.3 models
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 44
shifted from previous position = 0.00844
rotated from previous position = 0.00913 degrees
atoms outside contour = 1375, contour level = 0.0036964
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47525408 0.87647726 -0.07694909 158.53420343
-0.87868101 -0.47730886 -0.00979377 369.87324190
-0.04531250 0.06295917 0.99698691 112.96016999
Axis 0.04140865 -0.01800653 -0.99898002
Axis point 191.05150899 135.35845305 0.00000000
Rotation angle (degrees) 118.54103318
Shift along axis -112.94040061
> fitmap #25.3 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
postprocess_20231221.mrc (#1) using 3371 atoms
average map value = 0.004368, steps = 48
shifted from previous position = 0.0471
rotated from previous position = 0.0276 degrees
atoms outside contour = 1374, contour level = 0.0036964
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
-0.47516672 0.87649025 -0.07733961 158.59310079
-0.87873077 -0.47722253 -0.00953295 369.80611039
-0.04526374 0.06343095 0.99695922 112.92634766
Axis 0.04152685 -0.01825574 -0.99897059
Axis point 191.06980499 135.28411630 0.00000000
Rotation angle (degrees) 118.53627210
Shift along axis -112.97531167
> hide #25.3 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #!25.2 models
> show #!25.2 models
> hide #!25.2 models
> show #!25.2 models
> hide #!25.2 models
> hide #!25.4 models
> show #!25.4 models
> hide #!25.4 models
> show #!25.4 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.7 models
> show #!9 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #!9 models
> show #!9 models
> hide #!25.7 models
> show #!25.7 models
> hide #25.9 models
> show #25.9 models
> show #25.10 models
> hide #25.10 models
> show #25.10 models
> hide #25.10 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> hide #26.3 models
> show #26.3 models
> hide #26.3 models
> show #26.3 models
> hide #26.3 models
> hide #25.11 models
> show #25.11 models
> hide #25.11 models
> show #25.11 models
> hide #25.11 models
> show #25.11 models
> hide #25.8 models
> show #25.8 models
> show #!25.2 models
> hide #!25.2 models
> show #!25.2 models
> hide #!25.2 models
> show #!25.2 models
> show #4 models
> hide #4 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v10.cxs"
——— End of log from Thu Feb 15 12:14:52 2024 ———
opened ChimeraX session
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240325_GT.mrc"
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.00475, step 2, values float32
> hide #!33 models
> show #!33 models
> volume #33 step 1
> select add #33
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #33,1,0,0,72.57,0,1,0,86.032,0,0,1,68.458
> view matrix models #33,1,0,0,30.335,0,1,0,73.477,0,0,1,74.235
> volume #33 level 0.01231
> view matrix models #33,1,0,0,71.154,0,1,0,73.217,0,0,1,71.076
> view matrix models #33,1,0,0,72.64,0,1,0,67.127,0,0,1,85.835
> view matrix models #33,1,0,0,78.575,0,1,0,62.017,0,0,1,83.222
> volume #33 level 0.01173
> ui tool show "Fit in Map"
> fitmap #33 inMap #1
Fit map relion_locres_filtered_20240325_GT.mrc in map postprocess_20231221.mrc
using 44037 points
correlation = 0.6237, correlation about mean = 0.1262, overlap = 2.804
steps = 92, shift = 12.9, angle = 6.6 degrees
Position of relion_locres_filtered_20240325_GT.mrc (#33) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99949388 -0.02731098 0.01631250 -37.00560756
0.02888458 0.99398480 -0.10564043 -16.91209365
-0.01332924 0.10605815 0.99427059 -54.83653713
Axis 0.95779583 0.13410923 0.25424764
Axis point 0.00000000 386.91878756 -116.54834210
Rotation angle (degrees) 6.34491271
Shift along axis -51.65394478
> select subtract #33
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #33
2 models selected
> select subtract #33
Nothing selected
> hide #!33 models
> show #!33 models
> show #!1 models
> hide #!33 models
> hide #!1 models
> show #!33 models
> select add #33
2 models selected
> view matrix models
> #33,0.99957,-0.025838,0.01358,74.395,0.027189,0.99344,-0.1111,94.822,-0.01062,0.11142,0.99372,55.81
> view matrix models
> #33,0.99957,-0.025838,0.01358,73.428,0.027189,0.99344,-0.1111,96.48,-0.01062,0.11142,0.99372,62.53
> view matrix models
> #33,0.99957,-0.025838,0.01358,73.648,0.027189,0.99344,-0.1111,94.024,-0.01062,0.11142,0.99372,62.484
> view matrix models
> #33,0.99957,-0.025838,0.01358,69.414,0.027189,0.99344,-0.1111,91.313,-0.01062,0.11142,0.99372,57.683
> view matrix models
> #33,0.99957,-0.025838,0.01358,63.655,0.027189,0.99344,-0.1111,102,-0.01062,0.11142,0.99372,53.367
> fitmap #33 inMap #1
Fit map relion_locres_filtered_20240325_GT.mrc in map postprocess_20231221.mrc
using 44037 points
correlation = 0.857, correlation about mean = 0.4514, overlap = 5.569
steps = 76, shift = 3.2, angle = 5.89 degrees
Position of relion_locres_filtered_20240325_GT.mrc (#33) relative to
postprocess_20231221.mrc (#1) coordinates:
Matrix rotation and translation
0.99986659 -0.01403628 0.00835329 -48.07140361
0.01407399 0.99989095 -0.00447277 -38.51251840
-0.00828960 0.00458974 0.99995511 -34.90096404
Axis 0.26732008 0.49092094 0.82917827
Axis point 601.63878323 -2274.55915830 0.00000000
Rotation angle (degrees) 0.97124921
Shift along axis -60.69617408
> select subtract #33
Nothing selected
> volume #33 level 0.007732
> color #33 #b2b2b2b3 models
> hide #!9 models
> show #!9 models
> fitmap #9 inMap #33
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240325_GT.mrc
(#33) using 6673 atoms
average map value = 0.008961, steps = 52
shifted from previous position = 0.988
rotated from previous position = 0.57 degrees
atoms outside contour = 4166, contour level = 0.0077316
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240325_GT.mrc (#33) coordinates:
Matrix rotation and translation
0.49613377 -0.51960793 -0.69559965 274.31858527
0.53785070 -0.44499499 0.71602799 319.09443722
-0.68159218 -0.72937443 0.05869444 294.85363127
Axis -0.80704633 -0.00782113 0.59043633
Axis point -0.00000000 282.70437624 125.41603975
Rotation angle (degrees) 116.42867423
Shift along axis -49.79118899
> fitmap #9 inMap #33
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240325_GT.mrc
(#33) using 6673 atoms
average map value = 0.008961, steps = 64
shifted from previous position = 0.0124
rotated from previous position = 0.00857 degrees
atoms outside contour = 4169, contour level = 0.0077316
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240325_GT.mrc (#33) coordinates:
Matrix rotation and translation
0.49623907 -0.51951431 -0.69559447 274.30741330
0.53787534 -0.44494899 0.71603807 319.08787875
-0.68149608 -0.72946917 0.05863287 294.85903889
Axis -0.80708476 -0.00787170 0.59038312
Axis point 0.00000000 282.70154029 125.40339295
Rotation angle (degrees) 116.42580377
Shift along axis -49.82129739
> fitmap #9 inMap #33
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240325_GT.mrc
(#33) using 6673 atoms
average map value = 0.008961, steps = 80
shifted from previous position = 0.00724
rotated from previous position = 0.0138 degrees
atoms outside contour = 4169, contour level = 0.0077316
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240325_GT.mrc (#33) coordinates:
Matrix rotation and translation
0.49616295 -0.51945034 -0.69569653 274.30452132
0.53781312 -0.44516526 0.71595037 319.08560977
-0.68160060 -0.72938277 0.05849270 294.84858065
Axis -0.80708445 -0.00787127 0.59038354
Axis point -0.00000000 282.66374601 125.43104086
Rotation angle (degrees) 116.43964221
Shift along axis -49.82477444
> hide #24 models
> show #24 models
> hide #24 models
> show #24 models
> fitmap #24 inMap #33
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240325_GT.mrc (#33) using 1934 atoms
average map value = 0.008805, steps = 48
shifted from previous position = 0.97
rotated from previous position = 1.19 degrees
atoms outside contour = 905, contour level = 0.0077316
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240325_GT.mrc (#33) coordinates:
Matrix rotation and translation
0.23315837 0.94986433 -0.20831449 197.31839591
0.00055264 -0.21434801 -0.97675720 258.17011954
-0.97243862 0.22762399 -0.05050197 197.45063390
Axis 0.70293409 0.44597915 -0.55406341
Axis point 0.00000000 -45.05482516 254.37750939
Rotation angle (degrees) 121.05400663
Shift along axis 144.44014638
> select add #24
1934 atoms, 1950 bonds, 254 residues, 1 model selected
> view matrix models
> #24,0.22751,0.95373,-0.19658,261.64,0.013108,-0.20485,-0.9787,333.54,-0.97369,0.22008,-0.059107,273.86
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.20396,0.93399,-0.29337,260.27,-0.15499,-0.26508,-0.95169,335.09,-0.96663,0.23958,0.090695,276.18
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.20396,0.93399,-0.29337,258.7,-0.15499,-0.26508,-0.95169,335.39,-0.96663,0.23958,0.090695,278.18
> fitmap #24 inMap #33
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240325_GT.mrc (#33) using 1934 atoms
average map value = 0.008805, steps = 72
shifted from previous position = 1.23
rotated from previous position = 10.4 degrees
atoms outside contour = 903, contour level = 0.0077316
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240325_GT.mrc (#33) coordinates:
Matrix rotation and translation
0.23306458 0.94996117 -0.20797758 197.32356452
0.00057448 -0.21400168 -0.97683312 258.15005036
-0.97246109 0.22754572 -0.05042194 197.45698254
Axis 0.70285059 0.44613677 -0.55404244
Axis point 0.00000000 -45.14027322 254.39519192
Rotation angle (degrees) 121.04288590
Shift along axis 144.45966411
> fitmap #24 inMap #33
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240325_GT.mrc (#33) using 1934 atoms
average map value = 0.008805, steps = 44
shifted from previous position = 0.0314
rotated from previous position = 0.0236 degrees
atoms outside contour = 902, contour level = 0.0077316
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240325_GT.mrc (#33) coordinates:
Matrix rotation and translation
0.23331409 0.94994298 -0.20778080 197.36153623
0.00087375 -0.21388272 -0.97685895 258.14539493
-0.97240103 0.22773341 -0.05073187 197.45390626
Axis 0.70296074 0.44620738 -0.55384579
Axis point 0.00000000 -45.15246279 254.33489264
Rotation angle (degrees) 121.04092825
Shift along axis 144.56477865
> select subtract #24
Nothing selected
> volume #33 level 0.008296
> hide #32.2 models
> show #32.2 models
> hide #32.2 models
> show #32.2 models
> hide #32.2 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 2, values float32
> color #34 silver models
> color #34 #c0c0c0c3 models
> color #34 #c0c0c0b0 models
> color #34 #c0c0c0b6 models
> color #34 #c0c0c0b5 models
> volume #34 step 1
> volume #34 level 0.006879
> select add #34
2 models selected
> view matrix models #34,1,0,0,76.713,0,1,0,44.244,0,0,1,90.944
> view matrix models #34,1,0,0,68.467,0,1,0,67.193,0,0,1,95.122
> view matrix models #34,1,0,0,61.165,0,1,0,76.648,0,0,1,88.225
> view matrix models #34,1,0,0,60.385,0,1,0,81.766,0,0,1,79.991
> fitmap #34 inMap #33
Fit map relion_locres_filtered_20240326_GT.mrc in map
relion_locres_filtered_20240325_GT.mrc using 81080 points
correlation = 0.4928, correlation about mean = 0.147, overlap = 7.58
steps = 176, shift = 6.83, angle = 7.04 degrees
Position of relion_locres_filtered_20240326_GT.mrc (#34) relative to
relion_locres_filtered_20240325_GT.mrc (#33) coordinates:
Matrix rotation and translation
0.99429183 -0.08031793 0.07023384 6.18459749
0.08142673 0.99659370 -0.01306464 -10.59006941
-0.06894528 0.01870897 0.99744500 19.92687933
Axis 0.14728054 0.64513834 0.74973660
Axis point 203.43567918 46.00553043 0.00000000
Rotation angle (degrees) 6.19240989
Shift along axis 9.01872173
> select subtract #34
Nothing selected
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> select add #34
2 models selected
> view matrix models
> #34,0.9928,-0.092454,0.076157,67.203,0.094382,0.99529,-0.02212,64.594,-0.073753,0.029149,0.99685,82.392
> view matrix models
> #34,0.9928,-0.092454,0.076157,69.297,0.094382,0.99529,-0.02212,59.891,-0.073753,0.029149,0.99685,86.477
> fitmap #34 inMap #33
Fit map relion_locres_filtered_20240326_GT.mrc in map
relion_locres_filtered_20240325_GT.mrc using 81080 points
correlation = 0.9993, correlation about mean = 0.999, overlap = 24.37
steps = 88, shift = 2.2, angle = 6.19 degrees
Position of relion_locres_filtered_20240326_GT.mrc (#34) relative to
relion_locres_filtered_20240325_GT.mrc (#33) coordinates:
Matrix rotation and translation
1.00000000 -0.00007715 0.00001183 0.00492983
0.00007715 1.00000000 -0.00005101 -0.01559630
-0.00001183 0.00005101 1.00000000 -0.00690254
Axis 0.54709301 0.12689970 0.82739694
Axis point 193.95045006 99.30213635 0.00000000
Rotation angle (degrees) 0.00534241
Shift along axis -0.00499324
> hide #!33 models
> select subtract #34
Nothing selected
> volume #34 level 0.007468
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008451, steps = 44
shifted from previous position = 0.0262
rotated from previous position = 0.0727 degrees
atoms outside contour = 894, contour level = 0.0074676
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23425930 0.94987010 -0.20704919 197.40956475
0.00070050 -0.21314028 -0.97702136 258.09351163
-0.97217390 0.22873130 -0.05059548 197.38429803
Axis 0.70318792 0.44621627 -0.55355018
Axis point 0.00000000 -45.26642650 254.27476290
Rotation angle (degrees) 120.97995955
Shift along axis 144.71943025
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008451, steps = 44
shifted from previous position = 0.00229
rotated from previous position = 0.0546 degrees
atoms outside contour = 898, contour level = 0.0074676
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23353126 0.95014780 -0.20659697 197.39334641
0.00051751 -0.21259339 -0.97714061 258.06121856
-0.97234916 0.22808596 -0.05013891 197.42485509
Axis 0.70281335 0.44653916 -0.55376546
Axis point 0.00000000 -45.44733566 254.39921330
Rotation angle (degrees) 120.97075702
Shift along axis 144.63805233
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 6673 atoms
average map value = 0.008518, steps = 48
shifted from previous position = 0.0318
rotated from previous position = 0.0523 degrees
atoms outside contour = 4163, contour level = 0.0074676
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49550602 -0.51968681 -0.69598807 274.31952932
0.53772290 -0.44574109 0.71565981 319.08931419
-0.68214945 -0.72886247 0.05858011 294.80474301
Axis -0.80688849 -0.00773005 0.59065321
Axis point 0.00000000 282.58706202 125.53796346
Rotation angle (degrees) 116.47629292
Shift along axis -49.68447857
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 6673 atoms
average map value = 0.008518, steps = 104
shifted from previous position = 0.00642
rotated from previous position = 0.031 degrees
atoms outside contour = 4165, contour level = 0.0074676
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49574574 -0.51972562 -0.69578835 274.32666522
0.53787996 -0.44526973 0.71583519 319.08087152
-0.68185138 -0.72912286 0.05880943 294.81961287
Axis -0.80692092 -0.00778295 0.59060820
Axis point 0.00000000 282.65484655 125.47384425
Rotation angle (degrees) 116.44619964
Shift along axis -49.72043419
> show #8 models
> fitmap #8 inMap #34
Fit molecule CopD_Q5XJY5 (#8) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1462 atoms
average map value = 0.00841, steps = 156
shifted from previous position = 2.76
rotated from previous position = 12.4 degrees
atoms outside contour = 724, contour level = 0.0074676
Position of CopD_Q5XJY5 (#8) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.07140636 0.98850099 0.13329270 -99.10582965
-0.91228156 0.01069242 0.40942402 162.87483596
0.40329082 -0.15083595 0.90255473 445.96344647
Axis -0.28013823 -0.13500304 -0.95041925
Axis point -59.71258172 162.64687932 0.00000000
Rotation angle (degrees) 90.43964897
Shift along axis -418.07751033
> hide #8 models
> show #3 models
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 9810 atoms
average map value = 0.005549, steps = 72
shifted from previous position = 2.84
rotated from previous position = 1.34 degrees
atoms outside contour = 6409, contour level = 0.0074676
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90931516 0.39284566 0.13717951 209.67745401
-0.21905740 0.73223243 -0.64486395 282.20868279
-0.35377929 0.55633438 0.75188580 275.94887322
Axis 0.83725126 0.34220484 -0.42650460
Axis point 0.00000000 -384.56632735 515.35761515
Rotation angle (degrees) 45.83582590
Shift along axis 154.43242544
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 9810 atoms
average map value = 0.005549, steps = 60
shifted from previous position = 0.034
rotated from previous position = 0.0195 degrees
atoms outside contour = 6415, contour level = 0.0074676
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90917434 0.39314923 0.13724317 209.70451247
-0.21925634 0.73215869 -0.64488007 282.20950559
-0.35401788 0.55621698 0.75186036 275.96663282
Axis 0.83704470 0.34235989 -0.42678552
Axis point 0.00000000 -384.65716396 515.42335056
Rotation angle (degrees) 45.84540952
Shift along axis 154.37070138
> hide #3 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v11.cxs"
> show #4 models
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7501 atoms
average map value = 0.007457, steps = 148
shifted from previous position = 2.51
rotated from previous position = 2.87 degrees
atoms outside contour = 4420, contour level = 0.0074676
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.01680119 -0.69766311 0.71622895 219.87649830
-0.07060979 0.71536949 0.69516958 243.07737626
-0.99736251 -0.03889310 -0.06128091 272.76153712
Axis -0.37322028 0.87124316 0.31881340
Axis point 259.30872006 0.00000000 -51.77031004
Rotation angle (degrees) 100.44877054
Shift along axis 216.67716450
> hide #4 models
> show #5 models
> fitmap #5 inMap #34
Fit molecule hArf1_P84078 (#5) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1457 atoms
average map value = 0.007776, steps = 60
shifted from previous position = 3.87
rotated from previous position = 6.73 degrees
atoms outside contour = 819, contour level = 0.0074676
Position of hArf1_P84078 (#5) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.04242972 -0.02831736 0.99869807 172.65394789
-0.66600925 -0.74590924 0.00714571 238.26333147
0.74473578 -0.66544535 -0.05050834 212.55575199
Axis -0.69988454 0.26426798 -0.66356919
Axis point 0.00000000 166.46081014 -28.75809037
Rotation angle (degrees) 151.28184306
Shift along axis -198.91790665
> hide #5 models
> show #5 models
> hide #!26.1 models
> show #!26.1 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #!26.1 models
> show #!26.1 models
> hide #25.5 models
> show #5 models
> show #6 models
> hide #!26.1 models
> fitmap #6 inMap #34
Fit molecule hArf1_P84078 (#6) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1457 atoms
average map value = 0.01, steps = 72
shifted from previous position = 0.73
rotated from previous position = 2.1 degrees
atoms outside contour = 626, contour level = 0.0074676
Position of hArf1_P84078 (#6) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.84132215 -0.49459873 0.21805759 292.95471261
-0.49051987 0.52911808 -0.69240472 231.43475503
0.22708428 -0.68949701 -0.68776928 256.78767603
Axis 0.28166080 -0.87438969 0.39510742
Axis point 183.36285933 0.00000000 181.12263792
Rotation angle (degrees) 179.70425446
Shift along axis -18.39158846
> hide #6 models
> hide #5 models
> show #7 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7214 atoms
average map value = 0.008399, steps = 84
shifted from previous position = 0.843
rotated from previous position = 2.57 degrees
atoms outside contour = 3562, contour level = 0.0074676
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13431586 -0.22738621 -0.96449715 237.14149448
-0.00061001 -0.97329764 0.22954593 213.64544034
-0.99093838 0.03142001 0.13059060 275.37738819
Axis -0.65541234 0.08746916 0.75018918
Axis point 228.35039389 105.10157043 0.00000000
Rotation angle (degrees) 171.30665467
Shift along axis 69.84706251
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7214 atoms
average map value = 0.008399, steps = 44
shifted from previous position = 0.0128
rotated from previous position = 0.0342 degrees
atoms outside contour = 3562, contour level = 0.0074676
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13390870 -0.22779018 -0.96445844 237.15410914
-0.00039761 -0.97321119 0.22991264 213.64052796
-0.99099359 0.03117078 0.13023088 275.38236789
Axis -0.65555388 0.08752670 0.75005879
Axis point 228.37335345 105.12898072 0.00000000
Rotation angle (degrees) 171.28131559
Shift along axis 69.78491755
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7214 atoms
average map value = 0.008399, steps = 44
shifted from previous position = 0.0077
rotated from previous position = 0.0068 degrees
atoms outside contour = 3563, contour level = 0.0074676
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13397701 -0.22770446 -0.96446920 237.14731874
-0.00036520 -0.97323212 0.22982406 213.64279778
-0.99098437 0.03114337 0.13030757 275.38493157
Axis -0.65552905 0.08748443 0.75008542
Axis point 228.36528533 105.13378512 0.00000000
Rotation angle (degrees) 171.28368734
Shift along axis 69.79568160
> hide #7 models
> show #8 models
> fitmap #8 inMap #34
Fit molecule CopD_Q5XJY5 (#8) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1462 atoms
average map value = 0.00841, steps = 28
shifted from previous position = 0.0383
rotated from previous position = 0.0735 degrees
atoms outside contour = 722, contour level = 0.0074676
Position of CopD_Q5XJY5 (#8) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.07016472 0.98859876 0.13322696 -99.31004014
-0.91248006 0.00964302 0.40900753 163.18466590
0.40305963 -0.15026484 0.90275325 445.78508052
Axis -0.27964682 -0.13492146 -0.95057554
Axis point -59.54465786 162.68993060 0.00000000
Rotation angle (degrees) 90.49959742
Shift along axis -417.99777082
> fitmap #8 inMap #34
Fit molecule CopD_Q5XJY5 (#8) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1462 atoms
average map value = 0.00841, steps = 28
shifted from previous position = 0.0322
rotated from previous position = 0.0518 degrees
atoms outside contour = 723, contour level = 0.0074676
Position of CopD_Q5XJY5 (#8) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.07106380 0.98853589 0.13321692 -99.16933695
-0.91244747 0.01046829 0.40905994 162.89308632
0.40297587 -0.15062280 0.90273098 445.87345823
Axis -0.27985003 -0.13488365 -0.95052110
Axis point -59.63440143 162.62315862 0.00000000
Rotation angle (degrees) 90.45083426
Shift along axis -418.03120194
> hide #8 models
> show #10 models
> fitmap #10 inMap #34
Fit molecule CopZ1_P61924.pdb (#10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1420 atoms
average map value = 0.009234, steps = 48
shifted from previous position = 1.12
rotated from previous position = 1.79 degrees
atoms outside contour = 675, contour level = 0.0074676
Position of CopZ1_P61924.pdb (#10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.16424997 -0.94520201 -0.28216152 280.94831575
-0.37364491 0.20511456 -0.90460904 278.13209898
0.91291371 0.25401022 -0.31947985 253.91031297
Axis 0.65834031 -0.67905499 0.32476508
Axis point 174.97275092 0.00000000 294.15667076
Rotation angle (degrees) 118.36310421
Shift along axis 78.55381362
> fitmap #10 inMap #34
Fit molecule CopZ1_P61924.pdb (#10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1420 atoms
average map value = 0.009234, steps = 40
shifted from previous position = 0.0387
rotated from previous position = 0.022 degrees
atoms outside contour = 674, contour level = 0.0074676
Position of CopZ1_P61924.pdb (#10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.16427782 -0.94520359 -0.28214001 280.95341777
-0.37329087 0.20518314 -0.90473964 278.15427915
0.91305352 0.25394894 -0.31912883 253.87919273
Axis 0.65828937 -0.67902904 0.32492256
Axis point 174.96864287 0.00000000 294.21495040
Rotation angle (degrees) 118.34853786
Shift along axis 78.56489358
> hide #10 models
> show #11 models
> fitmap #11 inMap #34
Fit molecule Golph3_ Q9CRA5.pdb (#11) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2367 atoms
average map value = 0.007663, steps = 48
shifted from previous position = 0.709
rotated from previous position = 2.1 degrees
atoms outside contour = 1240, contour level = 0.0074676
Position of Golph3_ Q9CRA5.pdb (#11) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.65421830 -0.23794002 0.71790178 247.65193454
-0.70329335 -0.54051642 0.46175800 269.95611284
0.27816699 -0.80698609 -0.52095737 226.95063267
Axis -0.89276656 0.30942450 -0.32745129
Axis point 0.00000000 214.70262422 -10.31695525
Rotation angle (degrees) 134.71878815
Shift along axis -211.87960680
> fitmap #11 inMap #34
Fit molecule Golph3_ Q9CRA5.pdb (#11) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2367 atoms
average map value = 0.007663, steps = 28
shifted from previous position = 0.0299
rotated from previous position = 0.0482 degrees
atoms outside contour = 1239, contour level = 0.0074676
Position of Golph3_ Q9CRA5.pdb (#11) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.65431825 -0.23860616 0.71758953 247.67989817
-0.70349800 -0.54016367 0.46185903 269.95704958
0.27741339 -0.80702559 -0.52129790 226.95194987
Axis -0.89279567 0.30971086 -0.32710100
Axis point 0.00000000 214.77630651 -10.28288940
Rotation angle (degrees) 134.71426631
Shift along axis -211.75512060
> hide #11 models
> show #12 models
> fitmap #12 inMap #34
Fit molecule CopZ2_Q9CTG7.pdb (#12) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1463 atoms
average map value = 0.009106, steps = 44
shifted from previous position = 1.02
rotated from previous position = 1.24 degrees
atoms outside contour = 738, contour level = 0.0074676
Position of CopZ2_Q9CTG7.pdb (#12) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.82091914 0.29004883 -0.49189784 280.03421097
0.42279215 0.88773522 -0.18213459 278.62685215
0.38384711 -0.35748831 -0.85138918 253.04319994
Axis -0.19420328 -0.96988268 0.14701250
Axis point 75.80135238 0.00000000 175.21622813
Rotation angle (degrees) 153.16199409
Shift along axis -287.41840673
> fitmap #12 inMap #34
Fit molecule CopZ2_Q9CTG7.pdb (#12) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1463 atoms
average map value = 0.009106, steps = 40
shifted from previous position = 0.0192
rotated from previous position = 0.0109 degrees
atoms outside contour = 741, contour level = 0.0074676
Position of CopZ2_Q9CTG7.pdb (#12) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.82083085 0.29001682 -0.49206402 280.05037052
0.42282521 0.88772302 -0.18211730 278.62125297
0.38399948 -0.35754456 -0.85129685 253.05327012
Axis -0.19421314 -0.96987800 0.14703037
Axis point 75.79151350 0.00000000 175.23683625
Rotation angle (degrees) 153.15130828
Shift along axis -287.41157022
> hide #12 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> hide #24 models
> show #24 models
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 48
shifted from previous position = 0.0431
rotated from previous position = 0.0627 degrees
atoms outside contour = 895, contour level = 0.0074676
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23405376 0.94982303 -0.20749712 197.35570778
0.00020131 -0.21347264 -0.97694902 258.10756002
-0.97222364 0.22861682 -0.05015528 197.38522791
Axis 0.70310302 0.44599930 -0.55383279
Axis point 0.00000000 -45.20651034 254.35443028
Rotation angle (degrees) 120.98322448
Shift along axis 144.55877326
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #27.2 models
> hide #!30 models
> hide #25.1 models
> show #25.1 models
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 60
shifted from previous position = 0.904
rotated from previous position = 1.72 degrees
atoms outside contour = 1163, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50807931 0.84617772 -0.16074411 226.49375297
-0.85922710 -0.51091764 0.02630506 400.52629656
-0.05986824 0.15148075 0.98664551 146.92791984
Axis 0.07307543 -0.05888961 -0.99558626
Axis point 229.70717814 128.48284437 0.00000000
Rotation angle (degrees) 121.07607407
Shift along axis -153.31512685
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 44
shifted from previous position = 0.0149
rotated from previous position = 0.0266 degrees
atoms outside contour = 1160, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50771421 0.84636989 -0.16088590 226.45621049
-0.85944782 -0.51054152 0.02639693 400.53106900
-0.05979736 0.15167513 0.98661994 146.90491855
Axis 0.07311688 -0.05899892 -0.99557674
Axis point 229.74228973 128.45284652 0.00000000
Rotation angle (degrees) 121.05213979
Shift along axis -153.32824889
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 44
shifted from previous position = 0.0327
rotated from previous position = 0.0357 degrees
atoms outside contour = 1163, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50793455 0.84614433 -0.16137614 226.56209347
-0.85928642 -0.51082194 0.02622549 400.56407963
-0.06024392 0.15198915 0.98654445 146.96573947
Axis 0.07341508 -0.05903637 -0.99555258
Axis point 229.78643902 128.44653831 0.00000000
Rotation angle (degrees) 121.07141163
Shift along axis -153.32689327
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 60
shifted from previous position = 0.0217
rotated from previous position = 0.0104 degrees
atoms outside contour = 1163, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50794397 0.84616252 -0.16125102 226.54158397
-0.85929324 -0.51080380 0.02635510 400.52948403
-0.06006694 0.15194883 0.98656145 146.95116687
Axis 0.07331522 -0.05906611 -0.99555817
Axis point 229.75811826 128.43643924 0.00000000
Rotation angle (degrees) 121.07055136
Shift along axis -153.34720978
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 48
shifted from previous position = 0.022
rotated from previous position = 0.00674 degrees
atoms outside contour = 1160, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50788552 0.84621218 -0.16117454 226.52173670
-0.85933336 -0.51073460 0.02638836 400.51304405
-0.05998726 0.15190492 0.98657306 146.92661256
Axis 0.07326658 -0.05906508 -0.99556181
Axis point 229.74941295 128.43089793 0.00000000
Rotation angle (degrees) 121.06589357
Shift along axis -153.33438642
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 44
shifted from previous position = 0.0223
rotated from previous position = 0.0218 degrees
atoms outside contour = 1160, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50772527 0.84636665 -0.16086804 226.45629918
-0.85944082 -0.51055412 0.02638089 400.53445307
-0.05980394 0.15165080 0.98662329 146.90614497
Axis 0.07311256 -0.05898508 -0.99557788
Axis point 229.74200269 128.45676344 0.00000000
Rotation angle (degrees) 121.05281916
Shift along axis -153.32526360
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> show #27.2 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 72
shifted from previous position = 2.95
rotated from previous position = 3.29 degrees
atoms outside contour = 722, contour level = 0.0074676
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98952834 0.01496424 -0.14356094 -45.88490327
0.02378468 0.96410971 0.26443667 -113.51694283
0.14236559 -0.26508213 0.95365796 -31.11838703
Axis -0.87982037 -0.47508035 0.01465558
Axis point 0.00000000 -164.25502779 238.38714184
Rotation angle (degrees) 17.51313227
Shift along axis 93.84408321
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 44
shifted from previous position = 0.00588
rotated from previous position = 0.0147 degrees
atoms outside contour = 722, contour level = 0.0074676
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98951164 0.01477622 -0.14369546 -45.82658996
0.02398369 0.96414263 0.26429865 -113.49712905
0.14244826 -0.26497294 0.95367596 -31.13698708
Axis -0.87956809 -0.47552691 0.01530140
Axis point 0.00000000 -164.59272813 238.32826730
Rotation angle (degrees) 17.50987486
Shift along axis 93.80210585
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 48
shifted from previous position = 0.0111
rotated from previous position = 0.0591 degrees
atoms outside contour = 722, contour level = 0.0074676
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98953649 0.01421292 -0.14358105 -45.76249307
0.02436872 0.96437677 0.26340768 -113.35993219
0.14221003 -0.26415040 0.95393966 -31.30508543
Axis -0.87914478 -0.47625417 0.01692405
Axis point 0.00000000 -166.10252953 238.49904609
Rotation angle (degrees) 17.46003583
Shift along axis 93.69018859
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #!30 models
> hide #25.1 models
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 64
shifted from previous position = 1.57
rotated from previous position = 1.77 degrees
atoms outside contour = 1189, contour level = 0.0074676
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79092025 -0.51961367 0.32318231 236.68441941
-0.42094200 -0.07867712 0.90366905 306.91695679
-0.44413174 -0.85077115 -0.28095454 224.05164929
Axis -0.91499202 0.40017678 0.05146017
Axis point 0.00000000 298.33353283 -19.93137691
Rotation angle (degrees) 106.52033984
Shift along axis -82.21357901
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 36
shifted from previous position = 0.0111
rotated from previous position = 0.0267 degrees
atoms outside contour = 1193, contour level = 0.0074676
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79079468 -0.51987556 0.32306840 236.68351133
-0.42076432 -0.07839699 0.90377614 306.91406724
-0.44452354 -0.85063701 -0.28074101 224.04067556
Axis -0.91492583 0.40029892 0.05168648
Axis point 0.00000000 298.37775850 -19.93102356
Rotation angle (degrees) 106.50934092
Shift along axis -82.11061549
> show #25.1 models
> hide #!30 models
> hide #!25.2 models
> hide #32.1 models
> show #!25.2 models
> fitmap #25.2 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3198 atoms
average map value = 0.01621, steps = 112
shifted from previous position = 1.7
rotated from previous position = 0.599 degrees
atoms outside contour = 578, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50709287 0.85735527 -0.08831055 217.30498081
-0.86097460 -0.50861215 0.00603291 405.52318744
-0.03974347 0.07909238 0.99607471 147.10970162
Axis 0.04246242 -0.02822735 -0.99869923
Axis point 226.26182545 136.88589997 0.00000000
Rotation angle (degrees) 120.65151814
Shift along axis -149.13789725
> fitmap #25.2 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif B (#25.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3198 atoms
average map value = 0.01621, steps = 64
shifted from previous position = 0.0226
rotated from previous position = 0.0293 degrees
atoms outside contour = 579, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif B (#25.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50737829 0.85719270 -0.08824927 217.37021695
-0.86079235 -0.50892465 0.00567549 405.57999771
-0.04004724 0.07884392 0.99608225 147.17400146
Axis 0.04253439 -0.02802089 -0.99870199
Axis point 226.28039377 136.93300981 0.00000000
Rotation angle (degrees) 120.67118058
Shift along axis -149.10196826
> hide #!25.2 models
> show #32.1 models
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 112
shifted from previous position = 1.18
rotated from previous position = 1.16 degrees
atoms outside contour = 1336, contour level = 0.0074676
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99553808 -0.07926465 0.05119619 253.51290154
0.06867539 0.98071735 0.18296767 192.95843243
-0.06471186 -0.17863536 0.98178500 287.89564980
Axis -0.88731214 0.28441859 0.36301961
Axis point 0.00000000 1842.97375796 -962.27558149
Rotation angle (degrees) 11.75710465
Shift along axis -65.55234322
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 64
shifted from previous position = 0.0181
rotated from previous position = 0.024 degrees
atoms outside contour = 1339, contour level = 0.0074676
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99554242 -0.07909544 0.05137323 253.49477224
0.06845565 0.98067246 0.18329032 192.96194874
-0.06487774 -0.17895650 0.98171556 287.89837941
Axis -0.88774154 0.28489088 0.36159665
Axis point 0.00000000 1840.25528801 -961.24127973
Rotation angle (degrees) 11.77255744
Shift along axis -65.96165180
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 44
shifted from previous position = 0.0378
rotated from previous position = 0.0375 degrees
atoms outside contour = 1338, contour level = 0.0074676
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99552861 -0.07954903 0.05093861 253.51313438
0.06899044 0.98066323 0.18313913 192.97734679
-0.06452217 -0.17880596 0.98176643 287.91470617
Axis -0.88729246 0.28304702 0.36413799
Axis point 0.00000000 1841.49762982 -960.48331793
Rotation angle (degrees) 11.76864994
Shift along axis -65.47794715
> hide #32.1 models
> show #!25.2 models
> hide #!25.2 models
> show #4 models
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7501 atoms
average map value = 0.007457, steps = 84
shifted from previous position = 0.00986
rotated from previous position = 0.0149 degrees
atoms outside contour = 4418, contour level = 0.0074676
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.01692687 -0.69781792 0.71607516 219.88635890
-0.07055059 0.71522626 0.69532295 243.07545144
-0.99736457 -0.03874988 -0.06133800 272.75720508
Axis -0.37323686 0.87119266 0.31893196
Axis point 259.29199268 0.00000000 -51.78350649
Rotation angle (degrees) 100.45826756
Shift along axis 216.68684493
> hide #4 models
> show #!25.2 models
> show #25.3 models
> fitmap #25.3 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3371 atoms
average map value = 0.01534, steps = 84
shifted from previous position = 0.664
rotated from previous position = 0.704 degrees
atoms outside contour = 522, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.47952602 0.87307180 -0.08831997 209.44256838
-0.87665218 -0.48110979 0.00378334 404.39983371
-0.03918847 0.07924011 0.99608496 146.36841160
Axis 0.04306796 -0.02804246 -0.99867851
Axis point 226.30279310 136.28079993 0.00000000
Rotation angle (degrees) 118.83411947
Shift along axis -148.49509082
> fitmap #25.3 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif C (#25.3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3371 atoms
average map value = 0.01534, steps = 44
shifted from previous position = 0.00967
rotated from previous position = 0.00924 degrees
atoms outside contour = 522, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif C (#25.3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.47945371 0.87310077 -0.08842613 209.44463068
-0.87668580 -0.48104930 0.00368385 404.41695980
-0.03932096 0.07928817 0.99607592 146.39029199
Axis 0.04315051 -0.02802635 -0.99867540
Axis point 226.32606671 136.28067031 0.00000000
Rotation angle (degrees) 118.83007225
Shift along axis -148.49307228
> hide #25.3 models
> show #25.3 models
> hide #25.3 models
> show #25.3 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.008658, steps = 64
shifted from previous position = 1.03
rotated from previous position = 1.81 degrees
atoms outside contour = 3144, contour level = 0.0074676
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99803851 -0.02181724 0.05867833 -72.22086949
0.02067138 0.99958497 0.02006446 -76.16555965
-0.05909172 -0.01881214 0.99807528 -69.82650088
Axis -0.29654810 0.89834191 0.32410034
Axis point -850.35345607 0.00000000 1554.29607241
Rotation angle (degrees) 3.75835093
Shift along axis -69.63654543
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> hide #!25.4 models
> show #!25.4 models
> hide #!25.4 models
> show #!25.4 models
> fitmap #25.4 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif D (#25.4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 706 atoms
average map value = 0.01592, steps = 80
shifted from previous position = 0.636
rotated from previous position = 0.772 degrees
atoms outside contour = 40, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif D (#25.4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50259492 0.85687248 -0.11475140 219.26231166
-0.86423372 -0.50140934 0.04109425 401.64865313
-0.02232489 0.11982579 0.99254389 141.09944210
Axis 0.04563133 -0.05356868 -0.99752102
Axis point 225.86212363 132.07231659 0.00000000
Rotation angle (degrees) 120.37983597
Shift along axis -152.26021475
> fitmap #25.4 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif D (#25.4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 706 atoms
average map value = 0.01592, steps = 28
shifted from previous position = 0.0373
rotated from previous position = 0.0643 degrees
atoms outside contour = 40, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif D (#25.4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50212529 0.85727199 -0.11381966 219.06728753
-0.86451661 -0.50093569 0.04092016 401.63147027
-0.02193662 0.11894603 0.99265836 141.09360375
Axis 0.04520610 -0.05323457 -0.99755826
Axis point 225.82056137 132.11900207 0.00000000
Rotation angle (degrees) 120.34471710
Shift along axis -152.22659262
> show #25.5 models
> fitmap #25.5 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif F (#25.5) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.008629, steps = 108
shifted from previous position = 2.52
rotated from previous position = 6.05 degrees
atoms outside contour = 338, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif F (#25.5) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.74390514 0.41955755 0.52016977 246.08931688
-0.36884298 -0.90684067 0.20394814 333.22564308
0.55727909 -0.04014290 0.82935430 68.10850364
Axis -0.29545411 -0.04491808 -0.95430039
Axis point 149.46993327 142.24417457 0.00000000
Rotation angle (degrees) 155.60167823
Shift along axis -152.67192692
> show #5 models
> hide #5 models
> show #5 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #!25.6 models
> fitmap #25.6 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif G (#25.6) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3190 atoms
average map value = 0.01344, steps = 84
shifted from previous position = 0.406
rotated from previous position = 0.865 degrees
atoms outside contour = 1483, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif G (#25.6) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57147431 0.81988072 -0.03482392 221.54231101
-0.81988901 -0.57224165 -0.01793004 410.33209307
-0.03462819 0.01830519 0.99923260 151.13544845
Axis 0.02209236 -0.00011934 -0.99975593
Axis point 219.47770757 146.52154587 0.00000000
Rotation angle (degrees) 124.90669341
Shift along axis -146.25313402
> fitmap #25.6 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif G (#25.6) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3190 atoms
average map value = 0.01344, steps = 48
shifted from previous position = 0.0123
rotated from previous position = 0.0426 degrees
atoms outside contour = 1483, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif G (#25.6) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57128690 0.82001501 -0.03473701 221.50468882
-0.82004569 -0.57203843 -0.01723646 410.23469118
-0.03400507 0.01863897 0.99924783 151.05061499
Axis 0.02186922 -0.00044619 -0.99976074
Axis point 219.43497350 146.44850987 0.00000000
Rotation angle (degrees) 124.89251663
Shift along axis -146.35338032
> fitmap #25.7 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif K (#25.7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2239 atoms
average map value = 0.01256, steps = 52
shifted from previous position = 1.07
rotated from previous position = 0.975 degrees
atoms outside contour = 1129, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif K (#25.7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55272261 0.83288176 -0.02838457 218.72191943
-0.83335224 -0.55220263 0.02441902 405.50722908
0.00466412 0.03715129 0.99929876 143.32138373
Axis 0.00763962 -0.01982989 -0.99977418
Axis point 217.94279070 142.32445254 0.00000000
Rotation angle (degrees) 123.56022805
Shift along axis -149.65922830
> fitmap #25.7 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif K (#25.7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2239 atoms
average map value = 0.01256, steps = 48
shifted from previous position = 0.00983
rotated from previous position = 0.0758 degrees
atoms outside contour = 1127, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif K (#25.7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55336415 0.83247015 -0.02795643 218.83773390
-0.83292953 -0.55288209 0.02344748 405.67633701
0.00406271 0.03626073 0.99933410 143.56168250
Axis 0.00769215 -0.01922198 -0.99978565
Axis point 217.97393466 142.47245648 0.00000000
Rotation angle (degrees) 123.60443854
Shift along axis -149.64548098
> fitmap #25.7 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif K (#25.7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2239 atoms
average map value = 0.01256, steps = 44
shifted from previous position = 0.013
rotated from previous position = 0.027 degrees
atoms outside contour = 1127, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif K (#25.7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55355150 0.83234120 -0.02808664 218.90273150
-0.83280689 -0.55308296 0.02306328 405.73589241
0.00366228 0.03615745 0.99933939 143.63218421
Axis 0.00786200 -0.01906267 -0.99978738
Axis point 218.01141751 142.50521368 0.00000000
Rotation angle (degrees) 123.61761083
Shift along axis -149.61504017
> hide #25.8 models
> show #25.8 models
> fitmap #25.8 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif L (#25.8) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 555 atoms
average map value = 0.01074, steps = 80
shifted from previous position = 0.588
rotated from previous position = 3.23 degrees
atoms outside contour = 145, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif L (#25.8) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50467604 0.86246487 -0.03816319 206.27513790
-0.86298707 -0.50520155 -0.00497054 404.78071206
-0.02356702 0.03042583 0.99925915 148.79813129
Axis 0.02050921 -0.00845725 -0.99975389
Axis point 220.35656340 141.75148805 0.00000000
Rotation angle (degrees) 120.35188135
Shift along axis -147.95430385
> fitmap #25.8 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif L (#25.8) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 555 atoms
average map value = 0.01074, steps = 28
shifted from previous position = 0.0403
rotated from previous position = 0.073 degrees
atoms outside contour = 143, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif L (#25.8) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50517247 0.86222276 -0.03704961 206.30150521
-0.86270534 -0.50567988 -0.00522873 404.82655458
-0.02324358 0.02932149 0.99929974 148.95156873
Axis 0.02002529 -0.00800197 -0.99976745
Axis point 220.29338844 141.85869129 0.00000000
Rotation angle (degrees) 120.38289886
Shift along axis -148.02509348
> fitmap #25.9 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif M (#25.9) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01577, steps = 124
shifted from previous position = 0.71
rotated from previous position = 2.19 degrees
atoms outside contour = 69, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif M (#25.9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.53966745 0.84095711 0.03937224 209.53471555
-0.84152726 -0.54020254 0.00361411 405.93665350
0.02430829 -0.03118240 0.99921807 152.45933187
Axis -0.02067637 0.00895112 -0.99974615
Axis point 214.47181659 147.26852788 0.00000000
Rotation angle (degrees) 122.70583146
Shift along axis -153.11946032
> fitmap #25.9 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif M (#25.9) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01577, steps = 76
shifted from previous position = 0.0109
rotated from previous position = 0.0634 degrees
atoms outside contour = 71, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif M (#25.9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54017038 0.84066532 0.03870098 209.70718956
-0.84123061 -0.54066853 0.00293096 406.05692255
0.02338836 -0.03097324 0.99924653 152.52956116
Axis -0.02015339 0.00910216 -0.99975547
Axis point 214.56120528 147.30897566 0.00000000
Rotation angle (degrees) 122.73785558
Shift along axis -153.02257931
> show #25.10 models
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01241, steps = 88
shifted from previous position = 1.33
rotated from previous position = 3.32 degrees
atoms outside contour = 194, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57909157 0.81427968 -0.04001926 223.95348284
-0.80966806 -0.58016521 -0.08857739 418.65309158
-0.09534455 -0.01889210 0.99526504 159.84091487
Axis 0.04284677 0.03401737 -0.99850236
Axis point 224.35627291 152.90637180 0.00000000
Rotation angle (degrees) 125.59104470
Shift along axis -135.76437017
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.0124, steps = 180
shifted from previous position = 0.00625
rotated from previous position = 0.0139 degrees
atoms outside contour = 194, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57903412 0.81432513 -0.03992575 223.92618448
-0.80969492 -0.58009510 -0.08879070 418.66701441
-0.09546523 -0.01908517 0.99524978 159.88432576
Axis 0.04285711 0.03414738 -0.99849748
Axis point 224.36219273 152.92599870 0.00000000
Rotation angle (degrees) 125.58708831
Shift along axis -135.75088596
> fitmap #25.11 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 555 atoms
average map value = 0.01758, steps = 52
shifted from previous position = 0.864
rotated from previous position = 2.13 degrees
atoms outside contour = 29, contour level = 0.0074676
Position of 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54661403 0.83480638 -0.06566128 221.77840345
-0.83696530 -0.54713943 0.01129254 405.31468918
-0.02649879 0.06112887 0.99777806 145.35185938
Axis 0.02978909 -0.02340892 -0.99928206
Axis point 221.70681989 139.79750674 0.00000000
Rotation angle (degrees) 123.22907022
Shift along axis -148.12890886
> hide #25.11 models
> show #25.11 models
> hide #25.8 models
> show #25.8 models
> hide #31.1 models
> show #31.1 models
> fitmap #31.1 inMap #34
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.01025, steps = 52
shifted from previous position = 0.845
rotated from previous position = 1.26 degrees
atoms outside contour = 483, contour level = 0.0074676
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97543397 0.21971428 -0.01594367 223.15831279
-0.21945560 0.97548294 0.01650070 253.44359243
0.01917822 -0.01259642 0.99973673 253.90331968
Axis -0.06590038 -0.07954554 -0.99465052
Axis point 1140.29145699 -801.97494212 0.00000000
Rotation angle (degrees) 12.75402354
Shift along axis -287.41159217
> fitmap #31.1 inMap #34
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.01025, steps = 28
shifted from previous position = 0.0388
rotated from previous position = 0.107 degrees
atoms outside contour = 484, contour level = 0.0074676
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97529083 0.22021143 -0.01774054 223.17848705
-0.21993270 0.97537725 0.01639591 253.48098162
0.02091429 -0.01208906 0.99970818 253.85881041
Axis -0.06433566 -0.08730514 -0.99410197
Axis point 1127.72585108 -802.54669976 0.00000000
Rotation angle (degrees) 12.78996814
Shift along axis -288.85007223
> hide #31.1 models
> show #32.2 models
> hide #32.2 models
> show #32.2 models
> hide #32.2 models
> show #32.2 models
> fitmap #32.2 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1222 atoms
average map value = 0.00967, steps = 68
shifted from previous position = 0.749
rotated from previous position = 3.7 degrees
atoms outside contour = 496, contour level = 0.0074676
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97959844 0.04140448 0.19665342 249.12109135
-0.05617405 0.99595505 0.07012851 194.53555530
-0.19295433 -0.07974459 0.97796187 284.10527219
Axis -0.34960471 0.90882688 -0.22761866
Axis point 1632.36086288 0.00000000 -1141.96661413
Rotation angle (degrees) 12.37719153
Shift along axis 25.03757364
> fitmap #32.2 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1222 atoms
average map value = 0.009669, steps = 40
shifted from previous position = 0.0174
rotated from previous position = 0.0299 degrees
atoms outside contour = 497, contour level = 0.0074676
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97962421 0.04168681 0.19646529 249.12134924
-0.05651158 0.99591229 0.07046386 194.54450077
-0.19272478 -0.08013067 0.97797558 284.11629865
Axis -0.35127532 0.90782087 -0.22905658
Axis point 1633.21810015 0.00000000 -1141.58497569
Rotation angle (degrees) 12.37763046
Shift along axis 24.02266830
> hide #32.2 models
> show #32.1 models
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 76
shifted from previous position = 0.00598
rotated from previous position = 0.0249 degrees
atoms outside contour = 1338, contour level = 0.0074676
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99549389 -0.07975464 0.05129444 253.51897719
0.06913771 0.98067704 0.18300962 192.97132986
-0.06489914 -0.17863858 0.98177205 287.91294533
Axis -0.88640516 0.28479221 0.36493737
Axis point 0.00000000 1841.88880018 -960.63155214
Rotation angle (degrees) 11.77079789
Shift along axis -64.69360508
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 64
shifted from previous position = 0.0276
rotated from previous position = 0.0516 degrees
atoms outside contour = 1340, contour level = 0.0074676
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99555213 -0.07911083 0.05116079 253.49467224
0.06848984 0.98061581 0.18358045 192.96529574
-0.06469228 -0.17925991 0.98167245 287.91864772
Axis -0.88825599 0.28361561 0.36133569
Axis point 0.00000000 1838.11694158 -959.62478426
Rotation angle (degrees) 11.78519610
Shift along axis -66.40491008
> hide #32.1 models
> show #31.1 models
> hide #31.1 models
> show #31.1 models
> hide #31.1 models
> show #31.1 models
> hide #31.1 models
> show #31.1 models
> fitmap #31.1 inMap #34
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.01025, steps = 40
shifted from previous position = 0.025
rotated from previous position = 0.0414 degrees
atoms outside contour = 483, contour level = 0.0074676
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97536139 0.21995150 -0.01707324 223.17039763
-0.21968240 0.97543492 0.01632075 253.45807998
0.02024361 -0.01216794 0.99972103 253.88051004
Axis -0.06443458 -0.08440176 -0.99434628
Axis point 1132.84099748 -803.30257695 0.00000000
Rotation angle (degrees) 12.77169891
Shift along axis -288.21733823
> fitmap #31.1 inMap #34
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.01025, steps = 28
shifted from previous position = 0.034
rotated from previous position = 0.0637 degrees
atoms outside contour = 488, contour level = 0.0074676
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97526637 0.22028822 -0.01812743 223.18295814
-0.22000553 0.97536137 0.01636331 253.48943051
0.02128544 -0.01197045 0.99970177 253.84909039
Axis -0.06396440 -0.08897586 -0.99397779
Axis point 1125.16763021 -802.84882228 0.00000000
Rotation angle (degrees) 12.79601525
Shift along axis -289.15056334
> fitmap #31.1 inMap #34
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.01025, steps = 36
shifted from previous position = 0.00784
rotated from previous position = 0.0335 degrees
atoms outside contour = 487, contour level = 0.0074676
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97532297 0.21999563 -0.01862878 223.18772395
-0.21970776 0.97542913 0.01632549 253.47880020
0.02176259 -0.01182974 0.99969318 253.84507105
Axis -0.06363463 -0.09128996 -0.99378910
Axis point 1123.37013789 -804.72959050 0.00000000
Rotation angle (degrees) 12.78103464
Shift along axis -289.61100380
> hide #31.1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v12.cxs"
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.7 models
> show #!25.7 models
> hide #28.1 models
> show #28.1 models
> hide #28.1 models
> show #28.1 models
> hide #28.1 models
> hide #28.2 models
> show #28.2 models
> show #28.1 models
> hide #28.1 models
> hide #28.2 models
> show #28.2 models
> hide #28.2 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v13.cxs"
——— End of log from Tue Mar 26 13:48:19 2024 ———
opened ChimeraX session
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/20240229_COPI_budding/Symmetry_splitting_masks/cryosparc_P126_J1413_005_volume_map.mrc"
Opened cryosparc_P126_J1413_005_volume_map.mrc as #35, grid size 480,480,480,
pixel 0.953, shown at level 0.144, step 2, values float32
> select add #35
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #35,1,0,0,38.872,0,1,0,127.16,0,0,1,30.564
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.97306,-0.10077,-0.20734,114.45,-0.019022,-0.93144,0.36341,481.54,-0.22975,-0.34967,-0.90826,592.75
> view matrix models
> #35,0.93801,0.14095,0.31667,-45.352,0.021261,-0.93527,0.3533,473.56,0.34597,-0.32467,-0.88028,422.86
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.93801,0.14095,0.31667,-28.084,0.021261,-0.93527,0.3533,500.77,0.34597,-0.32467,-0.88028,428.08
> view matrix models
> #35,0.93801,0.14095,0.31667,-11.53,0.021261,-0.93527,0.3533,471.38,0.34597,-0.32467,-0.88028,495.07
> view matrix models
> #35,0.93801,0.14095,0.31667,-31.081,0.021261,-0.93527,0.3533,476.85,0.34597,-0.32467,-0.88028,521.42
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.90217,0.27291,0.33409,-54.42,0.12759,-0.90861,0.39768,431.92,0.41209,-0.31614,-0.85454,495.68
> ui tool show "Fit in Map"
> fitmap #35 inMap #34
Fit map cryosparc_P126_J1413_005_volume_map.mrc in map
relion_locres_filtered_20240326_GT.mrc using 138168 points
correlation = 0.7875, correlation about mean = 0.5223, overlap = 232.2
steps = 460, shift = 51.8, angle = 39.7 degrees
Position of cryosparc_P126_J1413_005_volume_map.mrc (#35) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.96692083 -0.25367451 0.02670869 70.21163555
-0.25379291 -0.96725797 0.00108444 522.06873341
0.02555910 -0.00782705 -0.99964267 447.02232309
Axis -0.99169569 0.12792986 -0.01317644
Axis point 0.00000000 266.06925773 222.45211839
Rotation angle (degrees) 179.74256592
Shift along axis -8.73056298
> hide #!35 models
> show #!35 models
> hide #!35 models
> show #!35 models
> volume #35 step 1
> volume #35 level 0.2171
> color #35 #73fdffff models
> color #35 #73fdffbf models
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.97012,-0.24173,0.020899,128.31,-0.242,-0.97021,0.011413,594.75,0.017517,-0.01613,-0.99972,528.01
> view matrix models
> #35,0.97012,-0.24173,0.020899,130.17,-0.242,-0.97021,0.011413,594.76,0.017517,-0.01613,-0.99972,528.11
> fitmap #35 inMap #34
Fit map cryosparc_P126_J1413_005_volume_map.mrc in map
relion_locres_filtered_20240326_GT.mrc using 251397 points
correlation = 0.8287, correlation about mean = 0.3769, overlap = 1089
steps = 52, shift = 1.44, angle = 0.114 degrees
Position of cryosparc_P126_J1413_005_volume_map.mrc (#35) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.96688100 -0.25361193 0.02867252 69.83312106
-0.25375364 -0.96726793 0.00135627 521.99028503
0.02739005 -0.00858711 -0.99958794 446.87697447
Axis -0.99168564 0.12790564 -0.01413325
Axis point 0.00000000 266.06324281 222.27972065
Rotation angle (degrees) 179.71275392
Shift along axis -8.80282672
> select subtract #35
Nothing selected
> hide #!34 models
> volume #35 level 0.1987
> hide #!35 models
> show #!34 models
> hide #!34 models
> show #!35 models
> hide #!35 models
> show #!35 models
> show #!34 models
> volume #35 level 0.1359
> hide #!35 models
> show #!35 models
> hide #!34 models
> hide #!35 models
> show #!34 models
> hide #!34 models
> show #!35 models
> show #!34 models
> hide #!35 models
> show #!35 models
> hide #!35 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v14.cxs"
> show #!35 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/20240229_COPI_budding/cryosparc_P126_J1449_008_volume_map_sharp.mrc"
Opened cryosparc_P126_J1449_008_volume_map_sharp.mrc as #36, grid size
480,480,480, pixel 0.953, shown at level 0.17, step 2, values float32
> color #36 #73fdffff models
> color #36 #73fdffc8 models
> select add #36
2 models selected
> color #36 #73fdffc7 models
> view matrix models #36,1,0,0,134.54,0,1,0,66.108,0,0,1,19.086
> view matrix models #36,1,0,0,137.13,0,1,0,64.787,0,0,1,117.11
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.056086,-0.92264,0.38156,461.04,-0.99189,-0.095145,-0.084268,550.52,0.11405,-0.37374,-0.92049,639.45
> view matrix models
> #36,0.81264,-0.57783,0.075758,289.88,-0.58232,-0.81023,0.066513,583.57,0.022949,-0.098166,-0.99491,615.85
> view matrix models
> #36,0.78553,-0.58331,0.20662,265.51,-0.59501,-0.80369,-0.0067434,602.61,0.16999,-0.11764,-0.9784,583.63
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.78553,-0.58331,0.20662,270.11,-0.59501,-0.80369,-0.0067434,598.27,0.16999,-0.11764,-0.9784,540.75
> view matrix models
> #36,0.78553,-0.58331,0.20662,259.65,-0.59501,-0.80369,-0.0067434,611.27,0.16999,-0.11764,-0.9784,540.23
> fitmap #36 inMap #34
Fit map cryosparc_P126_J1449_008_volume_map_sharp.mrc in map
relion_locres_filtered_20240326_GT.mrc using 137972 points
correlation = 0.5875, correlation about mean = 0.1014, overlap = 144.9
steps = 172, shift = 17.3, angle = 11.8 degrees
Position of cryosparc_P126_J1449_008_volume_map_sharp.mrc (#36) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79251646 -0.60801798 0.04724189 243.68438170
-0.60939626 -0.78655708 0.09982066 521.84571018
-0.02353432 -0.10789854 -0.99388331 498.85499284
Axis -0.94654323 0.32251585 -0.00628058
Axis point 0.00000000 316.92705286 232.83595470
Rotation angle (degrees) 173.70052777
Shift along axis -65.48739144
> select subtract #36
Nothing selected
> hide #!36 models
> show #!36 models
> hide #!35 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> ui mousemode right "rotate selected models"
> select add #36
2 models selected
> view matrix models
> #36,0.98096,-0.19407,-0.0076419,185.28,-0.19361,-0.98023,0.040778,563.9,-0.015405,-0.038522,-0.99914,559.02
> fitmap #36 inMap #34
Fit map cryosparc_P126_J1449_008_volume_map_sharp.mrc in map
relion_locres_filtered_20240326_GT.mrc using 137972 points
correlation = 0.6115, correlation about mean = 0.08318, overlap = 167.7
steps = 96, shift = 8.76, angle = 3.55 degrees
Position of cryosparc_P126_J1449_008_volume_map_sharp.mrc (#36) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.96606437 -0.25727564 0.02299707 141.59744497
-0.25752745 -0.96623177 0.00870514 506.06574925
0.01998088 -0.01433210 -0.99969763 472.20508693
Axis -0.99147951 0.12981117 -0.01083724
Axis point 0.00000000 263.68309230 233.81583547
Rotation angle (degrees) 179.33434506
Shift along axis -79.81537680
> view matrix models
> #36,0.95194,-0.28838,-0.10317,245.09,-0.29527,-0.9536,-0.058901,604.59,-0.081399,0.086533,-0.99292,546.63
> fitmap #36 inMap #34
Fit map cryosparc_P126_J1449_008_volume_map_sharp.mrc in map
relion_locres_filtered_20240326_GT.mrc using 137972 points
correlation = 0.7137, correlation about mean = 0.2763, overlap = 246.1
steps = 224, shift = 7.84, angle = 8.39 degrees
Position of cryosparc_P126_J1449_008_volume_map_sharp.mrc (#36) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.96625519 -0.25688299 0.01902743 148.49020627
-0.25700032 -0.96640321 0.00395959 513.54756791
0.01737102 -0.00871603 -0.99981112 475.85913570
Axis -0.99152782 0.12956988 -0.00917755
Axis point 0.00000000 267.24157646 236.39693055
Rotation angle (degrees) 179.63376510
Shift along axis -85.05909744
> select subtract #36
Nothing selected
> hide #!34 models
> volume #36 step 1
> volume #36 level 0.2273
> hide #!36 models
> show #!34 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v15.cxs"
> show #!36 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!36 models
> show #!36 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!35 models
> hide #!34 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!34 models
> show #!1 models
> hide #!34 models
> hide #!1 models
> show #!34 models
> show #7 models
> show #3 models
> hide #3 models
> show #3 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> hide #5 models
> show #25.5 models
> hide #25.5 models
> show #!26.1 models
> hide #!26.1 models
> show #25.5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #25.5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> select add #25.5
635 atoms, 634 bonds, 159 residues, 1 model selected
> hide #!34 models
> ui mousemode right "translate selected models"
> view matrix models
> #25.5,-0.73604,0.4305,0.52241,305.27,-0.38361,-0.90111,0.20209,413.36,0.55775,-0.051653,0.8284,142.68
> view matrix models
> #25.5,-0.73604,0.4305,0.52241,304.13,-0.38361,-0.90111,0.20209,415.06,0.55775,-0.051653,0.8284,144.4
> ui tool show Matchmaker
> matchmaker #25.5 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker hArf1_P84078, chain A (#5) with 5nzr_COPI_coat_leaf_2017.cif F,
chain F (#25.5), sequence alignment score = 612.9
RMSD between 91 pruned atom pairs is 1.407 angstroms; (across all 159 pairs:
2.595)
> select subtract #25.5
Nothing selected
> show #!34 models
> hide #5 models
> hide #7 models
> show #11 models
> volume #34 level 0.007041
> combine 25.5
Expected a keyword
> combine #25.5
> select add #37
635 atoms, 634 bonds, 159 residues, 1 model selected
> view matrix models
> #37,-0.53385,0.84429,0.046635,295.94,-0.84212,-0.53584,0.060952,498.92,0.07645,-0.0067325,0.99705,172.15
> view matrix models
> #37,-0.53385,0.84429,0.046635,290.65,-0.84212,-0.53584,0.060952,517.84,0.07645,-0.0067325,0.99705,203.74
> view matrix models
> #37,-0.53385,0.84429,0.046635,286.69,-0.84212,-0.53584,0.060952,511.7,0.07645,-0.0067325,0.99705,210.47
> view matrix models
> #37,-0.53385,0.84429,0.046635,288.46,-0.84212,-0.53584,0.060952,513.92,0.07645,-0.0067325,0.99705,208.92
> ui mousemode right "rotate selected models"
> view matrix models
> #37,-0.26547,0.96403,-0.013259,241.37,-0.93121,-0.25282,0.26256,499.47,0.24976,0.082049,0.96482,177.44
> view matrix models
> #37,-0.42633,0.87802,-0.21753,287,-0.89277,-0.3697,0.25746,499.75,0.14563,0.30397,0.94148,184.39
> view matrix models
> #37,0.013244,0.89027,0.45525,166.47,-0.96278,-0.11157,0.2462,498.21,0.26997,-0.44156,0.85565,210.01
> view matrix models
> #37,0.43692,0.89657,0.072551,121.99,-0.60427,0.23282,0.76201,384.07,0.6663,-0.37678,0.64349,155.11
> view matrix models
> #37,-0.17109,0.95269,-0.25123,242.73,-0.52973,0.12605,0.83875,372.12,0.83073,0.27659,0.4831,103.39
> view matrix models
> #37,-0.33767,0.94126,-0.00037941,253.75,-0.6278,-0.22492,0.74517,413.97,0.70132,0.25186,0.66687,113.58
> view matrix models
> #37,-0.13258,0.98137,-0.13904,226.98,-0.57174,0.038867,0.81951,385.18,0.80965,0.18814,0.55594,106.65
> view matrix models
> #37,-0.34901,0.8952,-0.27716,277.3,-0.5072,0.068249,0.85912,370.08,0.788,0.44042,0.43022,105.29
> view matrix models
> #37,-0.34953,0.91197,-0.21482,272.16,-0.52792,-0.0022859,0.84929,378.04,0.77403,0.41026,0.48224,105.65
> view matrix models
> #37,-0.23498,0.91143,-0.33776,261.6,-0.48984,0.1891,0.85106,361.2,0.83955,0.36543,0.40202,102.71
> ui mousemode right "translate selected models"
> view matrix models
> #37,-0.23498,0.91143,-0.33776,260.26,-0.48984,0.1891,0.85106,366.99,0.83955,0.36543,0.40202,106.91
> ui mousemode right "rotate selected models"
> view matrix models
> #37,-0.14164,0.96699,-0.21183,232.97,-0.55666,0.099149,0.82481,384.82,0.81858,0.23475,0.52424,109.03
> view matrix models
> #37,0.23062,0.55681,-0.79798,233.72,-0.082745,0.82834,0.55408,285.02,0.96952,-0.061755,0.23711,119.81
> view matrix models
> #37,-0.41519,0.77847,-0.47075,306.72,-0.24849,0.40074,0.88185,313.15,0.87514,0.48311,0.027061,120.55
> view matrix models
> #37,-0.54808,0.83523,-0.044679,296.3,-0.3291,-0.16623,0.92955,354.02,0.76896,0.52417,0.36598,112.57
> view matrix models
> #37,-0.22731,0.97035,-0.0822,238.1,-0.36299,-0.006099,0.93177,350.83,0.90364,0.24164,0.35361,106.28
> ui mousemode right "translate selected models"
> view matrix models
> #37,-0.22731,0.97035,-0.0822,237.53,-0.36299,-0.006099,0.93177,348.3,0.90364,0.24164,0.35361,106.02
> ui mousemode right "rotate selected models"
> view matrix models
> #37,-0.26817,0.94765,-0.17333,251.88,-0.31325,0.084372,0.94592,334.12,0.91102,0.30796,0.27422,106.69
> view matrix models
> #37,-0.29695,0.94968,-0.09959,251.47,-0.34179,-0.0083276,0.93974,344.34,0.89162,0.3131,0.32707,105.99
> view matrix models
> #37,-0.2546,0.96317,-0.086493,242.77,-0.35326,-0.0093715,0.93548,346.6,0.90022,0.26873,0.34263,105.88
> ui tool show "Fit in Map"
> fitmap #37 inMap #34
Fit molecule copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.009537, steps = 64
shifted from previous position = 3.04
rotated from previous position = 26.7 degrees
atoms outside contour = 177, contour level = 0.0070409
Position of copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.03518402 0.96625924 0.25515711 108.12871839
-0.42593365 -0.21646744 0.87847729 296.68750822
0.90407002 -0.13958836 0.40394614 42.99047607
Axis -0.55246929 -0.35214277 -0.75549530
Axis point 138.21037911 138.56100197 0.00000000
Rotation angle (degrees) 112.87168388
Shift along axis -196.69325894
> fitmap #37 inMap #34
Fit molecule copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.009537, steps = 36
shifted from previous position = 0.00551
rotated from previous position = 0.0232 degrees
atoms outside contour = 177, contour level = 0.0070409
Position of copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.03479145 0.96629551 0.25507356 108.20209154
-0.42596846 -0.21654561 0.87844115 296.70286695
0.90406881 -0.13921553 0.40407747 42.96077084
Axis -0.55229028 -0.35221482 -0.75559259
Axis point 138.22815027 138.53430087 0.00000000
Rotation angle (degrees) 112.88223694
Shift along axis -196.72295138
> fitmap #37 inMap #34
Fit molecule copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.009537, steps = 28
shifted from previous position = 0.02
rotated from previous position = 0.0771 degrees
atoms outside contour = 177, contour level = 0.0070409
Position of copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.03361578 0.96619871 0.25559736 108.38398615
-0.42634764 -0.21744143 0.87803582 296.85028859
0.90393454 -0.13848919 0.40462708 42.90508381
Axis -0.55186871 -0.35198052 -0.75600968
Axis point 138.29837629 138.51992435 0.00000000
Rotation angle (degrees) 112.92956801
Shift along axis -196.73590871
> fitmap #37 inMap #34
Fit molecule copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.009537, steps = 48
shifted from previous position = 0.0285
rotated from previous position = 0.113 degrees
atoms outside contour = 177, contour level = 0.0070409
Position of copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.03541471 0.96631473 0.25491495 108.10128492
-0.42588964 -0.21616037 0.87857424 296.65613018
0.90408174 -0.13968009 0.40388818 42.99770199
Axis -0.55251102 -0.35224187 -0.75541859
Axis point 138.20573010 138.55793198 0.00000000
Rotation angle (degrees) 112.85676625
Shift along axis -196.70312278
> fitmap #37 inMap #34
Fit molecule copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.009537, steps = 28
shifted from previous position = 0.032
rotated from previous position = 0.0961 degrees
atoms outside contour = 177, contour level = 0.0070409
Position of copy of 5nzr_COPI_coat_leaf_2017.cif F (#37) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.03392899 0.96620039 0.25554965 108.33940231
-0.42632747 -0.21727376 0.87808712 296.83434701
0.90393235 -0.13874044 0.40454589 42.92792536
Axis -0.55198231 -0.35197294 -0.75593028
Axis point 138.29150050 138.53365427 0.00000000
Rotation angle (degrees) 112.91713633
Shift along axis -196.72960858
> select subtract #37
Nothing selected
> show #!2 models
> hide #!34 models
> volume #2 level 0.1233
> show #!34 models
> volume #2 level 0.09309
> ui mousemode right label
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v16.cxs"
> hide #!34 models
> hide #!2 models
> show #!35 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!30 models
> hide #!30 models
> hide #3 models
> show #3 models
> show #!2 models
> volume #2 level 0.1866
> hide #!2 models
> hide #3 models
> hide #11 models
> hide #24 models
> show #24 models
> hide #!25.2 models
> show #!25.2 models
> hide #25.3 models
> show #25.3 models
> hide #!25.4 models
> show #!25.4 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.7 models
> show #!25.7 models
> hide #25.8 models
> show #25.8 models
> hide #25.9 models
> show #25.9 models
> hide #25.10 models
> show #25.10 models
> show #!26.1 models
> hide #!26.1 models
> show #!26.2 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> hide #37 models
> show #37 models
> hide #37 models
> show #37 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> hide #25.3 models
> show #25.3 models
> show #25.1 models
> show #!30 models
> show #28.2 models
> show #27.2 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> volume #34 level 0.005256
> volume #34 level 0.006446
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240328_leaf_fitting_v17.cxs"
——— End of log from Fri Mar 29 15:25:34 2024 ———
opened ChimeraX session
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> hide #37 models
> show #37 models
> hide #37 models
> show #37 models
> hide #37 models
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> hide #25.9 models
> show #25.9 models
> show #25.5 models
> hide #25.10 models
> show #25.10 models
> hide #25.10 models
> ui tool show Matchmaker
> show #25.10 models
> show #!26.1 models
> matchmaker #!26.1 to #25.10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif R, chain R (#25.10) with
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#26.1), sequence alignment
score = 773.4
RMSD between 92 pruned atom pairs is 1.282 angstroms; (across all 159 pairs:
2.182)
> hide #!34 models
> matchmaker #!26.1 to #25.10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif R, chain R (#25.10) with
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#26.1), sequence alignment
score = 773.4
RMSD between 92 pruned atom pairs is 1.282 angstroms; (across all 159 pairs:
2.182)
> show #!34 models
> hide #!34 models
> ui tool show "Fit in Map"
> show #!34 models
> fitmap #26.1 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#26.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008909, steps = 64
shifted from previous position = 0.77
rotated from previous position = 4.16 degrees
atoms outside contour = 520, contour level = 0.0064458
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#26.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.21066750 0.17815726 -0.96118634 330.74516316
0.67347295 0.73913574 -0.01060821 309.91319893
0.70855725 -0.64956781 -0.27569598 215.29865366
Axis -0.34442130 -0.90004949 0.26699227
Axis point -8.28188363 0.00000000 234.35961275
Rotation angle (degrees) 111.93866769
Shift along axis -335.36982072
> fitmap #26.1 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#26.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008909, steps = 48
shifted from previous position = 0.0112
rotated from previous position = 0.076 degrees
atoms outside contour = 521, contour level = 0.0064458
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#26.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.21042678 0.17939235 -0.96100934 330.82665780
0.67396729 0.73869774 -0.00968153 309.88279527
0.70815863 -0.64972612 -0.27634636 215.29149740
Axis -0.34506970 -0.89990494 0.26664209
Axis point -8.29655738 0.00000000 234.18876552
Rotation angle (degrees) 111.96484961
Shift along axis -335.61753797
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01241, steps = 96
shifted from previous position = 0.00308
rotated from previous position = 0.0115 degrees
atoms outside contour = 130, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57911686 0.81426097 -0.04003396 223.95598831
-0.80964168 -0.58019030 -0.08865414 418.66731589
-0.09541493 -0.01892795 0.99525761 159.85096414
Axis 0.04287302 0.03405247 -0.99850004
Axis point 224.36012870 152.91748322 0.00000000
Rotation angle (degrees) 125.59308112
Shift along axis -135.75286879
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01241, steps = 48
shifted from previous position = 0.00482
rotated from previous position = 0.0724 degrees
atoms outside contour = 131, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57945185 0.81399028 -0.04068608 224.09024031
-0.80945482 -0.58060406 -0.08764597 418.62233634
-0.09496547 -0.01785308 0.99532046 159.62444397
Axis 0.04292699 0.03338522 -0.99852026
Axis point 224.33339427 152.83275015 0.00000000
Rotation angle (degrees) 125.61724891
Shift along axis -135.79292122
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.0124, steps = 144
shifted from previous position = 0.0166
rotated from previous position = 0.048 degrees
atoms outside contour = 131, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57930230 0.81411152 -0.04038906 224.03717989
-0.80950866 -0.58041314 -0.08840991 418.66371837
-0.09541787 -0.01852077 0.99526499 159.78590532
Axis 0.04298079 0.03384191 -0.99850257
Axis point 224.36632488 152.89118575 0.00000000
Rotation angle (degrees) 125.60720577
Shift along axis -135.74896084
> hide #!34 models
> select add #25.10
635 atoms, 634 bonds, 159 residues, 1 model selected
> select subtract #25.10
Nothing selected
> select add #25.10
635 atoms, 634 bonds, 159 residues, 1 model selected
> select subtract #25.10
Nothing selected
> select add #26.1
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> show #!34 models
> select subtract #26.1
Nothing selected
> select add #26.1
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select subtract #26.1
Nothing selected
> hide #25.10 models
> show #25.10 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> hide #25.10 models
> show #25.10 models
> select add #25.10
635 atoms, 634 bonds, 159 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #25.10,-0.56979,0.82111,-0.033523,282.49,-0.81565,-0.57004,-0.098854,495.12,-0.10028,-0.028983,0.99454,238.05
> view matrix models
> #25.10,-0.56979,0.82111,-0.033523,282.64,-0.81565,-0.57004,-0.098854,495.27,-0.10028,-0.028983,0.99454,237.65
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01241, steps = 108
shifted from previous position = 1.77
rotated from previous position = 0.0348 degrees
atoms outside contour = 131, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57967028 0.81383264 -0.04072810 224.15941597
-0.80924405 -0.58081542 -0.08819020 418.69178013
-0.09542757 -0.01816226 0.99527067 159.71116751
Axis 0.04308066 0.03365071 -0.99850473
Axis point 224.37093318 152.88832243 0.00000000
Rotation angle (degrees) 125.63415139
Shift along axis -135.72614414
> view matrix models
> #25.10,-0.57016,0.82084,-0.033865,283.15,-0.81539,-0.57045,-0.098639,495.39,-0.10028,-0.028627,0.99455,238.98
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.0124, steps = 84
shifted from previous position = 1.46
rotated from previous position = 0.0732 degrees
atoms outside contour = 131, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57882830 0.81445493 -0.04026116 223.92057802
-0.80981808 -0.57992238 -0.08879576 418.64146532
-0.09566850 -0.01879328 0.99523582 159.85012424
Axis 0.04303278 0.03406067 -0.99849289
Axis point 224.39333634 152.88484856 0.00000000
Rotation angle (degrees) 125.57424627
Shift along axis -135.71407959
> select subtract #25.10
Nothing selected
> show #!26.1 models
> select add #26.1
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> view matrix models
> #26.1,-0.21464,0.16647,-0.9624,392.75,0.66418,0.74733,-0.01886,385.5,0.71609,-0.64326,-0.27097,291.62
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01241, steps = 80
shifted from previous position = 0.0105
rotated from previous position = 0.0343 degrees
atoms outside contour = 130, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57907990 0.81427973 -0.04018689 223.96868603
-0.80969368 -0.58017522 -0.08827713 418.62684340
-0.09519771 -0.01858044 0.99528496 159.77660424
Axis 0.04285338 0.03382370 -0.99850866
Axis point 224.35071346 152.87171941 0.00000000
Rotation angle (degrees) 125.59028400
Shift along axis -135.78100180
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01241, steps = 92
shifted from previous position = 0.0183
rotated from previous position = 0.0696 degrees
atoms outside contour = 132, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57960053 0.81387247 -0.04092444 224.16631037
-0.80934188 -0.58077628 -0.08754787 418.62643142
-0.09502075 -0.01762093 0.99531932 159.58864347
Axis 0.04301555 0.03327733 -0.99852005
Axis point 224.34840220 152.81747393 0.00000000
Rotation angle (degrees) 125.62859855
Shift along axis -135.77905230
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01241, steps = 112
shifted from previous position = 0.0135
rotated from previous position = 0.0187 degrees
atoms outside contour = 131, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57948580 0.81395203 -0.04096688 224.15145479
-0.80939248 -0.58066095 -0.08784456 418.63117192
-0.09528913 -0.01774640 0.99529143 159.63962880
Axis 0.04311703 0.03341335 -0.99851113
Axis point 224.37355418 152.82261696 0.00000000
Rotation angle (degrees) 125.62147319
Shift along axis -135.74933155
> fitmap #25.10 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif R (#25.10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 635 atoms
average map value = 0.01241, steps = 124
shifted from previous position = 0.0264
rotated from previous position = 0.0176 degrees
atoms outside contour = 131, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif R (#25.10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57946360 0.81397614 -0.04080154 224.11340702
-0.80944384 -0.58062769 -0.08759077 418.62341381
-0.09498731 -0.01772911 0.99532059 159.61256565
Axis 0.04296996 0.03332815 -0.99852031
Axis point 224.34354252 152.82263380 0.00000000
Rotation angle (degrees) 125.61849097
Shift along axis -135.79430071
> select subtract #26.1
Nothing selected
> select add #26.1
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select subtract #26.1
Nothing selected
> hide #25.10 models
> hide #!26.1 models
> show #!26.1 models
> show #!26.2 models
> hide #25.9 models
> show #25.9 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #26.3 models
> hide #26.3 models
> show #26.3 models
> hide #26.3 models
> hide #!26.1 models
> show #!26.1 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> fitmap #26.2 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2069 atoms
average map value = 0.01291, steps = 64
shifted from previous position = 0.946
rotated from previous position = 1.32 degrees
atoms outside contour = 709, contour level = 0.0064458
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.26676369 0.21060525 -0.94046933 331.59689306
0.69716374 0.71593433 -0.03742646 310.02523477
0.66543207 -0.66564514 -0.33781163 215.90163313
Axis -0.35062015 -0.89628248 0.27155705
Axis point -1.07432461 0.00000000 228.95265506
Rotation angle (degrees) 116.37987233
Shift along axis -335.50512764
> hide #!25.7 models
> show #!25.7 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!34 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!25.6 models
> show #!25.6 models
> fitmap #25.6 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif G (#25.6) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3190 atoms
average map value = 0.01344, steps = 60
shifted from previous position = 0.0136
rotated from previous position = 0.046 degrees
atoms outside contour = 1426, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif G (#25.6) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57150051 0.81986359 -0.03479709 221.54415607
-0.81986949 -0.57226792 -0.01798424 410.34012380
-0.03465788 0.01825107 0.99923256 151.14400112
Axis 0.02209290 -0.00008488 -0.99975592
Axis point 219.47799700 146.52998535 0.00000000
Rotation angle (degrees) 124.90852780
Shift along axis -146.24738522
> fitmap #25.6 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif G (#25.6) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3190 atoms
average map value = 0.01344, steps = 60
shifted from previous position = 0.00946
rotated from previous position = 0.0223 degrees
atoms outside contour = 1426, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif G (#25.6) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57139144 0.81993964 -0.03479654 221.52527143
-0.81995810 -0.57215219 -0.01762304 410.29097843
-0.03435875 0.01846205 0.99923902 151.09642121
Axis 0.02199915 -0.00026690 -0.99975795
Axis point 219.45935637 146.48992317 0.00000000
Rotation angle (degrees) 124.90044927
Shift along axis -146.29598725
> show #!34 models
> hide #!26.2 models
> show #!26.2 models
> hide #!25.6 models
> show #26.3 models
> hide #26.3 models
> hide #25.11 models
> show #25.11 models
> hide #!34 models
> show #26.3 models
> fitmap #26.3 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.01093, steps = 80
shifted from previous position = 0.986
rotated from previous position = 0.899 degrees
atoms outside contour = 358, contour level = 0.0064458
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.25043210 0.19248870 -0.94880549 329.67320722
0.71012646 0.70264192 -0.04488574 309.43538649
0.65803052 -0.68501271 -0.31265541 214.49028655
Axis -0.35455348 -0.88999420 0.28670916
Axis point -6.48640813 0.00000000 232.40025471
Rotation angle (degrees) 115.48170033
Shift along axis -330.78615344
> fitmap #25.11 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 555 atoms
average map value = 0.01758, steps = 44
shifted from previous position = 0.00184
rotated from previous position = 0.0428 degrees
atoms outside contour = 19, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54660847 0.83480197 -0.06576359 221.78872090
-0.83694728 -0.54718173 0.01055431 405.39457341
-0.02717388 0.06080973 0.99777941 145.43800115
Axis 0.03004001 -0.02306687 -0.99928250
Axis point 221.76468855 139.85093267 0.00000000
Rotation angle (degrees) 123.23028209
Shift along axis -148.02229824
> fitmap #25.11 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 555 atoms
average map value = 0.01758, steps = 44
shifted from previous position = 0.011
rotated from previous position = 0.0592 degrees
atoms outside contour = 19, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif Z (#25.11) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54623363 0.83511331 -0.06491964 221.64637607
-0.83721609 -0.54676420 0.01086763 405.33329553
-0.02642003 0.06028804 0.99783131 145.44742845
Axis 0.02953112 -0.02300541 -0.99929909
Axis point 221.70559607 139.84686651 0.00000000
Rotation angle (degrees) 123.20137237
Shift along axis -148.12487531
> show #!34 models
> hide #!2 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v18.cxs"
> close #25.11
> hide #!26.1 models
> show #!26.1 models
> hide #24 models
> show #24 models
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 44
shifted from previous position = 0.0138
rotated from previous position = 0.0468 degrees
atoms outside contour = 729, contour level = 0.0064458
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23357866 0.95002788 -0.20709425 197.36052025
-0.00017108 -0.21294573 -0.97706401 258.07204149
-0.97233789 0.22825674 -0.04957705 197.42047125
Axis 0.70280508 0.44620249 -0.55404726
Axis point 0.00000000 -45.38476117 254.49183049
Rotation angle (degrees) 120.96217309
Shift along axis 144.47809218
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 48
shifted from previous position = 0.0101
rotated from previous position = 0.0527 degrees
atoms outside contour = 727, contour level = 0.0064458
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23410930 0.94979349 -0.20756967 197.35969318
0.00022632 -0.21355609 -0.97693078 258.11291282
-0.97221026 0.22866161 -0.05021043 197.38370379
Axis 0.70313895 0.44596216 -0.55381708
Axis point 0.00000000 -45.18462452 254.34379884
Rotation angle (degrees) 120.98599951
Shift along axis 144.56541288
> hide #24 models
> show #24 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> hide #26.3 models
> show #26.3 models
> hide #!26.2 models
> show #!26.2 models
> show #27.1 models
> hide #25.3 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.008658, steps = 44
shifted from previous position = 0.0172
rotated from previous position = 0.0592 degrees
atoms outside contour = 2878, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99798654 -0.02155831 0.05964989 -72.41704393
0.02038086 0.99958663 0.02027796 -76.19302071
-0.06006239 -0.01902141 0.99801337 -69.77541800
Axis -0.29594138 0.90148559 0.31582026
Axis point -847.94280840 0.00000000 1529.19268245
Rotation angle (degrees) 3.80708140
Shift along axis -69.29220064
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.008658, steps = 48
shifted from previous position = 0.0145
rotated from previous position = 0.0556 degrees
atoms outside contour = 2881, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99803993 -0.02156149 0.05874854 -72.25761698
0.02042215 0.99959287 0.01992550 -76.13165864
-0.05915425 -0.01868667 0.99807394 -69.83557161
Axis -0.29480439 0.90018934 0.32054566
Axis point -853.82266054 0.00000000 1550.80156420
Rotation angle (degrees) 3.75486000
Shift along axis -69.61653459
> select add #27.1
6538 atoms, 6591 bonds, 911 residues, 1 model selected
> view matrix models
> #27.1,0.99735,-0.034033,0.064281,-7.3604,0.033414,0.99938,0.010672,1.0557,-0.064605,-0.0084954,0.99787,6.8613
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.008658, steps = 68
shifted from previous position = 2.62
rotated from previous position = 0.0326 degrees
atoms outside contour = 2881, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99806168 -0.02186237 0.05826591 -72.14158603
0.02073299 0.99958662 0.01991793 -76.13839887
-0.05867728 -0.01867130 0.99810238 -69.85512230
Axis -0.29614711 0.89746245 0.32689149
Axis point -852.22850225 0.00000000 1564.57377379
Rotation angle (degrees) 3.73558851
Shift along axis -69.80187603
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.008658, steps = 60
shifted from previous position = 0.0033
rotated from previous position = 0.02 degrees
atoms outside contour = 2881, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99808049 -0.02188794 0.05793316 -72.08240649
0.02077044 0.99958776 0.01982188 -76.12395187
-0.05834313 -0.01858053 0.99812366 -69.87297509
Axis -0.29615184 0.89669995 0.32897309
Axis point -854.08403980 0.00000000 1573.25797163
Rotation angle (degrees) 3.71741809
Shift along axis -69.89933488
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.008658, steps = 48
shifted from previous position = 0.0139
rotated from previous position = 0.0534 degrees
atoms outside contour = 2880, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99803390 -0.02166884 0.05881153 -72.25698973
0.02052243 0.99958878 0.02002748 -76.14999383
-0.05922132 -0.01878114 0.99806819 -69.82750912
Axis -0.29575854 0.89952239 0.32153750
Axis point -851.87721930 0.00000000 1550.05387539
Rotation angle (degrees) 3.76179925
Shift along axis -69.58016548
> select subtract #27.1
Nothing selected
> select add #27.2
1407 atoms, 1415 bonds, 194 residues, 1 model selected
> select subtract #27.2
Nothing selected
> select add #27.2
1407 atoms, 1415 bonds, 194 residues, 1 model selected
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.008658, steps = 48
shifted from previous position = 0.00355
rotated from previous position = 0.0108 degrees
atoms outside contour = 2881, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99804086 -0.02153848 0.05874132 -72.25917623
0.02040049 0.99959374 0.01990428 -76.12688742
-0.05914616 -0.01866693 0.99807479 -69.83738339
Axis -0.29458199 0.90034858 0.32030280
Axis point -854.19504449 0.00000000 1550.79158135
Rotation angle (degrees) 3.75370689
Shift along axis -69.62359268
> select subtract #27.2
Nothing selected
> hide #!30 models
> show #!30 models
> show #25.1 models
> hide #!34 models
> ui tool show Matchmaker
> matchmaker #27.2 to #25.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif A, chain A (#25.1) with
3mkq_yeast_alpha_betaprimeCOPI.cif B, chain B (#27.2), sequence alignment
score = 418.9
RMSD between 62 pruned atom pairs is 1.400 angstroms; (across all 175 pairs:
3.710)
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #!34 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 88
shifted from previous position = 2.49
rotated from previous position = 10 degrees
atoms outside contour = 654, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98954467 0.01425451 -0.14352057 -45.77357441
0.02436544 0.96427860 0.26376713 -113.41670488
0.14215368 -0.26450630 0.95384944 -31.24973114
Axis -0.87949755 -0.47560561 0.01683320
Axis point 0.00000000 -165.74194167 238.63704483
Rotation angle (degrees) 17.47723437
Shift along axis 93.67333471
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 44
shifted from previous position = 0.0121
rotated from previous position = 0.0235 degrees
atoms outside contour = 654, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98950284 0.01456273 -0.14377777 -45.78107200
0.02414939 0.96425692 0.26386627 -113.43225746
0.14248133 -0.26456857 0.95378328 -31.21802132
Axis -0.87916370 -0.47625287 0.01594945
Axis point 0.00000000 -165.26762153 238.24622898
Rotation angle (degrees) 17.48959966
Shift along axis 93.77358484
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 44
shifted from previous position = 0.0121
rotated from previous position = 0.0235 degrees
atoms outside contour = 654, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98950284 0.01456273 -0.14377777 -45.78107200
0.02414939 0.96425692 0.26386627 -113.43225746
0.14248133 -0.26456857 0.95378328 -31.21802132
Axis -0.87916370 -0.47625287 0.01594945
Axis point 0.00000000 -165.26762153 238.24622898
Rotation angle (degrees) 17.48959966
Shift along axis 93.77358484
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 88
shifted from previous position = 2.49
rotated from previous position = 10 degrees
atoms outside contour = 654, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98954467 0.01425451 -0.14352057 -45.77357441
0.02436544 0.96427860 0.26376713 -113.41670488
0.14215368 -0.26450630 0.95384944 -31.24973114
Axis -0.87949755 -0.47560561 0.01683320
Axis point 0.00000000 -165.74194167 238.63704483
Rotation angle (degrees) 17.47723437
Shift along axis 93.67333471
> select add #30
2737 atoms, 2622 bonds, 1 pseudobond, 505 residues, 2 models selected
> select subtract #30
Nothing selected
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #!30 models
> hide #27.2 models
> select add #25.1
3251 atoms, 3250 bonds, 813 residues, 1 model selected
> view matrix models
> #25.1,-0.49739,0.85348,-0.15546,287.51,-0.86504,-0.50149,0.014511,475.92,-0.065576,0.1417,0.98774,223.57
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 68
shifted from previous position = 2.11
rotated from previous position = 0.00909 degrees
atoms outside contour = 983, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50773664 0.84633078 -0.16102079 226.47717411
-0.85942981 -0.51057143 0.02640457 400.52408444
-0.05986562 0.15179263 0.98659773 146.90785450
Axis 0.07318292 -0.05903935 -0.99556949
Axis point 229.74919439 128.44033942 0.00000000
Rotation angle (degrees) 121.05463313
Shift along axis -153.32940131
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 48
shifted from previous position = 0.0158
rotated from previous position = 0.0116 degrees
atoms outside contour = 981, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50788469 0.84622701 -0.16109926 226.51308649
-0.85933646 -0.51072952 0.02638566 400.51616908
-0.05994989 0.15183934 0.98658543 146.92713917
Axis 0.07322941 -0.05904258 -0.99556588
Axis point 229.74511440 128.43760322 0.00000000
Rotation angle (degrees) 121.06528239
Shift along axis -153.33573453
> select subtract #25.1
Nothing selected
> hide #25.1 models
> show #27.2 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 88
shifted from previous position = 2.49
rotated from previous position = 10 degrees
atoms outside contour = 654, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98954467 0.01425451 -0.14352057 -45.77357441
0.02436544 0.96427860 0.26376713 -113.41670488
0.14215368 -0.26450630 0.95384944 -31.24973114
Axis -0.87949755 -0.47560561 0.01683320
Axis point 0.00000000 -165.74194167 238.63704483
Rotation angle (degrees) 17.47723437
Shift along axis 93.67333471
> hide #27.2 models
> show #27.2 models
> show #!30 models
> hide #!30 models
> hide #27.2 models
> show #27.2 models
> close #35
> close #36
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> hide #25.5 models
> show #25.5 models
> combine #26.1
> hide #!35 models
> show #!35 models
> select add #35
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> hide #!34 models
> select add #25.5
1941 atoms, 1965 bonds, 3 pseudobonds, 320 residues, 3 models selected
> select subtract #25.5
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select add #25.5
1941 atoms, 1965 bonds, 3 pseudobonds, 320 residues, 3 models selected
> select subtract #25.5
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> matchmaker #!35 to #25.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif F, chain F (#25.5) with copy of
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#35), sequence alignment
score = 720
RMSD between 92 pruned atom pairs is 1.327 angstroms; (across all 159 pairs:
2.577)
> show #!34 models
> close #25.5
> fitmap #35 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008638, steps = 44
shifted from previous position = 0.306
rotated from previous position = 3.66 degrees
atoms outside contour = 565, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.33621727 0.36097706 0.86985832 201.02429891
-0.22646712 -0.92751492 0.29736964 179.03665203
0.91415019 -0.09701350 0.39359598 210.27410806
Axis -0.55630275 -0.06247653 -0.82862774
Axis point 47.66462041 77.64958055 0.00000000
Rotation angle (degrees) 159.23915181
Shift along axis -297.25491863
> fitmap #35 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008638, steps = 48
shifted from previous position = 0.034
rotated from previous position = 0.0754 degrees
atoms outside contour = 565, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.33622679 0.36044176 0.87007659 200.96371480
-0.22735855 -0.92760278 0.29641384 179.04249014
0.91392539 -0.09815708 0.39383443 210.21005922
Axis -0.55627570 -0.06181911 -0.82869521
Axis point 47.69710519 77.73084221 0.00000000
Rotation angle (degrees) 159.22775321
Shift along axis -297.05954698
> fitmap #35 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008638, steps = 48
shifted from previous position = 0.0123
rotated from previous position = 0.0415 degrees
atoms outside contour = 562, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.33610588 0.36049797 0.87010001 200.95884938
-0.22803367 -0.92750642 0.29619667 179.05460852
0.91380166 -0.09885865 0.39394604 210.16812948
Axis -0.55627911 -0.06153647 -0.82871395
Axis point 47.74392439 77.76496889 0.00000000
Rotation angle (degrees) 159.20120342
Shift along axis -296.97686052
> hide #25.9 models
> show #25.9 models
> select subtract #35
Nothing selected
> hide #!34 models
> show #!34 models
> hide #!35 models
> show #!35 models
> show #37 models
> hide #37 models
> show #37 models
> combine #26.1
> matchmaker #!36 to #37
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 5nzr_COPI_coat_leaf_2017.cif F, chain F (#37) with copy of
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#36), sequence alignment
score = 720
RMSD between 92 pruned atom pairs is 1.327 angstroms; (across all 159 pairs:
2.577)
> fitmap #36 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#36) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.007274, steps = 68
shifted from previous position = 1.09
rotated from previous position = 1.54 degrees
atoms outside contour = 617, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#36) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.11537320 0.75636603 0.64389397 234.64544426
0.67225004 -0.53667322 0.50996247 244.70048176
0.73127895 0.37402175 -0.57038480 234.38875714
Axis -0.74616702 -0.47964867 -0.46170547
Axis point 0.00000000 48.44393250 42.99244610
Rotation angle (degrees) 174.77352811
Shift along axis -400.67352208
> select add #37
635 atoms, 634 bonds, 159 residues, 1 model selected
> select subtract #37
Nothing selected
> hide #!34 models
> select add #36
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select subtract #36
Nothing selected
> select add #36
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select subtract #36
Nothing selected
> select add #37
635 atoms, 634 bonds, 159 residues, 1 model selected
> select subtract #37
Nothing selected
> matchmaker #!36 to #37
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 5nzr_COPI_coat_leaf_2017.cif F, chain F (#37) with copy of
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#36), sequence alignment
score = 720
RMSD between 92 pruned atom pairs is 1.327 angstroms; (across all 159 pairs:
2.577)
> matchmaker #!36 to #37
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 5nzr_COPI_coat_leaf_2017.cif F, chain F (#37) with copy of
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#36), sequence alignment
score = 720
RMSD between 92 pruned atom pairs is 1.327 angstroms; (across all 159 pairs:
2.577)
> fitmap #36 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#36) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.007274, steps = 68
shifted from previous position = 1.09
rotated from previous position = 1.54 degrees
atoms outside contour = 617, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#36) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.11537320 0.75636603 0.64389397 234.64544426
0.67225004 -0.53667322 0.50996247 244.70048177
0.73127895 0.37402175 -0.57038480 234.38875714
Axis -0.74616702 -0.47964867 -0.46170547
Axis point 0.00000000 48.44393252 42.99244612
Rotation angle (degrees) 174.77352811
Shift along axis -400.67352206
> close #37
> show #!34 models
> fitmap #36 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#36) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.007274, steps = 40
shifted from previous position = 0.00738
rotated from previous position = 0.0209 degrees
atoms outside contour = 617, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#36) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.11505990 0.75631839 0.64400598 234.64753159
0.67216010 -0.53663003 0.51012645 244.70925801
0.73141097 0.37418003 -0.57011164 234.40153165
Axis -0.74606159 -0.47967061 -0.46185301
Axis point 0.00000000 48.43223574 42.96460006
Rotation angle (degrees) 174.77256767
Shift along axis -400.70040380
> fitmap #36 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#36) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.007274, steps = 40
shifted from previous position = 0.00299
rotated from previous position = 0.014 degrees
atoms outside contour = 617, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#36) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.11491296 0.75620763 0.64416227 234.64227089
0.67213072 -0.53667324 0.51011971 244.70806988
0.73146107 0.37434188 -0.56994109 234.41059083
Axis -0.74601371 -0.47965198 -0.46194969
Axis point 0.00000000 48.42873539 42.95258985
Rotation angle (degrees) 174.77873247
Shift along axis -400.70696272
> select add #35
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> fitmap #35 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008638, steps = 60
shifted from previous position = 0.021
rotated from previous position = 0.0989 degrees
atoms outside contour = 565, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.33695386 0.36047522 0.86978141 200.97071078
-0.22665166 -0.92769340 0.29667147 179.03519218
0.91383320 -0.09717280 0.39429218 210.27309495
Axis -0.55599565 -0.06218854 -0.82885549
Axis point 47.68614232 77.68205036 0.00000000
Rotation angle (degrees) 159.25684744
Shift along axis -297.15878789
> fitmap #35 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008638, steps = 40
shifted from previous position = 0.03
rotated from previous position = 0.0831 degrees
atoms outside contour = 564, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.33559289 0.36077052 0.87018506 201.01608465
-0.22676988 -0.92753054 0.29709005 179.02852543
0.91430456 -0.09763045 0.39308454 210.23157936
Axis -0.55657709 -0.06221087 -0.82846349
Axis point 47.64467346 77.68273633 0.00000000
Rotation angle (degrees) 159.23128706
Shift along axis -297.18765431
> select subtract #35
Nothing selected
> select add #36
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> fitmap #35 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008638, steps = 48
shifted from previous position = 0.00599
rotated from previous position = 0.0771 degrees
atoms outside contour = 564, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.33674425 0.36094457 0.86966793 201.01956439
-0.22639479 -0.92755279 0.29730658 179.03404178
0.91397412 -0.09677201 0.39406405 210.29209083
Axis -0.55607345 -0.06251924 -0.82877841
Axis point 47.68635638 77.63917676 0.00000000
Rotation angle (degrees) 159.24697513
Shift along axis -297.26026167
> fitmap #35 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.008638, steps = 40
shifted from previous position = 0.00259
rotated from previous position = 0.0467 degrees
atoms outside contour = 565, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#35) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.33600451 0.36092061 0.86996395 201.02317412
-0.22656995 -0.92751557 0.29728928 179.03525249
0.91420294 -0.09721716 0.39342318 210.25979761
Axis -0.55639525 -0.06239281 -0.82857194
Axis point 47.65908017 77.66051880 0.00000000
Rotation angle (degrees) 159.23597395
Shift along axis -297.23422034
> select subtract #36
Nothing selected
> show #25.10 models
> hide #25.10 models
> show #25.10 models
> hide #25.10 models
> select add #26.1
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select subtract #26.1
Nothing selected
> show #25.10 models
> hide #25.10 models
> close #25.10
> hide #25.9 models
> show #25.9 models
> combine #26.1
> select add #37
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select subtract #37
Nothing selected
> select add #37
1306 atoms, 1331 bonds, 3 pseudobonds, 161 residues, 2 models selected
> select subtract #37
Nothing selected
> hide #25.9 models
> show #25.9 models
> matchmaker #!37 to #25.9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif M, chain M (#25.9) with copy of
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#37), sequence alignment
score = 762.6
RMSD between 94 pruned atom pairs is 1.262 angstroms; (across all 159 pairs:
2.576)
> hide #!34 models
> fitmap #37 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.01088, steps = 104
shifted from previous position = 0.407
rotated from previous position = 3.96 degrees
atoms outside contour = 405, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#37) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54129972 -0.76666173 0.34528887 243.97507197
-0.38367034 -0.14020143 -0.91276537 216.04770294
0.74819227 -0.62655674 -0.21825437 215.75309840
Axis 0.45775576 -0.64439480 0.61254796
Axis point 179.85601116 0.00000000 234.95515780
Rotation angle (degrees) 161.78271137
Shift along axis 104.62009737
> close #25.9
> show #!34 models
> fitmap #37 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.01088, steps = 76
shifted from previous position = 0.00432
rotated from previous position = 0.0603 degrees
atoms outside contour = 406, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#37) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54069520 -0.76683005 0.34586176 243.96988302
-0.38360219 -0.14115007 -0.91264780 215.99229085
0.74866418 -0.62613762 -0.21783853 215.78179850
Axis 0.45807841 -0.64400884 0.61271264
Axis point 179.93311836 0.00000000 235.03686061
Rotation angle (degrees) 161.77613953
Shift along axis 104.86862749
> fitmap #37 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.01088, steps = 64
shifted from previous position = 0.00818
rotated from previous position = 0.0216 degrees
atoms outside contour = 406, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#37) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54084402 -0.76667433 0.34597429 243.97678854
-0.38342242 -0.14138288 -0.91268731 215.97017405
0.74864877 -0.62627577 -0.21749404 215.77421533
Axis 0.45800331 -0.64392046 0.61286165
Axis point 179.93402353 0.00000000 235.05958743
Rotation angle (degrees) 161.77954268
Shift along axis 104.91430511
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v19.cxs"
> hide #!26.1 models
> show #!26.1 models
> hide #!26.2 models
> show #!26.2 models
> hide #26.3 models
> show #26.3 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.2 models
> show #27.2 models
> hide #28.2 models
> show #28.2 models
> hide #28.2 models
> show #28.2 models
> hide #28.2 models
> show #28.2 models
> hide #28.2 models
> show #28.2 models
> hide #28.2 models
> show #28.1 models
> hide #28.1 models
> close #28
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> show #29 models
> hide #29 models
> close #29
> show #!30 models
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 36
shifted from previous position = 0.0233
rotated from previous position = 0.0317 degrees
atoms outside contour = 1051, contour level = 0.0064458
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79056596 -0.52023232 0.32305389 236.67743801
-0.42069457 -0.07803799 0.90383968 306.89868613
-0.44499613 -0.85045189 -0.28055309 224.02068804
Axis -0.91481745 0.40051812 0.05190635
Axis point 0.00000000 298.42661967 -19.93047147
Rotation angle (degrees) 106.49983377
Shift along axis -81.97007056
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 44
shifted from previous position = 0.0315
rotated from previous position = 0.0652 degrees
atoms outside contour = 1049, contour level = 0.0064458
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79098567 -0.51952120 0.32317084 236.68463732
-0.42093865 -0.07876264 0.90366316 306.91752169
-0.44401838 -0.85081971 -0.28098667 224.04980128
Axis -0.91502166 0.40011491 0.05141411
Axis point 0.00000000 298.31698751 -19.93413458
Rotation angle (degrees) 106.52190026
Shift along axis -82.24997222
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 28
shifted from previous position = 0.0253
rotated from previous position = 0.0264 degrees
atoms outside contour = 1051, contour level = 0.0064458
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79085843 -0.51970045 0.32319405 236.68274699
-0.42082895 -0.07837223 0.90374820 306.90197055
-0.44434891 -0.85074628 -0.28068633 224.03169942
Axis -0.91494800 0.40026452 0.05156031
Axis point 0.00000000 298.36397081 -19.96131267
Rotation angle (degrees) 106.50506268
Shift along axis -82.15929109
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009303, steps = 28
shifted from previous position = 0.0324
rotated from previous position = 0.0159 degrees
atoms outside contour = 1049, contour level = 0.0064458
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79092275 -0.51963452 0.32314267 236.68568073
-0.42088094 -0.07863185 0.90370143 306.92165118
-0.44418515 -0.85076260 -0.28089599 224.05512317
Axis -0.91498940 0.40017738 0.05150204
Axis point 0.00000000 298.34462200 -19.93270870
Rotation angle (degrees) 106.51716289
Shift along axis -82.20249073
> hide #25.8 models
> show #25.8 models
> combine #26.3
> hide #25.8 models
> show #25.8 models
> hide #26.3 models
> show #26.3 models
> hide #26.3 models
> show #26.3 models
> hide #26.3 models
> show #26.3 models
> hide #28 models
> show #28 models
> hide #28 models
> show #28 models
> hide #25.8 models
> show #25.8 models
> hide #26.3 models
> hide #28 models
> show #28 models
> show #26.3 models
> matchmaker #28 to #25.8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif L, chain L (#25.8) with copy of
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C, chain C (#28), sequence alignment
score = 662.5
RMSD between 94 pruned atom pairs is 1.180 angstroms; (across all 137 pairs:
1.871)
> hide #!34 models
> hide #25.8 models
> show #25.8 models
> hide #25.8 models
> show #25.8 models
> hide #28 models
> show #28 models
> show #!34 models
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007772, steps = 84
shifted from previous position = 1.17
rotated from previous position = 4.01 degrees
atoms outside contour = 477, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56993929 -0.71661199 0.40204035 245.68162516
-0.48485532 -0.10172533 -0.86865831 216.17526219
0.66338866 -0.69001391 -0.28947588 214.81018147
Axis 0.45533467 -0.66613308 0.59070895
Axis point 184.91540655 0.00000000 218.31168221
Rotation angle (degrees) 168.68702299
Shift along axis 94.75616540
> close #25.8
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> hide #!25.7 models
> show #!25.7 models
> combine #26.2
> hide #!25.7 models
> show #!25.7 models
> fitmap #25.7 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif K (#25.7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2239 atoms
average map value = 0.01256, steps = 44
shifted from previous position = 0.0318
rotated from previous position = 0.0204 degrees
atoms outside contour = 991, contour level = 0.0064458
Position of 5nzr_COPI_coat_leaf_2017.cif K (#25.7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55373559 0.83221893 -0.02808100 218.96063769
-0.83268549 -0.55327700 0.02279102 405.79166712
0.00343055 0.03600284 0.99934579 143.66486297
Axis 0.00793381 -0.01892296 -0.99978947
Axis point 218.03723218 142.54045039 0.00000000
Rotation angle (degrees) 123.63039976
Shift along axis -149.57620218
> matchmaker #!29 to #25.7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif K, chain K (#25.7) with copy of
3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B, chain B (#29), sequence alignment
score = 1196.5
RMSD between 133 pruned atom pairs is 1.377 angstroms; (across all 263 pairs:
3.376)
> hide #!25.7 models
> hide #!26.1 models
> show #!26.1 models
> hide #!35 models
> show #!35 models
> hide #!36 models
> show #!36 models
> hide #!37 models
> show #!37 models
> fitmap #37 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#37) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1306 atoms
average map value = 0.01088, steps = 48
shifted from previous position = 0.0334
rotated from previous position = 0.085 degrees
atoms outside contour = 406, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A (#37) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54161844 -0.76643163 0.34529989 243.99385836
-0.38372770 -0.14005578 -0.91276362 216.08584599
0.74793216 -0.62687074 -0.21824425 215.72724414
Axis 0.45761328 -0.64447172 0.61257350
Axis point 179.86152210 0.00000000 234.93773919
Rotation angle (degrees) 161.79764955
Shift along axis 104.54240724
> fitmap #29 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2069 atoms
average map value = 0.01228, steps = 56
shifted from previous position = 0.538
rotated from previous position = 0.789 degrees
atoms outside contour = 767, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55899489 -0.72614953 0.40028935 245.14925444
-0.44644233 -0.14323016 -0.88327479 214.34605641
0.69872309 -0.67245221 -0.24411896 213.92962783
Axis 0.45815304 -0.64854686 0.60785094
Axis point 184.70030066 0.00000000 225.19456914
Rotation angle (degrees) 166.69829003
Shift along axis 103.33974015
> fitmap #29 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2069 atoms
average map value = 0.01228, steps = 28
shifted from previous position = 0.0473
rotated from previous position = 0.0856 degrees
atoms outside contour = 765, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55790495 -0.72657367 0.40103958 245.11920271
-0.44743418 -0.14365178 -0.88270426 214.35988941
0.69895973 -0.67190390 -0.24494986 213.97654545
Axis 0.45879093 -0.64840052 0.60752585
Axis point 184.83003870 0.00000000 225.15640457
Rotation angle (degrees) 166.71854943
Shift along axis 103.46368548
> fitmap #29 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2069 atoms
average map value = 0.01228, steps = 40
shifted from previous position = 0.0493
rotated from previous position = 0.11 degrees
atoms outside contour = 764, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55914928 -0.72625234 0.39988700 245.15446634
-0.44598243 -0.14311765 -0.88352532 214.35117032
0.69889322 -0.67236513 -0.24387165 213.93318919
Axis 0.45802274 -0.64856757 0.60792703
Axis point 184.65421906 0.00000000 225.24447541
Rotation angle (degrees) 166.67273670
Shift along axis 103.32087343
> fitmap #29 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2069 atoms
average map value = 0.01228, steps = 28
shifted from previous position = 0.023
rotated from previous position = 0.0516 degrees
atoms outside contour = 765, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55860599 -0.72638775 0.40040000 245.14033651
-0.44669808 -0.14328398 -0.88313675 214.36057411
0.69887063 -0.67218340 -0.24443673 213.95623045
Axis 0.45836431 -0.64852387 0.60771617
Axis point 184.73389217 0.00000000 225.19547510
Rotation angle (degrees) 166.69613556
Shift along axis 103.37029320
> fitmap #29 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2069 atoms
average map value = 0.01228, steps = 44
shifted from previous position = 0.0115
rotated from previous position = 0.0231 degrees
atoms outside contour = 767, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55878243 -0.72637637 0.40017440 245.14104522
-0.44634487 -0.14327439 -0.88331687 214.35222183
0.69895525 -0.67219774 -0.24415516 213.94712879
Axis 0.45824170 -0.64851463 0.60781849
Axis point 184.69864831 0.00000000 225.22630823
Rotation angle (degrees) 166.68186027
Shift along axis 103.36431790
> show #!25.7 models
> hide #!25.7 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v20.cxs"
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/1pzd_Cow_Cterm_COPI_gamma.cif"
Summary of feedback from opening /Users/becca/Desktop/Postdoc/Structure
files/COPI structures/1pzd_Cow_Cterm_COPI_gamma.cif
---
note | Fetching CCD SO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif
1pzd_Cow_Cterm_COPI_gamma.cif title:
Structural Identification of a conserved appendage domain in the carboxyl-
terminus of the COPI gamma-subunit. [more info...]
Chain information for 1pzd_Cow_Cterm_COPI_gamma.cif #38
---
Chain | Description | UniProt
A | Coatomer gamma subunit | COPG_BOVIN 555-874
Non-standard residues in 1pzd_Cow_Cterm_COPI_gamma.cif #38
---
SO4 — sulfate ion
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> hide #38 models
> select add #38
2270 atoms, 2156 bonds, 426 residues, 1 model selected
> show #38 models
> view matrix models #38,1,0,0,-0.64529,0,1,0,23.842,0,0,1,-23.879
> view matrix models #38,1,0,0,-1.0009,0,1,0,24.244,0,0,1,-24.177
> view matrix models #38,1,0,0,59.65,0,1,0,285.42,0,0,1,-153.36
> view matrix models #38,1,0,0,237.46,0,1,0,84.435,0,0,1,-77.65
> view matrix models #38,1,0,0,227.02,0,1,0,211.76,0,0,1,-69.899
> view matrix models #38,1,0,0,221.44,0,1,0,318.77,0,0,1,-11.511
> view matrix models #38,1,0,0,221.36,0,1,0,404.89,0,0,1,96.545
> view matrix models #38,1,0,0,318.93,0,1,0,520.04,0,0,1,349.49
> view matrix models #38,1,0,0,383.63,0,1,0,467.83,0,0,1,382.24
> color #38 #00f900ff
> color #29 #00f900ff
> color #25.7 #00f900ff
> color #25.6 #00f900ff
> color #9 #00f900ff
> select subtract #38
Nothing selected
> show #!25.6 models
> hide #!25.6 models
> show #!25.7 models
> hide #!25.7 models
> show #!25.7 models
> matchmaker #38 to #25.7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif K, chain K (#25.7) with
1pzd_Cow_Cterm_COPI_gamma.cif, chain A (#38), sequence alignment score =
1222.3
RMSD between 131 pruned atom pairs is 1.315 angstroms; (across all 271 pairs:
5.906)
> hide #38 models
> show #38 models
> fitmap #38 inMap #34
Fit molecule 1pzd_Cow_Cterm_COPI_gamma.cif (#38) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2270 atoms
average map value = 0.005007, steps = 76
shifted from previous position = 3.75
rotated from previous position = 7.51 degrees
atoms outside contour = 1871, contour level = 0.0064458
Position of 1pzd_Cow_Cterm_COPI_gamma.cif (#38) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.75820373 -0.32963444 0.56255510 246.48716545
0.63653394 -0.18730372 0.74815898 188.08479567
-0.14125030 0.92534234 0.35183789 314.52014998
Axis 0.14662708 0.58243015 0.79954713
Axis point 103.49526445 19.07189728 0.00000000
Rotation angle (degrees) 142.82890022
Shift along axis 397.16163406
> fitmap #38 inMap #34
Fit molecule 1pzd_Cow_Cterm_COPI_gamma.cif (#38) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2270 atoms
average map value = 0.005007, steps = 76
shifted from previous position = 3.75
rotated from previous position = 7.51 degrees
atoms outside contour = 1871, contour level = 0.0064458
Position of 1pzd_Cow_Cterm_COPI_gamma.cif (#38) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.75820373 -0.32963444 0.56255510 246.48716545
0.63653394 -0.18730372 0.74815898 188.08479567
-0.14125030 0.92534234 0.35183789 314.52014998
Axis 0.14662708 0.58243015 0.79954713
Axis point 103.49526445 19.07189728 0.00000000
Rotation angle (degrees) 142.82890022
Shift along axis 397.16163406
> hide #!25.7 models
> show #!25.7 models
> hide #!34 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> hide #!29 models
> show #!29 models
> hide #38 models
> show #38 models
> hide #38 models
> hide #!29 models
> hide #!25.7 models
> show #38 models
> show #!29 models
> show #!25.7 models
> hide #!25.7 models
> close #25.7
> hide #38 models
> show #38 models
> show #!34 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v21.cxs"
——— End of log from Mon Apr 15 15:35:58 2024 ———
opened ChimeraX session
> hide #27.1 models
> show #27.1 models
> hide #!34 models
> hide #27.2 models
> color #26.2 #00f900ff
> hide #!30 models
> hide #!25.2 models
> hide #!25.6 models
> hide #!25.4 models
> ui mousemode right select
Drag select of 213 residues
> show #!34 models
> fitmap selection inMap #34 moveWholeMolecules false
Missing or invalid "atomsOrMap" argument: invalid objects specifier
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 116
shifted from previous position = 4.1
rotated from previous position = 12.8 degrees
atoms outside contour = 712, contour level = 0.0064458
> hide #!34 models
> select add #27.1
6538 atoms, 6591 bonds, 911 residues, 1 model selected
> ui tool show "Fit in Map"
> show #!34 models
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009087, steps = 64
shifted from previous position = 0.359
rotated from previous position = 0.614 degrees
atoms outside contour = 2707, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99755824 -0.01645506 0.06787330 -74.41438134
0.01499908 0.99964752 0.02190559 -76.65180827
-0.06820983 -0.02083407 0.99745344 -69.25669387
Axis -0.29260936 0.93166855 0.21534503
Axis point -861.70990518 -0.00000000 1343.67041359
Rotation angle (degrees) 4.18815100
Shift along axis -64.55381917
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009087, steps = 28
shifted from previous position = 0.04
rotated from previous position = 0.0543 degrees
atoms outside contour = 2708, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99753347 -0.01580353 0.06839024 -74.55393363
0.01436959 0.99966754 0.02140857 -76.52569111
-0.06870583 -0.02037302 0.99742892 -69.29634346
Axis -0.28527036 0.93604487 0.20601171
Axis point -864.49362817 0.00000000 1328.57141631
Rotation angle (degrees) 4.19961917
Shift along axis -64.63931133
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009088, steps = 40
shifted from previous position = 0.0404
rotated from previous position = 0.0851 degrees
atoms outside contour = 2701, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99744788 -0.01560279 0.06967261 -74.80797081
0.01409304 0.99965624 0.02210842 -76.65657376
-0.06999362 -0.02107009 0.99732489 -69.17622712
Axis -0.28945064 0.93626391 0.19906840
Axis point -856.59871046 0.00000000 1307.75000325
Rotation angle (degrees) 4.27749259
Shift along axis -63.88836937
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009088, steps = 28
shifted from previous position = 0.0256
rotated from previous position = 0.0724 degrees
atoms outside contour = 2702, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99738262 -0.01494067 0.07074384 -75.05761397
0.01341495 0.99966812 0.02199300 -76.61165845
-0.07104895 -0.02098641 0.99725203 -69.15128969
Axis -0.28491025 0.93994347 0.18796920
Axis point -854.68760792 0.00000000 1285.59288630
Rotation angle (degrees) 4.32571285
Shift along axis -63.62425729
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009088, steps = 44
shifted from previous position = 0.0101
rotated from previous position = 0.0174 degrees
atoms outside contour = 2698, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99737310 -0.01510216 0.07084371 -75.06002751
0.01355699 0.99966071 0.02224125 -76.66278390
-0.07115556 -0.02122240 0.99723944 -69.12245521
Axis -0.28737765 0.93888604 0.18949167
Axis point -852.18252975 0.00000000 1285.52549761
Rotation angle (degrees) 4.33691254
Shift along axis -63.50517285
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009088, steps = 44
shifted from previous position = 0.00135
rotated from previous position = 0.00484 degrees
atoms outside contour = 2701, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99737289 -0.01503306 0.07086129 -75.07004040
0.01349094 0.99966272 0.02219114 -76.65298501
-0.07117099 -0.02117685 0.99723930 -69.12606492
Axis -0.28678690 0.93924102 0.18862552
Axis point -852.79462738 0.00000000 1284.79440303
Rotation angle (degrees) 4.33628014
Shift along axis -63.50546312
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009088, steps = 44
shifted from previous position = 0.000948
rotated from previous position = 0.00317 degrees
atoms outside contour = 2701, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99737635 -0.01502750 0.07081379 -75.06232257
0.01348836 0.99966337 0.02216344 -76.64796013
-0.07112301 -0.02115013 0.99724329 -69.13037088
Axis -0.28662951 0.93927310 0.18870499
Axis point -853.26698506 0.00000000 1285.50345865
Rotation angle (degrees) 4.33321102
Shift along axis -63.52353651
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009088, steps = 44
shifted from previous position = 0.000891
rotated from previous position = 0.00255 degrees
atoms outside contour = 2701, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99737361 -0.01503364 0.07085101 -75.06823109
0.01349203 0.99966279 0.02218709 -76.65241101
-0.07116067 -0.02117289 0.99724013 -69.12677004
Axis -0.28677433 0.93923729 0.18866318
Axis point -852.87740114 0.00000000 1284.96331132
Rotation angle (degrees) 4.33566718
Shift along axis -63.50883719
> hide #!34 models
> select clear
Drag select of 213 residues
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 64
shifted from previous position = 0.231
rotated from previous position = 1.38 degrees
atoms outside contour = 713, contour level = 0.0064458
> show #!34 models
Drag select of 1 residues, 34 relion_locres_filtered_20240326_GT.mrc
> select clear
> hide #!34 models
Drag select of 213 residues
> show #!34 models
> ui mousemode right "translate selected models"
> view matrix models
> #27.1,0.9967,-0.027521,0.07635,-8.2465,0.026597,0.99956,0.013092,-2.2807,-0.076677,-0.011018,0.997,5.9858
> view matrix models
> #27.1,0.9967,-0.027521,0.07635,-9.0898,0.026597,0.99956,0.013092,-0.98399,-0.076677,-0.011018,0.997,6.4267
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 64
shifted from previous position = 1.2
rotated from previous position = 0.169 degrees
atoms outside contour = 716, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0112
rotated from previous position = 0.073 degrees
atoms outside contour = 714, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.00894
rotated from previous position = 0.0289 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0109
rotated from previous position = 0.0166 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0115
rotated from previous position = 0.0685 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0099
rotated from previous position = 0.0603 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0113
rotated from previous position = 0.0415 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009076, steps = 48
shifted from previous position = 0.846
rotated from previous position = 0.813 degrees
atoms outside contour = 2693, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99697850 -0.00319250 0.07761238 -77.02470711
0.00184708 0.99984689 0.01740065 -75.52589375
-0.07765605 -0.01720472 0.99683175 -69.23099659
Axis -0.21742804 0.97556263 0.03166404
Axis point -913.19688324 0.00000000 1122.51320803
Rotation angle (degrees) 4.56436218
Shift along axis -59.12504170
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009076, steps = 44
shifted from previous position = 0.0308
rotated from previous position = 0.0897 degrees
atoms outside contour = 2689, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99686897 -0.00260304 0.07902841 -77.33100146
0.00121206 0.99984360 0.01764388 -75.55803998
-0.07906198 -0.01749285 0.99671621 -69.14792570
Axis -0.21690282 0.97590907 0.02355103
Axis point -902.98601924 0.00000000 1103.56131090
Rotation angle (degrees) 4.64584567
Shift along axis -58.59296883
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 68
shifted from previous position = 0.456
rotated from previous position = 0.855 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0348
rotated from previous position = 0.0347 degrees
atoms outside contour = 717, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.0284
rotated from previous position = 0.0451 degrees
atoms outside contour = 716, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0273
rotated from previous position = 0.0318 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 60
shifted from previous position = 0.0254
rotated from previous position = 0.0716 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.00912, steps = 48
shifted from previous position = 0.259
rotated from previous position = 0.482 degrees
atoms outside contour = 2671, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99623283 0.00017687 0.08671860 -78.98362762
-0.00185569 0.99981242 0.01927914 -75.96257392
-0.08669893 -0.01936744 0.99604628 -68.64358733
Axis -0.21750268 0.97599269 -0.01143919
Axis point -845.44396193 0.00000000 1014.97033683
Rotation angle (degrees) 5.09696944
Shift along axis -56.17453882
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.00912, steps = 64
shifted from previous position = 0.037
rotated from previous position = 0.0375 degrees
atoms outside contour = 2678, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99623632 0.00063876 0.08667628 -79.01861460
-0.00227493 0.99982106 0.01877938 -75.84138965
-0.08664878 -0.01890588 0.99605951 -68.70039236
Axis -0.21243277 0.97703764 -0.01642454
Axis point -849.55401410 0.00000000 1012.46591456
Rotation angle (degrees) 5.08878185
Shift along axis -56.18537721
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.127
rotated from previous position = 0.39 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0109
rotated from previous position = 0.15 degrees
atoms outside contour = 716, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0044
rotated from previous position = 0.0418 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009126, steps = 40
shifted from previous position = 0.0991
rotated from previous position = 0.184 degrees
atoms outside contour = 2668, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99597070 0.00177957 0.08966155 -79.64525863
-0.00346690 0.99981975 0.01866660 -75.87705675
-0.08961217 -0.01890223 0.99579735 -68.56101837
Axis -0.20502187 0.97833853 -0.02863122
Axis point -828.87063691 0.00000000 978.95595835
Rotation angle (degrees) 5.25689876
Shift along axis -55.94144291
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0905
rotated from previous position = 0.143 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0183
rotated from previous position = 0.0546 degrees
atoms outside contour = 716, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 60
shifted from previous position = 0.0197
rotated from previous position = 0.0756 degrees
atoms outside contour = 716, contour level = 0.0064458
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 40
shifted from previous position = 0.051
rotated from previous position = 0.123 degrees
atoms outside contour = 2667, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99580165 0.00255344 0.09150166 -80.01967767
-0.00420302 0.99983203 0.01783972 -75.76301892
-0.09144073 -0.01814941 0.99564511 -68.54407390
Axis -0.19289763 0.98055039 -0.03621386
Axis point -817.44879003 0.00000000 955.84816463
Rotation angle (degrees) 5.35265165
Shift along axis -56.37160562
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 48
shifted from previous position = 0.0962
rotated from previous position = 0.132 degrees
atoms outside contour = 716, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 48
shifted from previous position = 0.0434
rotated from previous position = 0.0993 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.0133
rotated from previous position = 0.0949 degrees
atoms outside contour = 716, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.0188
rotated from previous position = 0.0254 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.0112
rotated from previous position = 0.0716 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 48
shifted from previous position = 0.0402
rotated from previous position = 0.0381 degrees
atoms outside contour = 714, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 48
shifted from previous position = 0.0399
rotated from previous position = 0.0162 degrees
atoms outside contour = 716, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.00454
rotated from previous position = 0.0271 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.000868
rotated from previous position = 0.00269 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 44
shifted from previous position = 0.00921
rotated from previous position = 0.0187 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.0172
rotated from previous position = 0.0878 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 36
shifted from previous position = 0.0299
rotated from previous position = 0.127 degrees
atoms outside contour = 2669, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99565516 0.00325095 0.09306036 -80.33588472
-0.00479502 0.99985445 0.01637330 -75.49861006
-0.09299359 -0.01674838 0.99552583 -68.61163257
Axis -0.17510766 0.98362995 -0.04253743
Axis point -808.91233658 0.00000000 933.27466357
Rotation angle (degrees) 5.42686925
Shift along axis -57.27670241
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 80
shifted from previous position = 0.00424
rotated from previous position = 0.0159 degrees
atoms outside contour = 2672, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99566955 0.00313415 0.09291031 -80.29974154
-0.00469500 0.99985142 0.01658570 -75.53846381
-0.09284452 -0.01695009 0.99553633 -68.59515076
Axis -0.17751313 0.98324548 -0.04144162
Axis point -809.32794560 0.00000000 935.78918938
Rotation angle (degrees) 5.42024293
Shift along axis -57.17590105
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 48
shifted from previous position = 0.0308
rotated from previous position = 0.0142 degrees
atoms outside contour = 2667, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99566015 0.00300970 0.09301513 -80.31036379
-0.00459013 0.99984864 0.01678183 -75.59942351
-0.09295054 -0.01713595 0.99552326 -68.56232670
Axis -0.17928253 0.98297714 -0.04017118
Axis point -807.40100433 0.00000000 935.91398650
Rotation angle (degrees) 5.42789937
Shift along axis -57.16003031
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 48
shifted from previous position = 0.0898
rotated from previous position = 0.141 degrees
atoms outside contour = 715, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 40
shifted from previous position = 0.0154
rotated from previous position = 0.0487 degrees
atoms outside contour = 718, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1674 atoms
average map value = 0.01022, steps = 52
shifted from previous position = 0.0362
rotated from previous position = 0.0578 degrees
atoms outside contour = 715, contour level = 0.0064458
> select add #27.1
6538 atoms, 6591 bonds, 911 residues, 1 model selected
> select subtract #27.1
Nothing selected
> show #27.2 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 44
shifted from previous position = 0.0121
rotated from previous position = 0.0235 degrees
atoms outside contour = 654, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98950284 0.01456273 -0.14377777 -45.78107200
0.02414939 0.96425692 0.26386627 -113.43225746
0.14248133 -0.26456857 0.95378328 -31.21802132
Axis -0.87916370 -0.47625287 0.01594945
Axis point 0.00000000 -165.26762153 238.24622898
Rotation angle (degrees) 17.48959966
Shift along axis 93.77358484
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 48
shifted from previous position = 0.00735
rotated from previous position = 0.0304 degrees
atoms outside contour = 655, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98957324 0.01436562 -0.14331239 -45.83372764
0.02419385 0.96429592 0.26371963 -113.40796082
0.14198405 -0.26443716 0.95389387 -31.25289470
Axis -0.87972357 -0.47520359 0.01637037
Axis point 0.00000000 -165.61758530 238.76706811
Rotation angle (degrees) 17.46861769
Shift along axis 93.70125911
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 48
shifted from previous position = 0.00376
rotated from previous position = 0.02 degrees
atoms outside contour = 654, contour level = 0.0064458
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98958048 0.01458074 -0.14324060 -45.88233885
0.02400733 0.96422242 0.26400525 -113.44903982
0.14196519 -0.26469327 0.95382564 -31.20027553
Axis -0.87999979 -0.47471486 0.01569022
Axis point 0.00000000 -165.08561338 238.78900449
Rotation angle (degrees) 17.48144690
Shift along axis 93.74285376
> hide #!29 models
> show #!29 models
> fitmap #29 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2069 atoms
average map value = 0.01228, steps = 28
shifted from previous position = 0.0214
rotated from previous position = 0.0489 degrees
atoms outside contour = 765, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55837192 -0.72641866 0.40067033 245.13415111
-0.44707968 -0.14334516 -0.88293370 214.36498407
0.69881367 -0.67213695 -0.24472711 213.96241331
Axis 0.45851933 -0.64851326 0.60761054
Axis point 184.77340267 0.00000000 225.16272815
Rotation angle (degrees) 166.71076992
Shift along axis 103.38602932
> fitmap #29 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2069 atoms
average map value = 0.01228, steps = 40
shifted from previous position = 0.0234
rotated from previous position = 0.0463 degrees
atoms outside contour = 766, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#29) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55871778 -0.72640821 0.40020688 245.13655175
-0.44637102 -0.14331619 -0.88329687 214.34807082
0.69899023 -0.67215443 -0.24417427 213.95068338
Axis 0.45827663 -0.64849787 0.60781003
Axis point 184.70215567 0.00000000 225.22715233
Rotation angle (degrees) 166.68139627
Shift along axis 103.37745705
> hide #!29 models
> show #!29 models
> hide #28 models
> show #28 models
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007773, steps = 48
shifted from previous position = 0.0338
rotated from previous position = 0.0799 degrees
atoms outside contour = 478, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56964807 -0.71670905 0.40228001 245.63471109
-0.48593724 -0.10104432 -0.86813307 216.22928932
0.66284694 -0.69001317 -0.29071592 214.86544464
Axis 0.45555491 -0.66641932 0.59021607
Axis point 184.94701523 0.00000000 218.18285260
Rotation angle (degrees) 168.72619893
Shift along axis 94.61776347
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v22.cxs"
> show #!30 models
> show #31.1 models
> fitmap #31.1 inMap #34
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.01025, steps = 28
shifted from previous position = 0.0462
rotated from previous position = 0.156 degrees
atoms outside contour = 434, contour level = 0.0064458
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97526237 0.22047467 -0.01594455 223.15731989
-0.22022010 0.97531421 0.01628817 253.45061674
0.01914207 -0.01237393 0.99974020 253.90603445
Axis -0.06469745 -0.07919918 -0.99475712
Axis point 1137.36188509 -800.30950272 0.00000000
Rotation angle (degrees) 12.79766331
Shift along axis -287.08562568
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> color #31 #fffb00ff models
> combine 31
Expected a keyword
> combine #31
> ui tool show Matchmaker
> matchmaker #39 to #28
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C, chain C (#28)
with copy of 5mc7_human_zeta1COPI.cif A, chain A (#39), sequence alignment
score = 650.6
RMSD between 129 pruned atom pairs is 0.558 angstroms; (across all 135 pairs:
1.041)
> matchmaker #39 to #28
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C, chain C (#28)
with copy of 5mc7_human_zeta1COPI.cif A, chain A (#39), sequence alignment
score = 650.6
RMSD between 129 pruned atom pairs is 0.558 angstroms; (across all 135 pairs:
1.041)
> fitmap #39 inMap #34
Fit molecule copy of 5mc7_human_zeta1COPI.cif A (#39) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.007568, steps = 64
shifted from previous position = 0.552
rotated from previous position = 4.03 degrees
atoms outside contour = 536, contour level = 0.0064458
Position of copy of 5mc7_human_zeta1COPI.cif A (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.45323339 -0.88826503 -0.07459701 293.41129101
0.73450969 0.41957092 -0.53334393 178.67488835
0.50504950 0.18693706 0.84260283 234.70272149
Axis 0.38565745 -0.31035804 0.86887641
Axis point -122.80676595 292.32051362 0.00000000
Rotation angle (degrees) 69.04076862
Shift along axis 261.63072132
> fitmap #39 inMap #34
Fit molecule copy of 5mc7_human_zeta1COPI.cif A (#39) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.007567, steps = 56
shifted from previous position = 0.0231
rotated from previous position = 0.0788 degrees
atoms outside contour = 535, contour level = 0.0064458
Position of copy of 5mc7_human_zeta1COPI.cif A (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.45367818 -0.88801865 -0.07482627 293.40168039
0.73362359 0.41982599 -0.53436182 178.70125616
0.50593728 0.18753399 0.84193732 234.67904282
Axis 0.38652479 -0.31095832 0.86827617
Axis point -123.26089371 292.36450112 0.00000000
Rotation angle (degrees) 69.03971476
Shift along axis 261.60460100
> fitmap #39 inMap #34
Fit molecule copy of 5mc7_human_zeta1COPI.cif A (#39) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.007567, steps = 28
shifted from previous position = 0.0272
rotated from previous position = 0.0732 degrees
atoms outside contour = 534, contour level = 0.0064458
Position of copy of 5mc7_human_zeta1COPI.cif A (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.45363623 -0.88804369 -0.07478346 293.38456518
0.73300647 0.41952936 -0.53544058 178.74461709
0.50686849 0.18807849 0.84125549 234.67417154
Axis 0.38731294 -0.31136889 0.86777768
Axis point -123.53315687 292.27092947 0.00000000
Rotation angle (degrees) 69.07101563
Shift along axis 261.62113379
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #39 models
> show #39 models
> fitmap #39 inMap #34
Fit molecule copy of 5mc7_human_zeta1COPI.cif A (#39) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.007568, steps = 44
shifted from previous position = 0.0439
rotated from previous position = 0.146 degrees
atoms outside contour = 536, contour level = 0.0064458
Position of copy of 5mc7_human_zeta1COPI.cif A (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.45344620 -0.88815635 -0.07459780 293.40980917
0.73441853 0.41975085 -0.53332789 178.66982431
0.50499105 0.18704950 0.84261291 234.69988042
Axis 0.38574095 -0.31035281 0.86884121
Axis point -122.87799694 292.33760915 0.00000000
Rotation angle (degrees) 69.02841056
Shift along axis 261.64642428
> hide #!31 models
> show #!31 models
> fitmap #31.1 inMap #34
Fit molecule 5mc7_human_zeta1COPI.cif A (#31.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1187 atoms
average map value = 0.01025, steps = 28
shifted from previous position = 0.0354
rotated from previous position = 0.114 degrees
atoms outside contour = 436, contour level = 0.0064458
Position of 5mc7_human_zeta1COPI.cif A (#31.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97523104 0.22046140 -0.01792165 223.17984380
-0.22018019 0.97532115 0.01641132 253.47497719
0.02109743 -0.01205883 0.99970470 253.85976196
Axis -0.06422597 -0.08802336 -0.99404573
Axis point 1125.53912289 -801.68454544 0.00000000
Rotation angle (degrees) 12.80540595
Shift along axis -288.99387215
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007771, steps = 64
shifted from previous position = 0.0341
rotated from previous position = 0.0862 degrees
atoms outside contour = 477, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.57010387 -0.71670663 0.40163810 245.69177739
-0.48464318 -0.10137131 -0.86881807 216.19575528
0.66340226 -0.68996771 -0.28955481 214.80984392
Axis 0.45521912 -0.66625559 0.59065984
Axis point 184.87677858 0.00000000 218.31793898
Rotation angle (degrees) 168.67089507
Shift along axis 94.68151187
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007772, steps = 44
shifted from previous position = 0.0293
rotated from previous position = 0.0689 degrees
atoms outside contour = 478, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56992216 -0.71677245 0.40177850 245.65582773
-0.48554024 -0.10070443 -0.86839466 216.24734258
0.66290225 -0.68999700 -0.29062818 214.85494562
Axis 0.45536928 -0.66653189 0.59023221
Axis point 184.89711462 0.00000000 218.20500299
Rotation angle (degrees) 168.70372386
Shift along axis 94.54267400
> fitmap #26.3 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.01093, steps = 48
shifted from previous position = 0.0209
rotated from previous position = 0.0503 degrees
atoms outside contour = 359, contour level = 0.0064458
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.25085728 0.19318279 -0.94855207 329.71382244
0.71030721 0.70246559 -0.04478560 309.43561010
0.65767339 -0.68499817 -0.31343773 214.51778716
Axis -0.35473060 -0.88998146 0.28652960
Axis point -6.40508156 0.00000000 232.30177959
Rotation angle (degrees) 115.52562396
Shift along axis -330.88583868
> fitmap #26.3 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.01093, steps = 60
shifted from previous position = 0.00782
rotated from previous position = 0.0168 degrees
atoms outside contour = 359, contour level = 0.0064458
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.25085273 0.19345219 -0.94849836 329.72015556
0.71028680 0.70249976 -0.04457284 309.42731387
0.65769717 -0.68488709 -0.31363052 214.53068781
Axis -0.35480140 -0.89000116 0.28638070
Axis point -6.39085838 0.00000000 232.25846266
Rotation angle (degrees) 115.53051522
Shift along axis -330.93839267
> hide #26.3 models
> show #26.3 models
> hide #!31 models
> hide #39 models
> hide #!30 models
> show #!30 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v23.cxs"
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> fitmap #1 inMap #34
Fit map postprocess_20231221.mrc in map relion_locres_filtered_20240326_GT.mrc
using 18952 points
correlation = 0.8013, correlation about mean = 0.3883, overlap = 1.793
steps = 48, shift = 0.0672, angle = 0.0779 degrees
Position of postprocess_20231221.mrc (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99987401 0.01319926 -0.00881724 48.68415658
-0.01316607 0.99990606 0.00381232 37.99834917
0.00886674 -0.00369575 0.99995386 34.88480185
Axis -0.23015011 -0.54207991 -0.80819571
Axis point 434.69758186 -2638.11488500 0.00000000
Rotation angle (degrees) 0.93460613
Shift along axis -59.99655265
> fitmap #2 inMap #34
Fit map emdb 3720 in map relion_locres_filtered_20240326_GT.mrc using 38639
points
correlation = 0.729, correlation about mean = 0.1842, overlap = 101.9
steps = 84, shift = 2.04, angle = 1.26 degrees
Position of emdb 3720 (#2) relative to relion_locres_filtered_20240326_GT.mrc
(#34) coordinates:
Matrix rotation and translation
-0.53788299 0.84160172 -0.04887165 217.95859619
-0.84291583 -0.53782153 0.01552156 404.43379129
-0.01322125 0.04954347 0.99868446 144.98895511
Axis 0.02018819 -0.02115452 -0.99957237
Axis point 220.37802412 140.14623835 0.00000000
Rotation angle (degrees) 122.58226757
Shift along axis -149.08236462
> show #3 models
> hide #!30 models
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 9810 atoms
average map value = 0.005549, steps = 104
shifted from previous position = 0.0315
rotated from previous position = 0.02 degrees
atoms outside contour = 6054, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90931116 0.39282847 0.13725523 209.68522691
-0.21900068 0.73225360 -0.64485917 282.21469801
-0.35382468 0.55631866 0.75187607 275.94393018
Axis 0.83724120 0.34229097 -0.42645523
Axis point 0.00000000 -384.59576759 515.32504904
Rotation angle (degrees) 45.83552825
Shift along axis 154.47892206
> hide #!34 models
> hide #27.1 models
> hide #27.2 models
> show #!34 models
> ui mousemode right select
Drag select of 132 residues
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v24.cxs"
> delete sel
Drag select of 19 residues, 2 pseudobonds
> select up
231 atoms, 234 bonds, 2 pseudobonds, 31 residues, 2 models selected
> select up
456 atoms, 465 bonds, 2 pseudobonds, 59 residues, 2 models selected
> select up
8735 atoms, 8933 bonds, 2 pseudobonds, 1101 residues, 2 models selected
> select down
456 atoms, 465 bonds, 2 pseudobonds, 59 residues, 2 models selected
> delete sel
Drag select of 56 residues, 2 pseudobonds
> delete sel
Drag select of 40 residues, 3 pseudobonds
> select up
1059 atoms, 1079 bonds, 3 pseudobonds, 142 residues, 2 models selected
> delete sel
Drag select of 4 residues, 1 pseudobonds
> select up
67 atoms, 69 bonds, 1 pseudobond, 8 residues, 2 models selected
> select up
84 atoms, 86 bonds, 1 pseudobond, 11 residues, 2 models selected
> delete sel
> select clear
Drag select of 1 pseudobonds, 34 relion_locres_filtered_20240326_GT.mrc
> select clear
[Repeated 1 time(s)]
> hide #!34 models
> hide #!35 models
> hide #!36 models
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008462, steps = 48
shifted from previous position = 0.0933
rotated from previous position = 0.112 degrees
atoms outside contour = 2966, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90891413 0.39398824 0.13655898 209.66442425
-0.22074322 0.73246747 -0.64402160 282.24312646
-0.35376194 0.55521587 0.75272027 276.03816129
Axis 0.83626314 0.34191503 -0.42867011
Axis point 0.00000000 -385.48459251 516.88628298
Rotation angle (degrees) 45.80912282
Shift along axis 153.50848796
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008462, steps = 40
shifted from previous position = 0.0321
rotated from previous position = 0.0123 degrees
atoms outside contour = 2960, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90889368 0.39409870 0.13637625 209.68451466
-0.22093480 0.73239839 -0.64403447 282.25152854
-0.35369490 0.55522860 0.75274239 276.05973913
Axis 0.83624278 0.34172524 -0.42886114
Axis point 0.00000000 -385.45306501 517.01562421
Rotation angle (degrees) 45.81181650
Shift along axis 153.40833872
Drag select of 233 residues, 1 pseudobonds
Drag select of 231 residues, 1 pseudobonds
> show #!34 models
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008823, steps = 80
shifted from previous position = 0.687
rotated from previous position = 3.7 degrees
atoms outside contour = 847, contour level = 0.0064458
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008573, steps = 60
shifted from previous position = 0.356
rotated from previous position = 0.186 degrees
atoms outside contour = 2928, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90782578 0.39663908 0.13612418 209.93249872
-0.22358555 0.73244000 -0.64307164 282.47841584
-0.35477013 0.55336161 0.75361068 275.87777154
Axis 0.83418023 0.34226258 -0.43243459
Axis point 0.00000000 -386.65044437 518.96879030
Rotation angle (degrees) 45.81812855
Shift along axis 152.50423879
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008825, steps = 60
shifted from previous position = 0.412
rotated from previous position = 0.174 degrees
atoms outside contour = 848, contour level = 0.0064458
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.00859, steps = 40
shifted from previous position = 0.164
rotated from previous position = 0.148 degrees
atoms outside contour = 2935, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90741514 0.39774698 0.13562849 210.01402558
-0.22549080 0.73319380 -0.64154558 282.65440494
-0.35461479 0.55156520 0.75499945 275.86129278
Axis 0.83284228 0.34221075 -0.43504659
Axis point 0.00000000 -388.23814513 521.16574384
Rotation angle (degrees) 45.74890070
Shift along axis 151.62342015
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008822, steps = 48
shifted from previous position = 0.235
rotated from previous position = 0.144 degrees
atoms outside contour = 846, contour level = 0.0064458
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008594, steps = 44
shifted from previous position = 0.0769
rotated from previous position = 0.124 degrees
atoms outside contour = 2940, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90696334 0.39875882 0.13567938 210.04607668
-0.22688465 0.73389108 -0.64025559 282.75835838
-0.35488145 0.54990477 0.75608457 275.85910636
Axis 0.83153588 0.34274283 -0.43712177
Axis point 0.00000000 -389.77558330 522.80729754
Rotation angle (degrees) 45.69565954
Shift along axis 150.99022935
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008823, steps = 48
shifted from previous position = 0.177
rotated from previous position = 0.129 degrees
atoms outside contour = 846, contour level = 0.0064458
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008597, steps = 44
shifted from previous position = 0.0361
rotated from previous position = 0.0972 degrees
atoms outside contour = 2946, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90682211 0.39903561 0.13580955 210.04444692
-0.22761279 0.73474399 -0.63901774 282.82199351
-0.35477609 0.54856343 0.75710770 275.87776428
Axis 0.83071778 0.34316661 -0.43834306
Axis point 0.00000000 -391.20321850 524.09410081
Rotation angle (degrees) 45.62617198
Shift along axis 150.61361762
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008824, steps = 44
shifted from previous position = 0.123
rotated from previous position = 0.131 degrees
atoms outside contour = 849, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008824, steps = 80
shifted from previous position = 0.00593
rotated from previous position = 0.042 degrees
atoms outside contour = 847, contour level = 0.0064458
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008598, steps = 48
shifted from previous position = 0.0603
rotated from previous position = 0.0823 degrees
atoms outside contour = 2941, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90688108 0.39906542 0.13532731 210.04151195
-0.22837904 0.73535901 -0.63803615 282.90230477
-0.35413232 0.54771699 0.75802136 275.90663773
Axis 0.83034228 0.34275181 -0.43937785
Axis point 0.00000000 -392.08196933 525.36366842
Rotation angle (degrees) 45.56250642
Shift along axis 150.14435832
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008598, steps = 44
shifted from previous position = 0.0329
rotated from previous position = 0.0136 degrees
atoms outside contour = 2938, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90688255 0.39899299 0.13553090 210.02036491
-0.22817718 0.73537741 -0.63808716 282.88222730
-0.35425867 0.54774505 0.75794204 275.89424066
Axis 0.83036376 0.34296885 -0.43916785
Axis point 0.00000000 -392.07575462 525.16889116
Rotation angle (degrees) 45.56489160
Shift along axis 150.24921009
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008823, steps = 48
shifted from previous position = 0.0934
rotated from previous position = 0.119 degrees
atoms outside contour = 848, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008822, steps = 56
shifted from previous position = 0.0149
rotated from previous position = 0.0989 degrees
atoms outside contour = 847, contour level = 0.0064458
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008599, steps = 40
shifted from previous position = 0.0254
rotated from previous position = 0.0438 degrees
atoms outside contour = 2940, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90676753 0.39927286 0.13547625 210.02601110
-0.22866700 0.73565368 -0.63759317 282.91435028
-0.35423725 0.54716983 0.75836740 275.91029921
Axis 0.82994946 0.34305381 -0.43988405
Axis point 0.00000000 -392.63867419 525.80518864
Rotation angle (degrees) 45.54135137
Shift along axis 149.99727922
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008599, steps = 44
shifted from previous position = 0.00445
rotated from previous position = 0.00461 degrees
atoms outside contour = 2938, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90673879 0.39932278 0.13552148 210.02748872
-0.22869189 0.73566610 -0.63756992 282.91049144
-0.35429475 0.54711671 0.75837887 275.91053727
Axis 0.82989319 0.34312462 -0.43993499
Axis point 0.00000000 -392.69123605 525.81905039
Rotation angle (degrees) 45.54154641
Shift along axis 149.99123777
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008821, steps = 48
shifted from previous position = 0.0616
rotated from previous position = 0.0475 degrees
atoms outside contour = 848, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008823, steps = 44
shifted from previous position = 0.0268
rotated from previous position = 0.0406 degrees
atoms outside contour = 847, contour level = 0.0064458
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008599, steps = 40
shifted from previous position = 0.034
rotated from previous position = 0.0427 degrees
atoms outside contour = 2943, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90665202 0.39949242 0.13560201 210.04475273
-0.22902990 0.73601982 -0.63704012 282.95219416
-0.35429846 0.54651680 0.75880957 275.92432789
Axis 0.82949980 0.34334837 -0.44050196
Axis point 0.00000000 -393.33709858 526.40128539
Rotation angle (degrees) 45.51353794
Shift along axis 149.83804876
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008823, steps = 48
shifted from previous position = 0.0706
rotated from previous position = 0.0499 degrees
atoms outside contour = 846, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008824, steps = 60
shifted from previous position = 0.0283
rotated from previous position = 0.0283 degrees
atoms outside contour = 849, contour level = 0.0064458
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.0086, steps = 44
shifted from previous position = 0.0265
rotated from previous position = 0.0385 degrees
atoms outside contour = 2936, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90667083 0.39942373 0.13567862 210.02682489
-0.22917090 0.73642362 -0.63652254 282.97962825
-0.35415915 0.54602283 0.75923010 275.91354666
Axis 0.82927246 0.34350392 -0.44080863
Axis point 0.00000000 -393.88759641 526.86229212
Rotation angle (degrees) 45.47967159
Shift along axis 149.74899838
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008822, steps = 48
shifted from previous position = 0.0331
rotated from previous position = 0.0295 degrees
atoms outside contour = 843, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1842 atoms
average map value = 0.008824, steps = 48
shifted from previous position = 0.0413
rotated from previous position = 0.0398 degrees
atoms outside contour = 847, contour level = 0.0064458
> hide #!3 models
> show #!3 models
> show #7 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7214 atoms
average map value = 0.008398, steps = 44
shifted from previous position = 0.0137
rotated from previous position = 0.0314 degrees
atoms outside contour = 3252, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13434959 -0.22741189 -0.96448640 237.13674547
-0.00067690 -0.97328915 0.22958174 213.64254218
-0.99093376 0.03149708 0.13060707 275.37371608
Axis -0.65540036 0.08750608 0.75019535
Axis point 228.34566768 105.09095173 0.00000000
Rotation angle (degrees) 171.30831886
Shift along axis 69.85959355
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7214 atoms
average map value = 0.008399, steps = 40
shifted from previous position = 0.00753
rotated from previous position = 0.021 degrees
atoms outside contour = 3254, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13415323 -0.22756384 -0.96447789 237.13727833
-0.00038925 -0.97326354 0.22969092 213.64331424
-0.99096052 0.03118920 0.13047787 275.38173050
Axis -0.65546554 0.08744736 0.75014524
Axis point 228.34699349 105.12967021 0.00000000
Rotation angle (degrees) 171.29074998
Shift along axis 69.82352552
> hide #!3 models
> select add #3
6692 atoms, 6847 bonds, 1 pseudobond, 833 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!3 models
> hide #!34 models
> hide #!3 models
Drag select of 14 residues
> select up
519 atoms, 525 bonds, 67 residues, 1 model selected
> show #!34 models
> hide #!34 models
> delete sel
> show #!34 models
> hide #!34 models
> show #27.1 models
> hide #27.1 models
> hide #7 models
> show #!34 models
> show #4 models
> hide #!34 models
> hide #24 models
> hide #26.3 models
> show #26.3 models
> color #26.3 #fffb00ff
> color #28 #fffb00ff
> hide #28 models
> hide #26.3 models
> hide #!26.2 models
> hide #!26.1 models
> hide #!29 models
> hide #!37 models
> hide #38 models
> show #!34 models
> hide #!34 models
Drag select of 24 residues
> select up
290 atoms, 293 bonds, 39 residues, 1 model selected
> delete sel
> show #!34 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.123
rotated from previous position = 0.437 degrees
atoms outside contour = 2761, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13064107 -0.23172439 -0.96396925 237.19381792
0.00542688 -0.97245471 0.23302870 213.64056466
-0.99141488 0.02521178 0.12830006 275.50575861
Axis -0.65657806 0.08671188 0.74925716
Axis point 228.27663105 105.89736307 0.00000000
Rotation angle (degrees) 170.89422511
Shift along axis 69.21358119
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009016, steps = 44
shifted from previous position = 0.0356
rotated from previous position = 0.0263 degrees
atoms outside contour = 2757, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13091454 -0.23172608 -0.96393174 237.20189942
0.00506406 -0.97244331 0.23308446 213.62990233
-0.99138072 0.02563274 0.12848044 275.47151700
Axis -0.65648217 0.08686245 0.74932374
Axis point 228.25761396 105.84342594 0.00000000
Rotation angle (degrees) 170.90902340
Shift along axis 69.25494684
> hide #!34 models
Drag select of 150 residues
> select up
1453 atoms, 1469 bonds, 190 residues, 1 model selected
> select up
3240 atoms, 3289 bonds, 418 residues, 1 model selected
> show #!34 models
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 64
shifted from previous position = 5.22
rotated from previous position = 5.34 degrees
atoms outside contour = 1418, contour level = 0.0064458
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009016, steps = 44
shifted from previous position = 0.0137
rotated from previous position = 0.0449 degrees
atoms outside contour = 2763, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13036235 -0.23227560 -0.96387432 237.21373396
0.00520236 -0.97231728 0.23360658 213.62030736
-0.99145277 0.02543909 0.12796194 275.47829542
Axis -0.65667635 0.08699781 0.74913787
Axis point 228.29490270 105.85984525 -0.00000000
Rotation angle (degrees) 170.88011010
Shift along axis 69.18307299
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009016, steps = 44
shifted from previous position = 0.00151
rotated from previous position = 0.00331 degrees
atoms outside contour = 2764, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13036477 -0.23227317 -0.96387457 237.21452052
0.00514485 -0.97231638 0.23361162 213.62130287
-0.99145275 0.02549573 0.12795081 275.47904292
Axis -0.65667680 0.08701857 0.74913507
Axis point 228.29894049 105.85286174 0.00000000
Rotation angle (degrees) 170.88239700
Shift along axis 69.18675920
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.008817, steps = 68
shifted from previous position = 1.01
rotated from previous position = 1.21 degrees
atoms outside contour = 3254, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.01860980 -0.70776039 0.70620741 220.19799781
-0.05500565 0.70598475 0.70608775 242.11894872
-0.99831260 -0.02570525 -0.05206905 272.56837572
Axis -0.37213564 0.86679245 0.33194264
Axis point 258.04675243 0.00000000 -54.69162162
Rotation angle (degrees) 100.50649879
Shift along axis 218.40042051
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 64
shifted from previous position = 1.1
rotated from previous position = 1.22 degrees
atoms outside contour = 1420, contour level = 0.0064458
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.008962, steps = 64
shifted from previous position = 0.523
rotated from previous position = 0.82 degrees
atoms outside contour = 3212, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02017469 -0.71402417 0.69983032 220.34435012
-0.04411501 0.69992680 0.71285086 241.61952198
-0.99882273 -0.01649148 -0.04561999 272.54737727
Axis -0.37093054 0.86390474 0.34070388
Axis point 257.10995134 0.00000000 -56.58617768
Rotation angle (degrees) 100.54070073
Shift along axis 219.86175039
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 60
shifted from previous position = 0.653
rotated from previous position = 0.827 degrees
atoms outside contour = 1418, contour level = 0.0064458
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.00902, steps = 84
shifted from previous position = 0.269
rotated from previous position = 0.578 degrees
atoms outside contour = 3184, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02126238 -0.71809220 0.69562310 220.37093889
-0.03610653 0.69587804 0.71725175 241.37668426
-0.99912173 -0.00986606 -0.04072384 272.58927506
Axis -0.36980760 0.86193669 0.34685368
Axis point 256.39793623 0.00000000 -57.91605031
Rotation angle (degrees) 100.54770288
Shift along axis 221.10516606
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 48
shifted from previous position = 0.379
rotated from previous position = 0.571 degrees
atoms outside contour = 1418, contour level = 0.0064458
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.009047, steps = 48
shifted from previous position = 0.169
rotated from previous position = 0.374 degrees
atoms outside contour = 3180, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02148076 -0.72058910 0.69302952 220.35457835
-0.03075639 0.69333767 0.71995619 241.26508197
-0.99929606 -0.00584988 -0.03705614 272.66881653
Axis -0.36910873 0.86063230 0.35081447
Axis point 256.00416174 0.00000000 -58.84211617
Rotation angle (degrees) 100.52121690
Shift along axis 221.96189033
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 48
shifted from previous position = 0.294
rotated from previous position = 0.378 degrees
atoms outside contour = 1420, contour level = 0.0064458
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.009066, steps = 44
shifted from previous position = 0.136
rotated from previous position = 0.344 degrees
atoms outside contour = 3188, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02175555 -0.72294654 0.69056136 220.33099503
-0.02590185 0.69090057 0.72248564 241.19819905
-0.99942773 -0.00216875 -0.03375658 272.74170203
Axis -0.36850260 0.85939641 0.35446247
Axis point 255.63636665 0.00000000 -59.69647871
Rotation angle (degrees) 100.50409379
Shift along axis 222.76901806
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 40
shifted from previous position = 0.269
rotated from previous position = 0.307 degrees
atoms outside contour = 1416, contour level = 0.0064458
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.00908, steps = 60
shifted from previous position = 0.144
rotated from previous position = 0.294 degrees
atoms outside contour = 3179, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02187099 -0.72521931 0.68817048 220.26525308
-0.02205057 0.68851761 0.72488432 241.14683477
-0.99951760 0.00067939 -0.03105006 272.81387189
Axis -0.36826682 0.85820946 0.35756967
Axis point 255.36293942 0.00000000 -60.42643654
Rotation angle (degrees) 100.49803006
Shift along axis 223.38807679
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 48
shifted from previous position = 0.213
rotated from previous position = 0.325 degrees
atoms outside contour = 1419, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 48
shifted from previous position = 0.00776
rotated from previous position = 0.0241 degrees
atoms outside contour = 1418, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 36
shifted from previous position = 0.0144
rotated from previous position = 0.0481 degrees
atoms outside contour = 1420, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 40
shifted from previous position = 0.031
rotated from previous position = 0.0424 degrees
atoms outside contour = 1418, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 36
shifted from previous position = 0.0136
rotated from previous position = 0.0235 degrees
atoms outside contour = 1416, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 44
shifted from previous position = 0.00504
rotated from previous position = 0.0201 degrees
atoms outside contour = 1418, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008342, steps = 44
shifted from previous position = 0.00145
rotated from previous position = 0.0365 degrees
atoms outside contour = 1419, contour level = 0.0064458
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.009093, steps = 48
shifted from previous position = 0.0942
rotated from previous position = 0.3 degrees
atoms outside contour = 3174, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02202831 -0.72743960 0.68581804 220.24647955
-0.01800794 0.68616191 0.72722593 241.13299244
-0.99959515 0.00366939 -0.02821467 272.86847264
Axis -0.36792593 0.85702663 0.36074348
Axis point 255.08370612 0.00000000 -61.21252613
Rotation angle (degrees) 100.48863782
Shift along axis 224.05852775
> hide #!34 models
> select clear
Drag select of 84 residues
> select up
797 atoms, 808 bonds, 106 residues, 1 model selected
> select up
3240 atoms, 3289 bonds, 418 residues, 1 model selected
> select down
797 atoms, 808 bonds, 106 residues, 1 model selected
> show #!34 models
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 797 atoms
average map value = 0.009017, steps = 52
shifted from previous position = 1.7
rotated from previous position = 6.56 degrees
atoms outside contour = 268, contour level = 0.0064458
> undo
Drag select of 188 residues
> select up
1720 atoms, 1745 bonds, 223 residues, 1 model selected
Drag select of 151 residues
> select up
1513 atoms, 1531 bonds, 200 residues, 1 model selected
> select up
3240 atoms, 3289 bonds, 418 residues, 1 model selected
> select down
1513 atoms, 1531 bonds, 200 residues, 1 model selected
> select clear
[Repeated 1 time(s)]Drag select of 43 residues
Drag select of 158 residues
> select up
1538 atoms, 1557 bonds, 203 residues, 1 model selected
> select up
3240 atoms, 3289 bonds, 418 residues, 1 model selected
> show #!34 models
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 48
shifted from previous position = 0.256
rotated from previous position = 0.202 degrees
atoms outside contour = 1414, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008402, steps = 44
shifted from previous position = 0.0114
rotated from previous position = 0.0342 degrees
atoms outside contour = 1413, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 44
shifted from previous position = 0.0109
rotated from previous position = 0.0247 degrees
atoms outside contour = 1413, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 44
shifted from previous position = 0.00781
rotated from previous position = 0.0287 degrees
atoms outside contour = 1413, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 36
shifted from previous position = 0.012
rotated from previous position = 0.0293 degrees
atoms outside contour = 1414, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 44
shifted from previous position = 0.0216
rotated from previous position = 0.0315 degrees
atoms outside contour = 1413, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 40
shifted from previous position = 0.0304
rotated from previous position = 0.00825 degrees
atoms outside contour = 1412, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 36
shifted from previous position = 0.00821
rotated from previous position = 0.0239 degrees
atoms outside contour = 1415, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 44
shifted from previous position = 0.0135
rotated from previous position = 0.011 degrees
atoms outside contour = 1411, contour level = 0.0064458
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008402, steps = 48
shifted from previous position = 0.00431
rotated from previous position = 0.0168 degrees
atoms outside contour = 1412, contour level = 0.0064458
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.009128, steps = 60
shifted from previous position = 0.105
rotated from previous position = 0.212 degrees
atoms outside contour = 3174, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02205954 -0.72904320 0.68411211 220.19108610
-0.01519801 0.68444410 0.72890692 241.09722099
-0.99964113 0.00568221 -0.02617852 272.91548671
Axis -0.36774727 0.85615942 0.36297794
Axis point 254.88464436 0.00000000 -61.75159142
Rotation angle (degrees) 100.48027313
Shift along axis 224.50529001
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.009128, steps = 48
shifted from previous position = 0.0147
rotated from previous position = 0.00889 degrees
atoms outside contour = 3170, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02200949 -0.72909117 0.68406260 220.18947119
-0.01532928 0.68439402 0.72895119 241.11096923
-0.99964023 0.00555765 -0.02623960 272.92257115
Axis -0.36783523 0.85613871 0.36293767
Axis point 254.91117447 0.00000000 -61.75060152
Rotation angle (degrees) 100.48205346
Shift along axis 224.48487369
> fitmap sel inMap #34 moveWholeMolecules false
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3240 atoms
average map value = 0.008403, steps = 44
shifted from previous position = 0.14
rotated from previous position = 0.2 degrees
atoms outside contour = 1413, contour level = 0.0064458
> select add #4
7211 atoms, 7324 bonds, 1 pseudobond, 914 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!3 models
> hide #!4 models
> hide #!3 models
> color #35 #ff2f92ff
> color #36 #ff2f92ff
> color #37 #ff2f92ff
> color #26.1 #ff2f92ff
> color #6 #ff2f92ff
> color #5 #ff2f92ff
> show #5 models
> ui tool show Matchmaker
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> show #!35 models
> matchmaker #5 to #35
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#35)
with hArf1_P84078, chain A (#5), sequence alignment score = 714.3
RMSD between 159 pruned atom pairs is 0.735 angstroms; (across all 159 pairs:
0.735)
> hide #!34 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show #6 models
> hide #5 models
> hide #!35 models
> show #!36 models
> hide #!36 models
> show #!37 models
> matchmaker #6 to #37
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#37)
with hArf1_P84078, chain A (#6), sequence alignment score = 714.3
RMSD between 159 pruned atom pairs is 0.735 angstroms; (across all 159 pairs:
0.735)
> matchmaker #6 to #37
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#37)
with hArf1_P84078, chain A (#6), sequence alignment score = 714.3
RMSD between 159 pruned atom pairs is 0.735 angstroms; (across all 159 pairs:
0.735)
> hide #!37 models
> hide #6 models
> show #!34 models
> show #7 models
> show #!3 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009016, steps = 44
shifted from previous position = 0.0015
rotated from previous position = 0.00327 degrees
atoms outside contour = 2762, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13040565 -0.23223349 -0.96387861 237.21405953
0.00513980 -0.97232561 0.23357331 213.62080010
-0.99144740 0.02550513 0.12799038 275.47756577
Axis -0.65666229 0.08700700 0.74914913
Axis point 228.29565523 105.85174821 0.00000000
Rotation angle (degrees) 170.88430171
Shift along axis 69.19075642
> hide #7 models
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6692 atoms
average map value = 0.008601, steps = 64
shifted from previous position = 0.0381
rotated from previous position = 0.0442 degrees
atoms outside contour = 2941, contour level = 0.0064458
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90671494 0.39954081 0.13503758 210.03056431
-0.22975457 0.73645358 -0.63627741 283.01088612
-0.35366770 0.54589674 0.75954979 275.94131079
Axis 0.82923738 0.34280286 -0.44141994
Axis point 0.00000000 -393.93203557 527.48012669
Rotation angle (degrees) 45.46384793
Shift along axis 149.37613895
> show #!4 models
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.009133, steps = 48
shifted from previous position = 0.0607
rotated from previous position = 0.175 degrees
atoms outside contour = 3169, contour level = 0.0064458
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02227576 -0.73059739 0.68244505 220.16670275
-0.01329774 0.68277057 0.73051182 241.11428481
-0.99966342 0.00719773 -0.02492453 272.95439119
Axis -0.36781473 0.85537428 0.36475630
Axis point 254.75617977 0.00000000 -62.17248178
Rotation angle (degrees) 100.49879570
Shift along axis 224.82423663
> show #5 models
> fitmap #5 inMap #34
Fit molecule hArf1_P84078 (#5) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1457 atoms
average map value = 0.007776, steps = 60
shifted from previous position = 0.26
rotated from previous position = 2.79 degrees
atoms outside contour = 719, contour level = 0.0064458
Position of hArf1_P84078 (#5) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.04234882 -0.02818621 0.99870521 172.65196320
-0.66605054 -0.74587192 0.00719247 238.26541094
0.74470346 -0.66549275 -0.05036024 212.55715318
Axis -0.69984360 0.26425660 -0.66361690
Axis point 0.00000000 166.46411478 -28.78247041
Rotation angle (degrees) 151.27561153
Shift along axis -198.92268355
> fitmap #5 inMap #34
Fit molecule hArf1_P84078 (#5) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1457 atoms
average map value = 0.007776, steps = 28
shifted from previous position = 0.0319
rotated from previous position = 0.0581 degrees
atoms outside contour = 720, contour level = 0.0064458
Position of hArf1_P84078 (#5) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.04231572 -0.02779859 0.99871748 172.67209877
-0.66534100 -0.74650277 0.00741217 238.24370144
0.74533933 -0.66480135 -0.05008434 212.54957544
Axis -0.69986868 0.26380224 -0.66377120
Axis point 0.00000000 166.36050683 -28.75252991
Rotation angle (degrees) 151.29875184
Shift along axis -199.08285740
> fitmap #5 inMap #34
Fit molecule hArf1_P84078 (#5) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1457 atoms
average map value = 0.007776, steps = 60
shifted from previous position = 0.26
rotated from previous position = 2.79 degrees
atoms outside contour = 719, contour level = 0.0064458
Position of hArf1_P84078 (#5) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.04234882 -0.02818621 0.99870521 172.65196320
-0.66605054 -0.74587192 0.00719247 238.26541094
0.74470346 -0.66549275 -0.05036024 212.55715318
Axis -0.69984360 0.26425660 -0.66361690
Axis point 0.00000000 166.46411478 -28.78247041
Rotation angle (degrees) 151.27561153
Shift along axis -198.92268355
> fitmap #5 inMap #34
Fit molecule hArf1_P84078 (#5) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1457 atoms
average map value = 0.007776, steps = 28
shifted from previous position = 0.0319
rotated from previous position = 0.0581 degrees
atoms outside contour = 720, contour level = 0.0064458
Position of hArf1_P84078 (#5) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.04231572 -0.02779859 0.99871748 172.67209877
-0.66534100 -0.74650277 0.00741217 238.24370144
0.74533933 -0.66480135 -0.05008434 212.54957544
Axis -0.69986868 0.26380224 -0.66377120
Axis point 0.00000000 166.36050683 -28.75252991
Rotation angle (degrees) 151.29875184
Shift along axis -199.08285740
> show #6 models
> fitmap #6 inMap #34
Fit molecule hArf1_P84078 (#6) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1457 atoms
average map value = 0.01, steps = 100
shifted from previous position = 0.303
rotated from previous position = 1.54 degrees
atoms outside contour = 540, contour level = 0.0064458
Position of hArf1_P84078 (#6) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.84109618 -0.49489980 0.21824615 292.94251604
-0.49080235 0.52875420 -0.69248251 231.43485077
0.22731089 -0.68956013 -0.68763113 256.77208513
Axis 0.28186120 -0.87428563 0.39519476
Axis point 183.38607825 0.00000000 181.13455437
Rotation angle (degrees) 179.70297261
Shift along axis -18.29605358
> fitmap #6 inMap #34
Fit molecule hArf1_P84078 (#6) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1457 atoms
average map value = 0.01, steps = 80
shifted from previous position = 0.0386
rotated from previous position = 0.0913 degrees
atoms outside contour = 538, contour level = 0.0064458
Position of hArf1_P84078 (#6) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.84141080 -0.49438517 0.21819978 292.95934934
-0.49075063 0.52999741 -0.69156817 231.45975086
0.22625573 -0.68897462 -0.68856539 256.78575999
Axis 0.28158432 -0.87464124 0.39460484
Axis point 183.39036692 0.00000000 180.99833258
Rotation angle (degrees) 179.73613569
Shift along axis -18.62257981
> show #7 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009016, steps = 44
shifted from previous position = 0.00265
rotated from previous position = 0.00798 degrees
atoms outside contour = 2763, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13031496 -0.23233256 -0.96386700 237.21589951
0.00511772 -0.97230159 0.23367373 213.62118254
-0.99145944 0.02551838 0.12789446 275.47979758
Axis -0.65669499 0.08704949 0.74911553
Axis point 228.30445679 105.84953601 0.00000000
Rotation angle (degrees) 170.88090756
Shift along axis 69.18331757
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009016, steps = 44
shifted from previous position = 0.00284
rotated from previous position = 0.0074 degrees
atoms outside contour = 2763, contour level = 0.0064458
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13036407 -0.23226920 -0.96387562 237.21339088
0.00520941 -0.97231900 0.23359927 213.62056134
-0.99145250 0.02543173 0.12796545 275.47872550
Axis -0.65667569 0.08699275 0.74913904
Axis point 228.29457997 105.86087578 0.00000000
Rotation angle (degrees) 170.88009904
Shift along axis 69.18304210
> show #8 models
> fitmap #8 inMap #34
Fit molecule CopD_Q5XJY5 (#8) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1462 atoms
average map value = 0.00841, steps = 44
shifted from previous position = 0.0258
rotated from previous position = 0.05 degrees
atoms outside contour = 660, contour level = 0.0064458
Position of CopD_Q5XJY5 (#8) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.07187504 0.98845136 0.13340879 -99.02438741
-0.91249811 0.01116004 0.40892868 162.65716677
0.40271726 -0.15112703 0.90276211 446.03007255
Axis -0.28003492 -0.13465763 -0.95049869
Axis point -59.66632563 162.61379915 0.00000000
Rotation angle (degrees) 90.40688381
Shift along axis -418.12374426
> fitmap #8 inMap #34
Fit molecule CopD_Q5XJY5 (#8) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1462 atoms
average map value = 0.00841, steps = 28
shifted from previous position = 0.0355
rotated from previous position = 0.0218 degrees
atoms outside contour = 658, contour level = 0.0064458
Position of CopD_Q5XJY5 (#8) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.07190905 0.98846257 0.13330736 -99.02728885
-0.91234566 0.01117639 0.40926824 162.68327434
0.40305644 -0.15105248 0.90262321 446.01125269
Axis -0.28016751 -0.13487798 -0.95042838
Axis point -59.73213470 162.60448549 0.00000000
Rotation angle (degrees) 90.40942063
Shift along axis -418.09991335
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #!9 models
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 6673 atoms
average map value = 0.008518, steps = 64
shifted from previous position = 0.00285
rotated from previous position = 0.0196 degrees
atoms outside contour = 3982, contour level = 0.0064458
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49555644 -0.51974611 -0.69590788 274.32281607
0.53779322 -0.44554954 0.71572624 319.08590355
-0.68205737 -0.72893730 0.05872099 294.81320826
Axis -0.80688147 -0.00773586 0.59066272
Axis point 0.00000000 282.61737441 125.51701713
Rotation angle (degrees) 116.46404027
Shift along axis -49.67923130
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 6673 atoms
average map value = 0.008518, steps = 72
shifted from previous position = 0.00472
rotated from previous position = 0.00969 degrees
atoms outside contour = 3982, contour level = 0.0064458
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49566394 -0.51961782 -0.69592714 274.31645257
0.53778966 -0.44556712 0.71571797 319.08334850
-0.68198206 -0.72901801 0.05859354 294.81271148
Axis -0.80693035 -0.00778876 0.59059524
Axis point -0.00000000 282.60556031 125.50928482
Rotation angle (degrees) 116.46524179
Shift along axis -49.72455120
> hide #!3 models
> hide #!4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #!26 models
> show #!26 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> ui mousemode right select
Drag select of 269 residues
> delete sel
> show #!34 models
> hide #!34 models
> show #!34 models
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 4566 atoms
average map value = 0.01074, steps = 72
shifted from previous position = 0.088
rotated from previous position = 0.409 degrees
atoms outside contour = 1879, contour level = 0.0064458
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49877213 -0.51940452 -0.69386259 274.34520892
0.54040314 -0.43953081 0.71747969 318.91808372
-0.67763619 -0.73282440 0.06146211 295.11334535
Axis -0.80736612 -0.00903304 0.58998165
Axis point 0.00000000 283.40502950 124.75091335
Rotation angle (degrees) 116.08144233
Shift along axis -50.26636765
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 4566 atoms
average map value = 0.01074, steps = 80
shifted from previous position = 0.0217
rotated from previous position = 0.0237 degrees
atoms outside contour = 1876, contour level = 0.0064458
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49908084 -0.51918554 -0.69380450 274.36159020
0.54045197 -0.43935907 0.71754810 318.91686111
-0.67736990 -0.73308252 0.06131916 295.12113417
Axis -0.80747365 -0.00914810 0.58983270
Axis point 0.00000000 283.42170468 124.71591629
Rotation angle (degrees) 116.07067825
Shift along axis -50.38514135
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 4566 atoms
average map value = 0.01074, steps = 64
shifted from previous position = 0.00684
rotated from previous position = 0.00808 degrees
atoms outside contour = 1875, contour level = 0.0064458
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49918805 -0.51909470 -0.69379534 274.36109060
0.54044465 -0.43934093 0.71756472 318.91338605
-0.67729673 -0.73315772 0.06122821 295.12739301
Axis -0.80751720 -0.00918364 0.58977253
Axis point 0.00000000 283.41958236 124.70941560
Rotation angle (degrees) 116.06958092
Shift along axis -50.42205343
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 4566 atoms
average map value = 0.01074, steps = 48
shifted from previous position = 0.0412
rotated from previous position = 0.051 degrees
atoms outside contour = 1881, contour level = 0.0064458
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49863214 -0.51967868 -0.69375792 274.34854819
0.54019886 -0.43962462 0.71757604 318.94247182
-0.67790204 -0.73257372 0.06151887 295.09515181
Axis -0.80731916 -0.00882719 0.59004903
Axis point -0.00000000 283.42057484 124.75295238
Rotation angle (degrees) 116.08708973
Shift along axis -50.18160021
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 4566 atoms
average map value = 0.01074, steps = 96
shifted from previous position = 0.0339
rotated from previous position = 0.0287 degrees
atoms outside contour = 1876, contour level = 0.0064458
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49883627 -0.51937283 -0.69384020 274.36535094
0.54046357 -0.43942649 0.71749808 318.92212104
-0.67754077 -0.73290942 0.06150022 295.12061589
Axis -0.80737825 -0.00907318 0.58996444
Axis point 0.00000000 283.42436703 124.74290900
Rotation angle (degrees) 116.07485371
Shift along axis -50.29958216
> show #!3 models
> show #!4 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #10 models
> fitmap #10 inMap #34
Fit molecule CopZ1_P61924.pdb (#10) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1420 atoms
average map value = 0.009234, steps = 36
shifted from previous position = 0.0309
rotated from previous position = 0.0395 degrees
atoms outside contour = 626, contour level = 0.0064458
Position of CopZ1_P61924.pdb (#10) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.16405062 -0.94536304 -0.28173769 280.95095994
-0.37368258 0.20476526 -0.90467261 278.13157944
0.91293413 0.25369256 -0.31967383 253.90027754
Axis 0.65834598 -0.67898053 0.32490923
Axis point 175.04449780 0.00000000 294.13537343
Rotation angle (degrees) 118.38728427
Shift along axis 78.61155290
> show #26.3 models
> matchmaker #10 to #26.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C, chain C (#26.3) with
CopZ1_P61924.pdb, chain A (#10), sequence alignment score = 682.7
RMSD between 136 pruned atom pairs is 0.539 angstroms; (across all 140 pairs:
0.678)
> matchmaker #10 to #26.3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C, chain C (#26.3) with
CopZ1_P61924.pdb, chain A (#10), sequence alignment score = 682.7
RMSD between 136 pruned atom pairs is 0.539 angstroms; (across all 140 pairs:
0.678)
> show #11 models
> show #24 models
> matchmaker #11 to #24
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3kn1_Golph3_xtal.cif, chain A (#24) with Golph3_ Q9CRA5.pdb, chain
A (#11), sequence alignment score = 1235.4
RMSD between 224 pruned atom pairs is 0.677 angstroms; (across all 239 pairs:
1.230)
> matchmaker #11 to #24
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3kn1_Golph3_xtal.cif, chain A (#24) with Golph3_ Q9CRA5.pdb, chain
A (#11), sequence alignment score = 1235.4
RMSD between 224 pruned atom pairs is 0.677 angstroms; (across all 239 pairs:
1.230)
> show #28 models
> close #12
> combine #10
> matchmaker #12 to #28
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C, chain C (#28)
with copy of CopZ1_P61924.pdb, chain A (#12), sequence alignment score = 682.7
RMSD between 136 pruned atom pairs is 0.539 angstroms; (across all 140 pairs:
0.678)
> fitmap #12 inMap #34
Fit molecule copy of CopZ1_P61924.pdb (#12) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1420 atoms
average map value = 0.006745, steps = 64
shifted from previous position = 0.39
rotated from previous position = 4.83 degrees
atoms outside contour = 736, contour level = 0.0064458
Position of copy of CopZ1_P61924.pdb (#12) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.27949610 0.26259205 0.92354066 296.75539420
0.23510266 -0.95131032 0.19933746 181.82495698
0.93091819 0.16141282 -0.32762361 253.34470051
Axis -0.79981086 -0.15558823 -0.57973691
Axis point 0.00000000 62.15359640 18.24995244
Rotation angle (degrees) 178.64147557
Shift along axis -412.51128564
> fitmap #12 inMap #34
Fit molecule copy of CopZ1_P61924.pdb (#12) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1420 atoms
average map value = 0.006745, steps = 28
shifted from previous position = 0.0184
rotated from previous position = 0.0572 degrees
atoms outside contour = 738, contour level = 0.0064458
Position of copy of CopZ1_P61924.pdb (#12) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.27909472 0.26258099 0.92366519 296.74803660
0.23427529 -0.95144081 0.19968845 181.83677489
0.93124714 0.16065994 -0.32705834 253.33531105
Axis -0.79968349 -0.15535216 -0.57997588
Axis point 0.00000000 62.20182981 18.15991470
Rotation angle (degrees) 178.60170243
Shift along axis -412.48161185
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007773, steps = 48
shifted from previous position = 0.0142
rotated from previous position = 0.0418 degrees
atoms outside contour = 478, contour level = 0.0064458
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56968892 -0.71660451 0.40240837 245.63689092
-0.48577288 -0.10134922 -0.86818952 216.21258450
0.66293230 -0.69007702 -0.29036951 214.84991857
Axis 0.45553213 -0.66630374 0.59036413
Axis point 184.95393002 0.00000000 218.20954457
Rotation angle (degrees) 168.72610284
Shift along axis 94.67192673
> matchmaker #12 to #28
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C, chain C (#28)
with copy of CopZ1_P61924.pdb, chain A (#12), sequence alignment score = 682.7
RMSD between 136 pruned atom pairs is 0.539 angstroms; (across all 140 pairs:
0.678)
> hide #12 models
> hide #10 models
> hide #11 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #!4 models
> hide #!3 models
> hide #24 models
> show #24 models
> show #!26.1 models
> show #!26.2 models
> show #27.1 models
> show #27.2 models
> show #!29 models
> show #!30 models
> show #!31 models
> hide #!31 models
> show #32.1 models
> show #32.2 models
> fitmap #32.2 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1222 atoms
average map value = 0.00967, steps = 40
shifted from previous position = 0.021
rotated from previous position = 0.0347 degrees
atoms outside contour = 445, contour level = 0.0064458
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97959254 0.04144497 0.19667426 249.11650249
-0.05619291 0.99596256 0.07000672 194.53498036
-0.19297878 -0.07962976 0.97796641 284.10165336
Axis -0.34907553 0.90899186 -0.22777197
Axis point 1632.26880529 0.00000000 -1141.93249083
Rotation angle (degrees) 12.37637091
Shift along axis 25.15984564
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 48
shifted from previous position = 0.0261
rotated from previous position = 0.0371 degrees
atoms outside contour = 1247, contour level = 0.0064458
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99553470 -0.07935222 0.05112623 253.52559741
0.06877173 0.98070360 0.18300518 192.96746113
-0.06466154 -0.17867197 0.98178165 287.89707254
Axis -0.88727983 0.28405486 0.36338320
Axis point 0.00000000 1842.64101745 -961.84044084
Rotation angle (degrees) 11.75998331
Shift along axis -65.51784426
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 48
shifted from previous position = 0.0296
rotated from previous position = 0.0293 degrees
atoms outside contour = 1245, contour level = 0.0064458
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99549817 -0.07949331 0.05161596 253.50777442
0.06882177 0.98069682 0.18302269 192.95935324
-0.06516868 -0.17864645 0.98175276 287.89709900
Axis -0.88650634 0.28625700 0.36354291
Axis point 0.00000000 1841.69475761 -961.45966514
Rotation angle (degrees) 11.77012642
Shift along axis -64.83733407
> show #!35 models
> show #!36 models
> show #!37 models
> show #38 models
> show #39 models
> hide #24,28,38-39#26.3#27.1-2#32.1-2#!29-30,35-37#!26.1-2 atoms
> show #25.3 models
> hide #25.3 models
> show #25.3 models
> hide #25.3 models
> show #25.3 models
> hide #25.3 models
> show #!25.4 models
> close #25.4
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #25.3 models
> hide #25.3 models
> show #!25.2 models
> hide #!25.2 models
> show #!25.2 models
> hide #!25.2 models
> show #!25.2 models
> hide #!25.2 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> show #!25.2 models
> show #25.3 models
> show #!25.6 models
> hide #!25.6 models
> hide #25.3 models
> hide #!25.2 models
> hide #25.1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v25.cxs"
[Repeated 1 time(s)]
——— End of log from Mon Apr 15 16:36:47 2024 ———
opened ChimeraX session
> show #!25.2 models
> hide #!25.2 models
> show #!4 models
> show #!9 models
> show #!3 models
> hide #!32 models
> show #!32 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif"
Chain information for fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif #40
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #40,1,0,0,234.59,0,1,0,391.2,0,0,1,309.71
> view matrix models #40,1,0,0,284.73,0,1,0,301.14,0,0,1,305.21
> view matrix models #40,1,0,0,402.41,0,1,0,470.42,0,0,1,302.24
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.16022,0.94225,0.29411,411.46,0.73565,0.31265,-0.60089,467.05,-0.65814,0.12009,-0.74326,318.3
> view matrix models
> #40,0.86,0.41775,0.29305,400.37,-0.0030509,0.57848,-0.81569,476.76,-0.51028,0.7006,0.49877,307.01
> view matrix models
> #40,0.85383,0.41387,-0.31573,403.09,-0.00082885,-0.60545,-0.79589,484.53,-0.52055,0.67981,-0.5166,311.64
> ui mousemode right "translate selected models"
> view matrix models
> #40,0.85383,0.41387,-0.31573,252.84,-0.00082885,-0.60545,-0.79589,386.37,-0.52055,0.67981,-0.5166,265.49
> view matrix models
> #40,0.85383,0.41387,-0.31573,331.52,-0.00082885,-0.60545,-0.79589,336.66,-0.52055,0.67981,-0.5166,323.89
> ui mousemode right "rotate selected models"
> view matrix models
> #40,0.57393,0.75462,-0.31803,333.26,0.64193,-0.65572,-0.39744,326.1,-0.50846,0.023945,-0.86075,329.56
> view matrix models
> #40,0.52833,0.8481,0.039831,331.76,0.82036,-0.49783,-0.28139,322,-0.21882,0.18134,-0.95877,324.79
> ui mousemode right "translate selected models"
> view matrix models
> #40,0.52833,0.8481,0.039831,328.27,0.82036,-0.49783,-0.28139,321.63,-0.21882,0.18134,-0.95877,318.64
> ui tool show "Fit in Map"
> fitmap #40 inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 39508 atoms
average map value = 0.004388, steps = 200
shifted from previous position = 8.17
rotated from previous position = 17.6 degrees
atoms outside contour = 32899, contour level = 0.0064458
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.58472728 0.79380900 -0.16721630 266.82467508
0.79525538 -0.60160797 -0.07507824 245.55671941
-0.16019644 -0.08907937 -0.98305746 234.46350673
Axis -0.89014628 -0.44629997 0.09195612
Axis point 0.00000000 56.47232383 130.79238037
Rotation angle (degrees) 179.54939215
Shift along axis -325.54459557
> ui mousemode right "rotate selected models"
> view matrix models
> #40,0.37648,0.90384,-0.20331,331.11,0.78777,-0.42782,-0.44315,322.32,-0.48752,0.006674,-0.87309,323.28
> view matrix models
> #40,0.31321,0.93565,-0.16265,331.63,0.79103,-0.3518,-0.5005,322.01,-0.52551,0.028098,-0.85032,323.58
> view matrix models
> #40,0.24573,0.95264,-0.17917,332.55,0.91774,-0.28814,-0.27335,318.8,-0.31203,-0.097263,-0.94508,321.77
> ui mousemode right "translate selected models"
> view matrix models
> #40,0.24573,0.95264,-0.17917,321.28,0.91774,-0.28814,-0.27335,321.98,-0.31203,-0.097263,-0.94508,328.46
> view matrix models
> #40,0.24573,0.95264,-0.17917,312.5,0.91774,-0.28814,-0.27335,316.29,-0.31203,-0.097263,-0.94508,326.49
> view matrix models
> #40,0.24573,0.95264,-0.17917,320.62,0.91774,-0.28814,-0.27335,305.75,-0.31203,-0.097263,-0.94508,330.28
> view matrix models
> #40,0.24573,0.95264,-0.17917,306.25,0.91774,-0.28814,-0.27335,324.27,-0.31203,-0.097263,-0.94508,339.84
> fitmap #40 inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 39508 atoms
average map value = 0.004497, steps = 208
shifted from previous position = 31.1
rotated from previous position = 15.5 degrees
atoms outside contour = 31836, contour level = 0.0064458
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.21859002 0.87498356 -0.43199791 268.05474712
0.89192099 -0.35873760 -0.27528948 246.27440060
-0.39584766 -0.32513247 -0.85883265 245.13026030
Axis -0.78050970 -0.56609006 0.26522945
Axis point 0.00000000 29.20665060 167.23281914
Rotation angle (degrees) 178.17024775
Shift along axis -283.61705421
> view matrix models
> #40,0.20524,0.87745,-0.43353,298.83,0.89848,-0.34457,-0.27203,322.09,-0.38808,-0.33369,-0.8591,337.92
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.011958,0.99618,0.086488,298.92,0.92221,0.04442,-0.38413,319.64,-0.38651,0.075166,-0.91922,335.43
> view matrix models
> #40,0.096569,0.99434,0.044315,297.56,0.9034,-0.068875,-0.42323,320.83,-0.41778,0.080905,-0.90494,335.78
> view matrix models
> #40,0.24162,0.97007,-0.024311,295.94,0.87677,-0.22898,-0.42289,322.28,-0.4158,0.080863,-0.90586,335.76
> view matrix models
> #40,0.0047045,0.99981,-0.018662,299.1,0.89663,-0.01248,-0.44261,320.63,-0.44276,-0.01465,-0.89652,336.74
> ui mousemode right "translate selected models"
> view matrix models
> #40,0.0047045,0.99981,-0.018662,314.77,0.89663,-0.01248,-0.44261,320.29,-0.44276,-0.01465,-0.89652,340.63
> hide #39 models
> hide #38 models
> hide #!37 models
> hide #!36 models
> hide #!35 models
> show #!35 models
> show #!36 models
> show #!37 models
> show #38 models
> show #39 models
> select subtract #40
Nothing selected
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> hide #!34 models
> view matrix models
> #40,0.0047045,0.99981,-0.018662,303.33,0.89663,-0.01248,-0.44261,331.3,-0.44276,-0.01465,-0.89652,331.63
> view matrix models
> #40,0.0047045,0.99981,-0.018662,312.1,0.89663,-0.01248,-0.44261,323.64,-0.44276,-0.01465,-0.89652,350.59
> view matrix models
> #40,0.0047045,0.99981,-0.018662,297.07,0.89663,-0.01248,-0.44261,331.48,-0.44276,-0.01465,-0.89652,341.31
> view matrix models
> #40,0.0047045,0.99981,-0.018662,298.07,0.89663,-0.01248,-0.44261,326.15,-0.44276,-0.01465,-0.89652,341.83
> view matrix models
> #40,0.0047045,0.99981,-0.018662,298.51,0.89663,-0.01248,-0.44261,325.59,-0.44276,-0.01465,-0.89652,334.13
> view matrix models
> #40,0.0047045,0.99981,-0.018662,306.69,0.89663,-0.01248,-0.44261,325.39,-0.44276,-0.01465,-0.89652,325.25
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.092242,0.9883,0.12146,307.55,0.8583,0.14075,-0.49347,325.14,-0.5048,0.058726,-0.86124,325.49
> show #!34 models
> fitmap #40 inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 39508 atoms
average map value = 0.004389, steps = 164
shifted from previous position = 13.9
rotated from previous position = 12.3 degrees
atoms outside contour = 32253, contour level = 0.0064458
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.10637774 0.98314105 0.14871942 249.35910865
0.72385981 0.17911285 -0.66629241 251.93157492
-0.68169698 0.03677333 -0.73070990 236.30563794
Axis 0.62855969 0.74241460 -0.23180441
Axis point 80.49126806 0.00000000 143.53994937
Rotation angle (degrees) 145.99485923
Shift along axis 288.99807412
> hide #!34 models
> show #!34 models
> select subtract #40
Nothing selected
> hide #40 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240521_leaf_fitting_v26.cxs"
> hide #39 models
> hide #38 models
> hide #!37 models
> hide #!36 models
> hide #!35 models
> hide #!34 models
> show #!34 models
> hide #!30 models
> hide #!29 models
> hide #28 models
> hide #!27 models
> hide #!26 models
> hide #!25 models
> hide #24 models
> hide #!9 models
> hide #!4 models
> hide #!3 models
> hide #!32 models
> show #40 models
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> view matrix models
> #40,0.49541,0.86394,0.090463,304.34,0.73844,-0.36401,-0.56763,331.05,-0.45747,0.34801,-0.8183,308.13
> ui mousemode right "translate selected models"
> view matrix models
> #40,0.49541,0.86394,0.090463,229.31,0.73844,-0.36401,-0.56763,383.49,-0.45747,0.34801,-0.8183,249.02
> view matrix models
> #40,0.49541,0.86394,0.090463,253.32,0.73844,-0.36401,-0.56763,374.1,-0.45747,0.34801,-0.8183,201.17
> select subtract #40
Nothing selected
> select #40/A
9740 atoms, 9959 bonds, 1224 residues, 1 model selected
> color sel blue
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select subtract #40
Nothing selected
> select #40/b
7507 atoms, 7626 bonds, 953 residues, 1 model selected
> color sel dark green
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select subtract #40
Nothing selected
> select #40/c
7218 atoms, 7376 bonds, 906 residues, 1 model selected
> color sel cyan
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select subtract #40
Nothing selected
> select #40/d
4011 atoms, 4079 bonds, 511 residues, 1 model selected
> color sel chocolate
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select subtract #40
Nothing selected
> select #40/e
2423 atoms, 2468 bonds, 308 residues, 1 model selected
> select #40/e
2423 atoms, 2468 bonds, 308 residues, 1 model selected
> color sel orange
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select subtract #40
Nothing selected
> select #40/f
6841 atoms, 6958 bonds, 874 residues, 1 model selected
> color sel lime
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select subtract #40
Nothing selected
> select #40/g
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> color sel yellow
> select #40/j
Nothing selected
> hbonds
119 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
22431 hydrogen bonds found
> select #40/h
348 atoms, 347 bonds, 28 pseudobonds, 47 residues, 2 models selected
> color sel purple
> select add #40
39508 atoms, 40254 bonds, 4621 pseudobonds, 5000 residues, 2 models selected
> select subtract #40
Nothing selected
> select add #40
39508 atoms, 40254 bonds, 4621 pseudobonds, 5000 residues, 2 models selected
> select subtract #40
Nothing selected
> close #41
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select subtract #40
Nothing selected
> show #38 models
> hide #38 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #40 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA_F8WHL2.pdb, chain A (#3) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain A (#40), sequence
alignment score = 5650.7
RMSD between 321 pruned atom pairs is 0.997 angstroms; (across all 824 pairs:
9.767)
> hide #!3 models
> show #!3 models
> hide #40 models
> show #40 models
> hide #40 models
> show #40 models
> hide #!34 models
> hide #40 models
> show #40 models
> hide #40 models
> show #40 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui mousemode right select
> hide #40 models
> show #40 models
> ui tool show Matchmaker
> matchmaker #40 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_Q9JIF7.pdb, chain A (#4) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 4735.7
RMSD between 278 pruned atom pairs is 1.072 angstroms; (across all 914 pairs:
6.141)
> show #!34 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> hide #!34 models
> ui mousemode right select
> select #40/A:634
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select #40/H:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/H:8
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #40/H:9
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #40/H:10
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #40/H:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #40/H:12
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40/H:13
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!34 models
> volume #34 level 0.01184
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #!9 models
> show #8 models
> hide #8 models
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select #40/B #40/h
7855 atoms, 7973 bonds, 1000 residues, 1 model selected
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 96
shifted from previous position = 1.99
rotated from previous position = 4.54 degrees
atoms outside contour = 5565, contour level = 0.011843
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55133787 0.81826284 0.16270371 218.63511633
0.82536859 0.56340587 -0.03661333 261.19268218
-0.12162755 0.11410422 -0.98599543 268.92489827
Axis 0.46823282 0.88332933 0.02207537
Axis point 52.07818554 0.00000000 128.45275782
Rotation angle (degrees) 170.73836738
Shift along axis 339.02791132
> hide #40/A
> hide #40/C
> hide #40/D
> hide #40/E
> hide #40/F
> hide #40/g
> select #40/A
9740 atoms, 9959 bonds, 1224 residues, 1 model selected
> cartoon hide sel
> select #40/C
7218 atoms, 7376 bonds, 906 residues, 1 model selected
> cartoon hide sel
> select #40/D
4011 atoms, 4079 bonds, 511 residues, 1 model selected
> cartoon hide sel
> select #40/E
2423 atoms, 2468 bonds, 308 residues, 1 model selected
> cartoon hide sel
> select #40/F
6841 atoms, 6958 bonds, 874 residues, 1 model selected
> cartoon hide sel
> select #40/G
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> cartoon hide sel
> hide #!9 models
> volume #34 level 0.00987
> select #40/B #40/h
7855 atoms, 7973 bonds, 1000 residues, 1 model selected
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 124
shifted from previous position = 0.0117
rotated from previous position = 0.0075 degrees
atoms outside contour = 5046, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55130906 0.81830346 0.16259698 218.64123658
0.82538951 0.56337101 -0.03667798 261.20229085
-0.12161615 0.11398494 -0.98601063 268.92086397
Axis 0.46825276 0.88332007 0.02202309
Axis point 52.07086061 0.00000000 128.45942589
Rotation angle (degrees) 170.74215114
Shift along axis 339.02705427
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 180
shifted from previous position = 0.0115
rotated from previous position = 0.0183 degrees
atoms outside contour = 5042, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55153846 0.81816881 0.16249657 218.63118093
0.82522764 0.56360153 -0.03677871 261.19672471
-0.12167451 0.11381178 -0.98602343 268.91088302
Axis 0.46813192 0.88338610 0.02194336
Axis point 52.08757088 0.00000000 128.46507520
Rotation angle (degrees) 170.74423093
Shift along axis 338.98659745
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.5624,0.81178,0.15722,286.27,0.81949,0.57256,-0.024894,338.86,-0.11023,0.11484,-0.98725,346.69
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 100
shifted from previous position = 5.48
rotated from previous position = 0.0362 degrees
atoms outside contour = 5046, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55125874 0.81829194 0.16282541 218.64816997
0.82544073 0.56331488 -0.03638629 261.18746369
-0.12149658 0.11434447 -0.98598374 268.92316731
Axis 0.46827538 0.88330341 0.02220914
Axis point 52.07588489 0.00000000 128.43293399
Rotation angle (degrees) 170.73839773
Shift along axis 339.06788680
> view matrix models
> #40,-0.56212,0.81191,0.15755,285.77,0.8197,0.57227,-0.024498,339.44,-0.11005,0.11537,-0.98721,347.33
> view matrix models
> #40,-0.56212,0.81191,0.15755,283.72,0.8197,0.57227,-0.024498,336.84,-0.11005,0.11537,-0.98721,347.63
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 128
shifted from previous position = 2.9
rotated from previous position = 0.0265 degrees
atoms outside contour = 5047, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55131009 0.81833243 0.16244765 218.64835717
0.82540593 0.56334930 -0.03664183 261.20608081
-0.12149997 0.11388425 -0.98603659 268.91792299
Axis 0.46826242 0.88331540 0.02200455
Axis point 52.06055817 0.00000000 128.46307893
Rotation angle (degrees) 170.75082647
Shift along axis 339.02958194
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 84
shifted from previous position = 0.0194
rotated from previous position = 0.0131 degrees
atoms outside contour = 5049, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55143936 0.81821808 0.16258478 218.65494305
0.82531597 0.56348672 -0.03655513 261.19084196
-0.12152443 0.11402588 -0.98601720 268.91027226
Axis 0.46818717 0.88335369 0.02206879
Axis point 52.08652545 0.00000000 128.44728030
Rotation angle (degrees) 170.74592104
Shift along axis 339.02985803
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 104
shifted from previous position = 0.0107
rotated from previous position = 0.0337 degrees
atoms outside contour = 5045, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55110129 0.81836999 0.16296607 218.65986733
0.82553973 0.56317113 -0.03636548 261.18645049
-0.12153820 0.11449390 -0.98596127 268.92250550
Axis 0.46835240 0.88326133 0.02225891
Axis point 52.07542258 0.00000000 128.42422789
Rotation angle (degrees) 170.73196224
Shift along axis 339.09168542
> show #!4 models
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.009133, steps = 44
shifted from previous position = 0.0217
rotated from previous position = 0.00877 degrees
atoms outside contour = 4184, contour level = 0.0098704
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02212550 -0.73061751 0.68242839 220.16058213
-0.01331212 0.68275028 0.73053052 241.09652572
-0.99966657 0.00707878 -0.02483226 272.96568751
Axis -0.36787702 0.85534950 0.36475159
Axis point 254.78423417 0.00000000 -62.18356583
Rotation angle (degrees) 100.49232066
Shift along axis 224.79444223
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!34 models
> hide #!4 models
> show #!4 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!4 models
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> select subtract #40
Nothing selected
> show #!34 models
> show #!3 models
> show #5 models
> hide #5 models
> show #39 models
> show #38 models
> hide #38 models
> show #38 models
> hide #38 models
> show #!37 models
> show #!36 models
> show #!35 models
> hide #!35 models
> show #!35 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!31 models
> show #!30 models
> hide #!30 models
> show #!30 models
> show #!29 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> hide #39 models
> show #39 models
> show #!27 models
> show #!26 models
> hide #!26 models
> show #!26 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!9 models
> hide #!3 models
> show #!3 models
> show #24 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> ui tool show "Side View"
> hide #!34 models
> show #!34 models
> select #40/B #40/h
7855 atoms, 7973 bonds, 1000 residues, 1 model selected
> view matrix models
> #40,-0.56197,0.81199,0.15769,282.69,0.8198,0.57212,-0.024475,337.55,-0.11009,0.11552,-0.98719,345.61
> view matrix models
> #40,-0.56197,0.81199,0.15769,283.28,0.8198,0.57212,-0.024475,338.86,-0.11009,0.11552,-0.98719,344.99
> view matrix models
> #40,-0.56197,0.81199,0.15769,284.14,0.8198,0.57212,-0.024475,340.07,-0.11009,0.11552,-0.98719,345.26
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 92
shifted from previous position = 4.57
rotated from previous position = 0.022 degrees
atoms outside contour = 5048, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55110014 0.81840479 0.16279514 218.64168819
0.82551278 0.56318841 -0.03670801 261.19751669
-0.12172635 0.11415968 -0.98597681 268.91351797
Axis 0.46835241 0.88326616 0.02206600
Axis point 52.06701893 0.00000000 128.44776774
Rotation angle (degrees) 170.73144763
Shift along axis 339.04213420
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 72
shifted from previous position = 0.0174
rotated from previous position = 0.0142 degrees
atoms outside contour = 5048, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55119683 0.81835465 0.16271979 218.65690501
0.82548023 0.56325066 -0.03648423 261.19361936
-0.12150907 0.11421198 -0.98599756 268.91895596
Axis 0.46831203 0.88328562 0.02214385
Axis point 52.06914221 0.00000000 128.44120503
Rotation angle (degrees) 170.74126999
Shift along axis 339.06312999
> hide #!34 models
> show #!34 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240521_leaf_fitting_v27.cxs"
> hide #!37 models
> hide #!36 models
> hide #!35 models
> hide #39 models
> hide #!32 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!27 models
> hide #!26 models
> hide #!25 models
> hide #24 models
> hide #!9 models
> hide #!3 models
> view matrix models
> #40,-0.56206,0.81197,0.15744,283.54,0.81974,0.57221,-0.024597,339.16,-0.11006,0.11524,-0.98722,345.42
> view matrix models
> #40,-0.56206,0.81197,0.15744,283.87,0.81974,0.57221,-0.024597,340.09,-0.11006,0.11524,-0.98722,345.18
> view matrix models
> #40,-0.56206,0.81197,0.15744,283.79,0.81974,0.57221,-0.024597,340.89,-0.11006,0.11524,-0.98722,345.03
> view matrix models
> #40,-0.56206,0.81197,0.15744,283.46,0.81974,0.57221,-0.024597,341.23,-0.11006,0.11524,-0.98722,346.54
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7855 atoms
average map value = 0.008027, steps = 108
shifted from previous position = 5.26
rotated from previous position = 0.0235 degrees
atoms outside contour = 5046, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.55145473 0.81819682 0.16263963 218.63191357
0.82528315 0.56352552 -0.03669766 261.19416657
-0.12167749 0.11398665 -0.98600286 268.91645801
Axis 0.46817099 0.88336356 0.02201698
Axis point 52.08701783 0.00000000 128.45637404
Rotation angle (degrees) 170.73919393
Shift along axis 339.00725471
> hide #!34 models
> ui mousemode right select
> select clear
> ui mousemode right select
Drag select of 148 residues
> select up
1263 atoms, 1277 bonds, 164 residues, 1 model selected
> select up
7855 atoms, 7973 bonds, 1000 residues, 1 model selected
> select down
1263 atoms, 1277 bonds, 164 residues, 1 model selected
> select clear
Drag select of 154 residues
> select up
1311 atoms, 1327 bonds, 171 residues, 1 model selected
> show #!34 models
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1311 atoms
average map value = 0.007817, steps = 64
shifted from previous position = 6.37
rotated from previous position = 3.82 degrees
atoms outside contour = 825, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.49959872 0.84635064 0.18463943 219.53809976
0.85843903 0.51228436 -0.02543959 267.69551574
-0.11611871 0.14579210 -0.98247703 270.53710887
Axis 0.49446431 0.86849670 0.03490754
Axis point 46.53717373 0.00000000 127.56693591
Rotation angle (degrees) 170.02905866
Shift along axis 350.49021168
> hide #!34 models
> surface sel
> show #!34 models
> surface hidePatches (#!40 & sel)
> hide #!34 models
> ui mousemode right select
> select clear
Drag select of 78 residues
> select up
928 atoms, 935 bonds, 119 residues, 2 models selected
> select up
7507 atoms, 7626 bonds, 953 residues, 2 models selected
> select down
928 atoms, 935 bonds, 119 residues, 2 models selected
> select clear
Drag select of 118 residues
> select down
921 atoms, 118 residues, 2 models selected
> select up
1380 atoms, 1394 bonds, 175 residues, 2 models selected
> select up
7507 atoms, 7626 bonds, 953 residues, 2 models selected
> select down
1380 atoms, 1394 bonds, 175 residues, 2 models selected
> ui mousemode right select
Drag select of 272 residues
> select up
2962 atoms, 2997 bonds, 372 residues, 2 models selected
> select up
7507 atoms, 7626 bonds, 953 residues, 2 models selected
> select down
2962 atoms, 2997 bonds, 372 residues, 2 models selected
> cartoon hide (#!40 & sel)
Drag select of 48 residues
> select up
652 atoms, 656 bonds, 84 residues, 2 models selected
> cartoon hide (#!40 & sel)
Drag select of 29 residues
> select up
436 atoms, 439 bonds, 54 residues, 2 models selected
> cartoon hide (#!40 & sel)
Drag select of 3 residues
> cartoon hide (#!40 & sel)
Drag select of 7 residues
> select up
92 atoms, 92 bonds, 12 residues, 2 models selected
> cartoon hide (#!40 & sel)
Drag select of 8 residues
> select up
7507 atoms, 7626 bonds, 953 residues, 2 models selected
> select down
65 atoms, 8 residues, 2 models selected
Drag select of 9 residues
Drag select of 10 residues
> cartoon hide (#!40 & sel)
Drag select of 267 residues
> select up
2188 atoms, 2221 bonds, 280 residues, 2 models selected
> cartoon hide (#!40 & sel)
Drag select of 2 residues
> cartoon hide (#!40 & sel)
Drag select of 1 residues
> select up
39 atoms, 38 bonds, 6 residues, 2 models selected
> cartoon hide (#!40 & sel)
Drag select of 2 residues
> cartoon hide (#!40 & sel)
> show #!34 models
> show #!4 models
> hide #!34 models
> hide #!4 models
Drag select of 50 residues
> select up
477 atoms, 484 bonds, 62 residues, 2 models selected
> select up
7507 atoms, 7626 bonds, 953 residues, 2 models selected
> show #!34 models
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7507 atoms
average map value = 0.008297, steps = 84
shifted from previous position = 6.62
rotated from previous position = 3.71 degrees
atoms outside contour = 4721, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.54880618 0.81993615 0.16283888 218.74247183
0.82669165 0.56124221 -0.03985101 261.18604987
-0.12406733 0.11274707 -0.98584756 268.81795879
Axis 0.46948367 0.88269650 0.02078400
Axis point 52.04192904 0.00000000 128.56927986
Rotation angle (degrees) 170.64698297
Shift along axis 338.83114217
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 2 models selected
> select subtract #40
2 models selected
> ui tool show Matchmaker
> matchmaker #!40 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_Q9JIF7.pdb, chain A (#4) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 4735.7
RMSD between 278 pruned atom pairs is 1.072 angstroms; (across all 914 pairs:
6.141)
> undo
[Repeated 2 time(s)]Drag select of 172 residues
> fitmap sel inMap #34
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1325 atoms
average map value = 0.007953, steps = 76
shifted from previous position = 5.45
rotated from previous position = 2.57 degrees
atoms outside contour = 827, contour level = 0.0098704
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50508390 0.84461041 0.17754866 219.44757134
0.85545379 0.51718857 -0.02673585 267.71204628
-0.11440752 0.13838082 -0.98374879 270.68842562
Axis 0.49202156 0.86998319 0.03231156
Axis point 46.61766015 0.00000000 128.06969832
Rotation angle (degrees) 170.34040927
Shift along axis 349.62428175
> show #!34 models
> show #!4 models
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 3 models selected
> select subtract #40
2 models selected
> show #39 models
> show #38 models
> hide #38 models
> show #!37 models
> show #!36 models
> show #!35 models
> show #!32 models
> show #!31 models
> show #!30 models
> show #!29 models
> show #28 models
> hide #28 models
> show #!27 models
> show #!26 models
> show #!25.6 models
> hide #!25.6 models
> show #24 models
> show #!9 models
> show #!3 models
> show #!2 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240521_leaf_fitting_v28.cxs"
> hide #!2 models
> hide #!34 models
> select #4/A:625
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #4/A:661
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #!34 models
> show #!2 models
> hide #24 models
> show #24 models
> volume #34 level 0.006418
> hide #!34 models
> select add #24
1945 atoms, 1960 bonds, 255 residues, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> style sel sphere
Changed 1945 atom styles
> ui tool show "Color Actions"
> style sel stick
Changed 1945 atom styles
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> show sel atoms
> hide sel atoms
> select subtract #24
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #24/A:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel red
> select #24/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select clear
> select #24/A:156
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #24/A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select #24/A:262
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> select #24/A:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> select #24/A:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel yellow
> show sel atoms
> select #24/A:75
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel lime
> select #24/A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel lime
> select clear
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240521_leaf_fitting_v29_mutations_labeled.cxs"
> show #!34 models
> hide #!2 models
> hide #!25 models
> show #!25 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> select add #24
1934 atoms, 1950 bonds, 254 residues, 1 model selected
> surface sel
> ui tool show "Surface Color"
> color electrostatic #24.1 map #2 palette -10,#ff0000:0,#ffffff:10,#0000ff
Map values for surface "3kn1_Golph3_xtal.cif_A SES surface": minimum -0.2153,
mean -0.04639, maximum 0.1938
> color single #24.1
> ui tool show "Surface Color"
> color electrostatic #24.1 map #2 palette -10,#ff0000:0,#ffffff:10,#0000ff
Map values for surface "3kn1_Golph3_xtal.cif_A SES surface": minimum -0.2153,
mean -0.04639, maximum 0.1938
> color single #24.1
> surface hidePatches (#!24 & sel)
> select subtract #24
1 model selected
> show #!34 models
> volume #34 level 0.005871
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #11 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!2 models
> hide #!2 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> select #24/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #24/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!34 models
Drag select of 1 residues, 34 relion_locres_filtered_20240326_GT.mrc
> select add #34
5 atoms, 1 residue, 4 models selected
> select subtract #34
5 atoms, 1 residue, 1 model selected
> hide #!34 models
> select #30/A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #24/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #11/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:97
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:95
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #30/A:94
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #30/A:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:94
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select #30/A:97
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select #3/A:321
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:320
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!34 models
> hide #!34 models
> hide #!30 models
> show #!34 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!25 models
> show #!25 models
> hide #!34 models
> volume #2 level 0.1204
> show #!34 models
> fitmap #2 inMap #34
Fit map emdb 3720 in map relion_locres_filtered_20240326_GT.mrc using 87829
points
correlation = 0.6926, correlation about mean = 0.2583, overlap = 150.4
steps = 48, shift = 0.101, angle = 0.106 degrees
Position of emdb 3720 (#2) relative to relion_locres_filtered_20240326_GT.mrc
(#34) coordinates:
Matrix rotation and translation
-0.53796983 0.84155370 -0.04874257 218.00766540
-0.84283572 -0.53799705 0.01367977 404.60666989
-0.01471110 0.04844128 0.99871769 145.34757683
Axis 0.02062885 -0.02019562 -0.99958321
Axis point 220.50645392 140.27828970 0.00000000
Rotation angle (degrees) 122.59005790
Shift along axis -148.96103027
> fitmap #2 inMap #34
Fit map emdb 3720 in map relion_locres_filtered_20240326_GT.mrc using 87829
points
correlation = 0.6927, correlation about mean = 0.2585, overlap = 150.4
steps = 44, shift = 0.0342, angle = 0.00493 degrees
Position of emdb 3720 (#2) relative to relion_locres_filtered_20240326_GT.mrc
(#34) coordinates:
Matrix rotation and translation
-0.53792909 0.84158316 -0.04868350 217.96400146
-0.84286283 -0.53795369 0.01371436 404.61662806
-0.01464769 0.04841086 0.99872010 145.33292296
Axis 0.02058960 -0.02019753 -0.99958398
Axis point 220.49090624 140.29322173 0.00000000
Rotation angle (degrees) 122.58711660
Shift along axis -148.95692510
> fitmap #2 inMap #34
Fit map emdb 3720 in map relion_locres_filtered_20240326_GT.mrc using 87829
points
correlation = 0.6927, correlation about mean = 0.2585, overlap = 150.4
steps = 44, shift = 0.00301, angle = 0.00163 degrees
Position of emdb 3720 (#2) relative to relion_locres_filtered_20240326_GT.mrc
(#34) coordinates:
Matrix rotation and translation
-0.53795122 0.84156844 -0.04869343 217.96879525
-0.84284862 -0.53797589 0.01371664 404.62013148
-0.01465240 0.04842007 0.99871959 145.33197166
Axis 0.02059406 -0.02020097 -0.99958382
Axis point 220.49098314 140.29514343 0.00000000
Rotation angle (degrees) 122.58864151
Shift along axis -148.95634306
> hide #!2 models
> select add #3
6692 atoms, 6847 bonds, 1 pseudobond, 833 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!30 models
> show #!34 models
> hide #!30 models
> hide #!34 models
> show #!2 models
> show #!34 models
> hide #!34 models
> hide #!2 models
> select #11/A:90
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #11
2367 atoms, 2398 bonds, 298 residues, 1 model selected
> select subtract #11
Nothing selected
> hide #11 models
> select #24/A:90
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel cyan
> select #24/A:171
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #24/A:90
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #24/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> select #24/A:81
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> show #!34 models
> select clear
> volume #34 level 0.008609
> volume #34 level 0.006418
> volume #34 level 0.005871
> hide #!34 models
> show #!34 models
> hide #!34 models
> select #40/H:10
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #40/H:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #40/H:12
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40/H:13
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/H:14
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #40/B:848
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/H:14
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 3 residues
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel stick
Changed 29 atom styles
> select clear
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera
> sessions/20240521_leaf_fitting_v30_mutations_interactions_labeled.cxs"
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> select #24/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> select #24/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #24/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!34 models
> select #34
2 models selected
> hide #!34 models
> select #3/A:13
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> select #24/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #24/A:185
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 2 time(s)]
> select #3/A:269
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!34 models
> hide #!34 models
> select clear
> select #3/A:293
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!34 models
> select #3/A:269@CD
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!34 models
> select #3/A:269
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:293
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #24/A:185
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #24/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!34 models
> show #!2 models
> hide #!2 models
> hide #!34 models
> select #3/A:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:291
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:291
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:291
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!30 models
> select #30/A:298
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #30/A:297
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!34 models
> select add #30
2737 atoms, 2622 bonds, 1 pseudobond, 505 residues, 2 models selected
> select subtract #30
Nothing selected
> hide #!34 models
> hide #!30 models
> select #3/A:291@CE1
1 atom, 1 residue, 1 model selected
> show #!34 models
> volume #34 level 0.007331
> hide #!34 models
> show #!34 models
> hide #!34 models
> hide #39 models
> show #39 models
> hide #26.3 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!34 models
> select #31.1/A:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #31.1/A:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera
> sessions/20240521_leaf_fitting_v31_mutations_interactions_labeled.cxs"
——— End of log from Tue May 21 23:56:29 2024 ———
opened ChimeraX session
> show #!34 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240522_leaf_fitting_v32_labelled.cxs"
——— End of log from Mon Jun 3 13:56:09 2024 ———
opened ChimeraX session
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!9 models
> show #!9 models
> hide #!24 models
> show #!24 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!24 models
> show #!24 models
> show #26.3 models
> hide #31.1 models
> hide #26.3 models
> show #26.3 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #26.3 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.01093, steps = 60
shifted from previous position = 0.0301
rotated from previous position = 0.115 degrees
atoms outside contour = 396, contour level = 0.0073311
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.25015197 0.19166485 -0.94904613 329.61451129
0.70993523 0.70281569 -0.04518920 309.45965141
0.65834334 -0.68506545 -0.31188036 214.46027109
Axis -0.35429978 -0.89001229 0.28696654
Axis point -6.56266263 0.00000000 232.51267062
Rotation angle (degrees) 115.44270597
Shift along axis -330.66231699
> fitmap #26.3 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.01093, steps = 40
shifted from previous position = 0.0136
rotated from previous position = 0.056 degrees
atoms outside contour = 396, contour level = 0.0073311
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.25044191 0.19256066 -0.94878830 329.65987834
0.71001093 0.70276508 -0.04478510 309.44631735
0.65815144 -0.68486613 -0.31272200 214.49855120
Axis -0.35452366 -0.89004067 0.28660178
Axis point -6.47767297 0.00000000 232.37808000
Rotation angle (degrees) 115.48021628
Shift along axis -330.81636809
> fitmap #26.3 inMap #34
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.01093, steps = 48
shifted from previous position = 0.0249
rotated from previous position = 0.0425 degrees
atoms outside contour = 393, contour level = 0.0073311
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#26.3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.25077607 0.19313625 -0.94858302 329.70656717
0.71021693 0.70256140 -0.04471441 309.44271618
0.65780184 -0.68491303 -0.31335423 214.51452240
Axis -0.35469842 -0.89000844 0.28648562
Axis point -6.41176068 0.00000000 232.30159949
Rotation angle (degrees) 115.51735370
Shift along axis -330.89769971
> hide #!27 models
> show #!27 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> show #28 models
> hide #28 models
> hide #39 models
> show #28 models
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007773, steps = 64
shifted from previous position = 0.00753
rotated from previous position = 0.0352 degrees
atoms outside contour = 593, contour level = 0.0073311
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56977216 -0.71673503 0.40205793 245.64427258
-0.48588719 -0.10076147 -0.86819396 216.24614809
0.66277698 -0.69002755 -0.29084129 214.86790721
Axis 0.45547881 -0.66652294 0.59015780
Axis point 184.92723986 0.00000000 218.17465974
Rotation angle (degrees) 168.72130754
Shift along axis 94.55871550
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007773, steps = 44
shifted from previous position = 0.00467
rotated from previous position = 0.0259 degrees
atoms outside contour = 592, contour level = 0.0073311
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56974234 -0.71665127 0.40224944 245.64234236
-0.48572977 -0.10117318 -0.86823416 216.22185965
0.66291798 -0.69005429 -0.29045622 214.85271487
Axis 0.45549464 -0.66636665 0.59032204
Axis point 184.94036291 0.00000000 218.20662049
Rotation angle (degrees) 168.72084168
Shift along axis 94.63802762
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007773, steps = 76
shifted from previous position = 0.00297
rotated from previous position = 0.0032 degrees
atoms outside contour = 592, contour level = 0.0073311
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56977869 -0.71664593 0.40220745 245.64658784
-0.48569764 -0.10113646 -0.86825642 216.22256444
0.66291027 -0.69006522 -0.29044784 214.85034197
Axis 0.45547257 -0.66637964 0.59032441
Axis point 184.93644775 0.00000000 218.20641252
Rotation angle (degrees) 168.71956173
Shift along axis 94.63037015
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007773, steps = 80
shifted from previous position = 0.003
rotated from previous position = 0.0126 degrees
atoms outside contour = 592, contour level = 0.0073311
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56975507 -0.71676535 0.40202808 245.64499671
-0.48563061 -0.10100146 -0.86830962 216.23091799
0.66297968 -0.68996096 -0.29053710 214.85692881
Axis 0.45547043 -0.66642348 0.59027657
Axis point 184.92158374 0.00000000 218.21261815
Rotation angle (degrees) 168.70940821
Shift along axis 94.60768454
> fitmap #28 inMap #34
Fit molecule copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1128 atoms
average map value = 0.007772, steps = 28
shifted from previous position = 0.0343
rotated from previous position = 0.0983 degrees
atoms outside contour = 594, contour level = 0.0073311
Position of copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif C (#28) relative
to relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.56976373 -0.71640192 0.40266310 245.66998860
-0.48493373 -0.10249149 -0.86852447 216.13776532
0.66348214 -0.69011867 -0.28901152 214.79452675
Axis 0.45545972 -0.66585597 0.59092492
Axis point 184.97144152 0.00000000 218.33697098
Rotation angle (degrees) 168.70547428
Shift along axis 94.90360191
> hide #32.1 models
> show #32.1 models
> hide #32.2 models
> show #32.2 models
> hide #32.1 models
> show #32.1 models
> hide #32.2 models
> show #32.2 models
> hide #!35 models
> show #!35 models
> hide #!36 models
> show #!36 models
> hide #!37 models
> show #!37 models
> show #38 models
> hide #38 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!9 models
> show #!9 models
> show #8 models
> close #1
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/AF-Q5XJY5-CopD.pdb"
AF-Q5XJY5-CopD.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit δ (Q5XJY5) [more
info...]
Chain information for AF-Q5XJY5-CopD.pdb #1
---
Chain | Description | UniProt
A | coatomer subunit δ | COPD_MOUSE 1-511
> color #1 #b55c00ff
> select add #1
4014 atoms, 4084 bonds, 511 residues, 2 models selected
> view orient
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.22845,0.95367,-0.19576,582.24,0.012859,-0.20401,-0.97888,618.31,-0.97347,0.22111,-0.058869,274.42,#1,1,0,0,322.45,0,1,0,284.52,0,0,1,0
> view matrix models
> #24,0.22845,0.95367,-0.19576,714.03,0.012859,-0.20401,-0.97888,717.94,-0.97347,0.22111,-0.058869,470.12,#1,1,0,0,454.24,0,1,0,384.15,0,0,1,195.7
> view matrix models
> #24,0.22845,0.95367,-0.19576,714.38,0.012859,-0.20401,-0.97888,741.01,-0.97347,0.22111,-0.058869,482.72,#1,1,0,0,454.59,0,1,0,407.22,0,0,1,208.3
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #1 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopD_Q5XJY5, chain A (#8) with AF-Q5XJY5-CopD.pdb, chain A (#1),
sequence alignment score = 2127.5
RMSD between 179 pruned atom pairs is 0.000 angstroms; (across all 179 pairs:
0.000)
> ui mousemode right select
> select subtract #1
1 bond, 1 model selected
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #!3 models
> hide #!4 models
> hide #!9 models
> hide #!34 models
> show #!34 models
> show #!3 models
> show #!4 models
> show #!9 models
> hide #1 models
> show #8 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #!30 models
> hide #!3 models
> select add #24
1934 atoms, 1950 bonds, 254 residues, 1 model selected
> select subtract #24
1 model selected
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> select add #24
1934 atoms, 1950 bonds, 254 residues, 1 model selected
> view orient
Drag select of 7 atoms, 38 residues, 4 bonds
Drag select of 95 atoms, 239 residues, 82 bonds
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.22845,0.95367,-0.19576,311.99,0.012859,-0.20401,-0.97888,299.49,-0.97347,0.22111,-0.058869,482.72
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!24 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Golph3_ Q9CRA5.pdb, chain A (#11) with 3kn1_Golph3_xtal.cif, chain
A (#24), sequence alignment score = 1235.4
RMSD between 224 pruned atom pairs is 0.677 angstroms; (across all 239 pairs:
1.230)
> select add #24
1934 atoms, 1950 bonds, 254 residues, 2 models selected
> select subtract #24
1 model selected
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 44
shifted from previous position = 0.00199
rotated from previous position = 0.00237 degrees
atoms outside contour = 870, contour level = 0.0073311
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23411882 0.94979669 -0.20754429 197.36124212
0.00020207 -0.21352478 -0.97693763 258.11108339
-0.97220797 0.22867754 -0.05018209 197.38531977
Axis 0.70313521 0.44596483 -0.55381969
Axis point 0.00000000 -45.19312295 254.34939772
Rotation angle (degrees) 120.98368854
Shift along axis 144.56422808
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 44
shifted from previous position = 0.00409
rotated from previous position = 0.0477 degrees
atoms outside contour = 871, contour level = 0.0073311
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23367514 0.95001198 -0.20705835 197.35573015
-0.00012509 -0.21292467 -0.97706861 258.07355956
-0.97231472 0.22834255 -0.04963637 197.41034193
Axis 0.70284348 0.44620082 -0.55399988
Axis point 0.00000000 -45.37463902 254.47002005
Rotation angle (degrees) 120.96022808
Shift along axis 144.49751519
> hide #!24 models
> show #11 models
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 44
shifted from previous position = 0.0328
rotated from previous position = 0.0458 degrees
atoms outside contour = 868, contour level = 0.0073311
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23415440 0.94986066 -0.20721111 197.39669232
0.00041715 -0.21323457 -0.97700094 258.09433832
-0.97219933 0.22868264 -0.05032604 197.39158985
Axis 0.70313034 0.44612570 -0.55369630
Axis point 0.00000000 -45.26326865 254.32962611
Rotation angle (degrees) 120.97761199
Shift along axis 144.64312646
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 36
shifted from previous position = 0.0198
rotated from previous position = 0.0176 degrees
atoms outside contour = 868, contour level = 0.0073311
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23408490 0.94982276 -0.20746319 197.37337718
0.00020395 -0.21344001 -0.97695615 258.10559803
-0.97221614 0.22864837 -0.05015680 197.38961043
Axis 0.70311025 0.44600500 -0.55381903
Axis point 0.00000000 -45.22107900 254.35958148
Rotation angle (degrees) 120.98114440
Shift along axis 144.57350888
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 40
shifted from previous position = 0.0111
rotated from previous position = 0.0115 degrees
atoms outside contour = 870, contour level = 0.0073311
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23420658 0.94976056 -0.20761057 197.36474823
0.00016749 -0.21358949 -0.97692349 258.11341680
-0.97218684 0.22876713 -0.05018314 197.37895020
Axis 0.70317380 0.44591041 -0.55381451
Axis point 0.00000000 -45.17503829 254.34330682
Rotation angle (degrees) 120.98295329
Shift along axis 144.56585129
> hide #11 models
> show #!24 models
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 44
shifted from previous position = 0.00201
rotated from previous position = 0.0533 degrees
atoms outside contour = 871, contour level = 0.0073311
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23369916 0.95001506 -0.20701710 197.35800882
-0.00011063 -0.21288690 -0.97707684 258.07126543
-0.97230895 0.22836494 -0.04964639 197.41036117
Axis 0.70284861 0.44621343 -0.55398322
Axis point 0.00000000 -45.38179119 254.46707755
Rotation angle (degrees) 120.95849874
Shift along axis 144.50563895
> fitmap #24 inMap #34
Fit molecule 3kn1_Golph3_xtal.cif (#24) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1934 atoms
average map value = 0.008452, steps = 40
shifted from previous position = 0.00765
rotated from previous position = 0.0189 degrees
atoms outside contour = 870, contour level = 0.0073311
Position of 3kn1_Golph3_xtal.cif (#24) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.23388251 0.94996011 -0.20706223 197.36980604
0.00013398 -0.21300044 -0.97705209 258.08065054
-0.97226486 0.22848765 -0.04994435 197.39999665
Axis 0.70296183 0.44619702 -0.55385276
Axis point 0.00000000 -45.33519202 254.40462393
Rotation angle (degrees) 120.96612115
Shift along axis 144.56772497
> show #!3 models
> hide #!3 models
> hide #!30 models
> show #!30 models
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 28
shifted from previous position = 0.0444
rotated from previous position = 0.043 degrees
atoms outside contour = 1169, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79065852 -0.52006743 0.32309283 236.67837552
-0.42071527 -0.07811133 0.90382370 306.89589708
-0.44481206 -0.85054600 -0.28055970 224.01788859
Axis -0.91485641 0.40044166 0.05180947
Axis point 0.00000000 298.40681607 -19.94524805
Rotation angle (degrees) 106.49945673
Shift along axis -82.02658130
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 44
shifted from previous position = 0.00604
rotated from previous position = 0.0155 degrees
atoms outside contour = 1170, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79062785 -0.52015485 0.32302715 236.68246447
-0.42057503 -0.07792376 0.90390516 306.90046176
-0.44499917 -0.85050974 -0.28037283 224.02093681
Axis -0.91483143 0.40048372 0.05192543
Axis point 0.00000000 298.44102839 -19.95437080
Rotation angle (degrees) 106.48918577
Shift along axis -81.98353244
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 40
shifted from previous position = 0.0346
rotated from previous position = 0.0549 degrees
atoms outside contour = 1171, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79089557 -0.51967170 0.32314940 236.68458374
-0.42088694 -0.07860174 0.90370126 306.91730947
-0.44422786 -0.85074267 -0.28088879 224.04967298
Axis -0.91497749 0.40020254 0.05151822
Axis point 0.00000000 298.34590809 -19.93277897
Rotation angle (degrees) 106.51686013
Shift along axis -82.18933752
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 28
shifted from previous position = 0.0248
rotated from previous position = 0.0349 degrees
atoms outside contour = 1171, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79075543 -0.51989715 0.32312971 236.68339373
-0.42069040 -0.07810589 0.90383575 306.90424046
-0.44466330 -0.85065059 -0.28047840 224.03220543
Axis -0.91489129 0.40037196 0.05173217
Axis point 0.00000000 298.41110765 -19.96559274
Rotation angle (degrees) 106.49396960
Shift along axis -82.07405001
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 36
shifted from previous position = 0.0193
rotated from previous position = 0.00966 degrees
atoms outside contour = 1169, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79077253 -0.51990541 0.32307457 236.68582329
-0.42071618 -0.07826985 0.90380957 306.91632187
-0.44460848 -0.85063048 -0.28062626 224.04469682
Axis -0.91490879 0.40033284 0.05172539
Axis point 0.00000000 298.40008943 -19.94137991
Rotation angle (degrees) 106.50277513
Shift along axis -82.08845700
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 44
shifted from previous position = 0.00798
rotated from previous position = 0.0359 degrees
atoms outside contour = 1173, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79095030 -0.51957998 0.32316292 236.68460133
-0.42092107 -0.07870379 0.90367648 306.91900688
-0.44409806 -0.85078926 -0.28095295 224.05143643
Axis -0.91500463 0.40014880 0.05145348
Axis point 0.00000000 298.32918230 -19.93282662
Rotation angle (degrees) 106.52019122
Shift along axis -82.22601095
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 28
shifted from previous position = 0.0246
rotated from previous position = 0.0351 degrees
atoms outside contour = 1170, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79079859 -0.51980952 0.32316506 236.68350793
-0.42074402 -0.07819437 0.90380314 306.90476290
-0.44453579 -0.85069602 -0.28054274 224.03459739
Axis -0.91491347 0.40033068 0.05165939
Axis point 0.00000000 298.39624004 -19.96672359
Rotation angle (degrees) 106.49724595
Shift along axis -82.10804416
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 28
shifted from previous position = 0.013
rotated from previous position = 0.0168 degrees
atoms outside contour = 1169, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79073436 -0.51999363 0.32302601 236.68295257
-0.42075309 -0.07838298 0.90378258 306.91348854
-0.44464144 -0.85056613 -0.28076905 224.03795392
Axis -0.91490274 0.40034291 0.05175450
Axis point 0.00000000 298.38336978 -19.91695214
Rotation angle (degrees) 106.51156264
Shift along axis -82.07627243
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!30 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA_F8WHL2.pdb, chain A (#3) with 4j87_yeast_alphaCOPI.cif, chain
A (#30), sequence alignment score = 1380.7
RMSD between 297 pruned atom pairs is 0.540 angstroms; (across all 309 pairs:
2.943)
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 48
shifted from previous position = 0.484
rotated from previous position = 2.47 degrees
atoms outside contour = 1170, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79086817 -0.51973337 0.32311726 236.68392710
-0.42085373 -0.07856391 0.90372001 306.91790359
-0.44430810 -0.85070849 -0.28086542 224.04826702
Axis -0.91496466 0.40022553 0.05156744
Axis point 0.00000000 298.35339518 -19.92897462
Rotation angle (degrees) 106.51585001
Shift along axis -82.16745292
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 48
shifted from previous position = 0.484
rotated from previous position = 2.47 degrees
atoms outside contour = 1170, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79086817 -0.51973337 0.32311726 236.68392710
-0.42085373 -0.07856391 0.90372001 306.91790359
-0.44430810 -0.85070849 -0.28086542 224.04826702
Axis -0.91496466 0.40022553 0.05156744
Axis point 0.00000000 298.35339518 -19.92897462
Rotation angle (degrees) 106.51585001
Shift along axis -82.16745292
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 48
shifted from previous position = 0.484
rotated from previous position = 2.47 degrees
atoms outside contour = 1170, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79086817 -0.51973337 0.32311726 236.68392710
-0.42085373 -0.07856391 0.90372001 306.91790359
-0.44430810 -0.85070849 -0.28086542 224.04826702
Axis -0.91496466 0.40022553 0.05156744
Axis point 0.00000000 298.35339518 -19.92897462
Rotation angle (degrees) 106.51585001
Shift along axis -82.16745292
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 48
shifted from previous position = 0.484
rotated from previous position = 2.47 degrees
atoms outside contour = 1170, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79086817 -0.51973337 0.32311726 236.68392710
-0.42085373 -0.07856391 0.90372001 306.91790359
-0.44430810 -0.85070849 -0.28086542 224.04826702
Axis -0.91496466 0.40022553 0.05156744
Axis point 0.00000000 298.35339518 -19.92897462
Rotation angle (degrees) 106.51585001
Shift along axis -82.16745292
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 28
shifted from previous position = 0.0215
rotated from previous position = 0.0203 degrees
atoms outside contour = 1170, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79080859 -0.51979573 0.32316277 236.68283087
-0.42075840 -0.07823684 0.90379277 306.90558108
-0.44450439 -0.85070053 -0.28057879 224.03446005
Axis -0.91492010 0.40031735 0.05164525
Axis point 0.00000000 298.38989078 -19.96369190
Rotation angle (degrees) 106.49929346
Shift along axis -82.11593248
> hide #!37 models
> show #!37 models
> hide #!36 models
> show #!36 models
> hide #!35 models
> show #!35 models
> show #!3 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #!26.1 models
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> ui mousemode right select
> hide #6 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #7 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240708_leaf_fitting_v33_labelled.cxs"
> hide #!40 models
> hide #!37 models
> hide #!36 models
> hide #!34 models
> show #!34 models
> hide #!35 models
> hide #!34 models
> hide #32.2 models
> hide #32.1 models
> hide #!32 models
> show #!32 models
> show #32.1 models
> show #32.2 models
> hide #!32 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #28 models
> hide #27.2 models
> show #27.2 models
> hide #!27 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> hide #!26.1 models
> hide #!26.2 models
> hide #26.3 models
> hide #27.1 models
> hide #27.2 models
> hide #!24 models
> hide #!25 models
> hide #!9 models
> hide #8 models
> hide #7 models
> hide #!4 models
> show #27.2 models
> show #!30 models
> hide #!30 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!34 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 48
shifted from previous position = 0.00273
rotated from previous position = 0.0242 degrees
atoms outside contour = 718, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98956810 0.01433697 -0.14335073 -45.82491729
0.02422267 0.96431254 0.26365620 -113.39654732
0.14201494 -0.26437811 0.95390564 -31.26296098
Axis -0.87962783 -0.47537740 0.01646812
Axis point 0.00000000 -165.70831636 238.71953494
Rotation angle (degrees) 17.46639833
Shift along axis 93.70018662
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 48
shifted from previous position = 0.000499
rotated from previous position = 0.00154 degrees
atoms outside contour = 718, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98956841 0.01434068 -0.14334821 -45.82626387
0.02422224 0.96430547 0.26368210 -113.40009857
0.14201285 -0.26440369 0.95389886 -31.25752997
Axis -0.87965054 -0.47533566 0.01646006
Axis point 0.00000000 -165.67596109 238.72518972
Rotation angle (degrees) 17.46769067
Shift along axis 93.69970795
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 48
shifted from previous position = 0.00016
rotated from previous position = 0.00118 degrees
atoms outside contour = 718, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98956880 0.01435531 -0.14334403 -45.82936380
0.02420915 0.96430157 0.26369756 -113.40235253
0.14201233 -0.26441712 0.95389522 -31.25478351
Axis -0.87966536 -0.47530985 0.01641326
Axis point 0.00000000 -165.64407090 238.72526660
Rotation angle (degrees) 17.46837305
Shift along axis 93.70276671
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 48
shifted from previous position = 0.000232
rotated from previous position = 0.0016 degrees
atoms outside contour = 718, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98956798 0.01433731 -0.14335150 -45.82514046
0.02422547 0.96430711 0.26367580 -113.39913149
0.14201527 -0.26439788 0.95390011 -31.25869132
Axis -0.87964184 -0.47535137 0.01647125
Axis point 0.00000000 -165.68626076 238.72206913
Rotation angle (degrees) 17.46745538
Shift along axis 93.69927359
> hide #27.2 models
> show #27.2 models
> show #25.1 models
> hide #!34 models
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 44
shifted from previous position = 0.0255
rotated from previous position = 0.0165 degrees
atoms outside contour = 1139, contour level = 0.0073311
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50785617 0.84619728 -0.16134517 226.54486618
-0.85933572 -0.51073828 0.02623942 400.55682789
-0.06020143 0.15197552 0.98654914 146.95470423
Axis 0.07339469 -0.05903963 -0.99555389
Axis point 229.78625014 128.44128536 0.00000000
Rotation angle (degrees) 121.06583536
Shift along axis -153.32286545
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 40
shifted from previous position = 0.0282
rotated from previous position = 0.0262 degrees
atoms outside contour = 1141, contour level = 0.0073311
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50777141 0.84631853 -0.16097555 226.47710304
-0.85941279 -0.51059812 0.02644248 400.51128673
-0.05981505 0.15177118 0.98660410 146.91059784
Axis 0.07314968 -0.05904360 -0.99557168
Axis point 229.73837123 128.43746238 0.00000000
Rotation angle (degrees) 121.05647504
Shift along axis -153.34093340
> fitmap #25.1 inMap #34
Fit molecule 5nzr_COPI_coat_leaf_2017.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3251 atoms
average map value = 0.01111, steps = 44
shifted from previous position = 0.0343
rotated from previous position = 0.0212 degrees
atoms outside contour = 1138, contour level = 0.0073311
Position of 5nzr_COPI_coat_leaf_2017.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.50786213 0.84621309 -0.16124345 226.53567475
-0.85933666 -0.51073604 0.02625237 400.56152237
-0.06013775 0.15189499 0.98656543 146.95013683
Axis 0.07333980 -0.05901717 -0.99555926
Axis point 229.78005640 128.45021909 0.00000000
Rotation angle (degrees) 121.06541504
Shift along axis -153.32349619
> hide #25.1 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009081, steps = 48
shifted from previous position = 0.000571
rotated from previous position = 0.00345 degrees
atoms outside contour = 718, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98956980 0.01437573 -0.14333510 -45.83431014
0.02419063 0.96429507 0.26372303 -113.40605851
0.14200855 -0.26443971 0.95388952 -31.25014824
Axis -0.87969326 -0.47526049 0.01634743
Axis point 0.00000000 -165.59514953 238.72926707
Rotation angle (degrees) 17.46944224
Shift along axis 93.70669324
> show #!34 models
> hide #!34 models
> show #!3 models
> select clear
[Repeated 3 time(s)]
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> ui mousemode right select
Drag select of 1 pseudobonds
> delete sel
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
[Repeated 1 time(s)]
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!3 models
> show #!3 models
> hide #27.2 models
Drag select of 179 residues
> delete sel
Drag select of 1 pseudobonds
> delete sel
> undo
[Repeated 1 time(s)]Undo failed, probably because structures have been
modified.
> close #1
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/Structure
> files/alphafold/CopA-F8WHL2.pdb"
CopA-F8WHL2.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit α (F8WHL2) [more
info...]
Chain information for CopA-F8WHL2.pdb #1
---
Chain | Description | UniProt
A | coatomer subunit α | F8WHL2_MOUSE 1-1233
> color #1 #0024ffff
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA_F8WHL2.pdb, chain A (#3) with CopA-F8WHL2.pdb, chain A (#1),
sequence alignment score = 5565.8
RMSD between 598 pruned atom pairs is 0.000 angstroms; (across all 654 pairs:
1.682)
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #32.2 models
> hide #32.1 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!34 models
> hide #!34 models
> hide #!3 models
Drag select of 156 residues
> select up
1558 atoms, 1584 bonds, 194 residues, 1 model selected
> select up
9810 atoms, 10032 bonds, 1233 residues, 1 model selected
> select down
1558 atoms, 1584 bonds, 194 residues, 1 model selected
Drag select of 197 residues
> select up
1710 atoms, 1739 bonds, 214 residues, 1 model selected
> delete sel
Drag select of 89 residues, 3 pseudobonds
> select up
1348 atoms, 1375 bonds, 3 pseudobonds, 177 residues, 2 models selected
> delete sel
Drag select of 8 residues
> delete sel
> show #!3 models
> hide #!3 models
> show #!30 models
> hide #!30 models
> show #27.2 models
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6696 atoms
average map value = 0.007765, steps = 68
shifted from previous position = 0.739
rotated from previous position = 0.952 degrees
atoms outside contour = 3587, contour level = 0.0073311
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.74504812 0.59199968 0.30731039 209.86635543
-0.12528750 0.57673472 -0.80726706 282.53055788
-0.65513841 0.56295065 0.50386528 266.54966434
Axis 0.75219668 0.52834728 -0.39376300
Axis point 0.00000000 -289.36381832 369.37988482
Rotation angle (degrees) 65.61763811
Shift along axis 202.17763230
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6696 atoms
average map value = 0.007764, steps = 40
shifted from previous position = 0.0353
rotated from previous position = 0.0293 degrees
atoms outside contour = 3596, contour level = 0.0073311
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.74507195 0.59194685 0.30735439 209.84046391
-0.12490471 0.57649071 -0.80750064 282.51296927
-0.65518441 0.56325606 0.50346400 266.52699347
Axis 0.75237628 0.52831502 -0.39346305
Axis point 0.00000000 -289.07271763 369.13608189
Rotation angle (degrees) 65.63718359
Shift along axis 202.26631021
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6696 atoms
average map value = 0.007764, steps = 28
shifted from previous position = 0.0364
rotated from previous position = 0.0161 degrees
atoms outside contour = 3589, contour level = 0.0073311
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.74506354 0.59198084 0.30730929 209.86888132
-0.12512801 0.57661233 -0.80737922 282.52551876
-0.65515136 0.56309582 0.50368621 266.54833056
Axis 0.75228442 0.52831619 -0.39363710
Axis point 0.00000000 -289.24096229 369.28145085
Rotation angle (degrees) 65.62663487
Shift along axis 202.22058227
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6696 atoms
average map value = 0.007764, steps = 44
shifted from previous position = 0.0344
rotated from previous position = 0.0145 degrees
atoms outside contour = 3594, contour level = 0.0073311
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.74510831 0.59194177 0.30727603 209.84031429
-0.12496767 0.57647605 -0.80750136 282.51167816
-0.65513105 0.56327640 0.50351068 266.53073234
Axis 0.75240063 0.52825170 -0.39350150
Axis point 0.00000000 -289.06685996 369.16873400
Rotation angle (degrees) 65.63503331
Shift along axis 202.24101644
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #27.2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA-F8WHL2.pdb, chain A (#1) with
3mkq_yeast_alpha_betaprimeCOPI.cif B, chain B (#27.2), sequence alignment
score = 481.9
RMSD between 128 pruned atom pairs is 0.920 angstroms; (across all 175 pairs:
3.040)
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6696 atoms
average map value = 0.007764, steps = 44
shifted from previous position = 0.0344
rotated from previous position = 0.0145 degrees
atoms outside contour = 3594, contour level = 0.0073311
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.74510831 0.59194177 0.30727603 209.84031429
-0.12496767 0.57647605 -0.80750136 282.51167816
-0.65513105 0.56327640 0.50351068 266.53073234
Axis 0.75240063 0.52825170 -0.39350150
Axis point 0.00000000 -289.06685996 369.16873400
Rotation angle (degrees) 65.63503331
Shift along axis 202.24101644
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009083, steps = 96
shifted from previous position = 11.1
rotated from previous position = 14.2 degrees
atoms outside contour = 717, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98957852 0.01454291 -0.14325800 -45.84740165
0.02408635 0.96415153 0.26425685 -113.49444007
0.14196549 -0.26495346 0.95375336 -31.15818392
Axis -0.88017677 -0.47438057 0.01587254
Axis point 0.00000000 -164.91280797 238.91025494
Rotation angle (degrees) 17.49528335
Shift along axis 93.69881529
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!1 to #27.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3mkq_yeast_alpha_betaprimeCOPI.cif B, chain B (#27.2) with
CopA-F8WHL2.pdb, chain A (#1), sequence alignment score = 481.9
RMSD between 128 pruned atom pairs is 0.920 angstroms; (across all 175 pairs:
3.040)
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
Drag select of 13 residues
> delete sel
Drag select of 149 residues
Drag select of 154 residues
> select up
1232 atoms, 1254 bonds, 155 residues, 1 model selected
> delete sel
> show #27.2 models
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 5369 atoms
average map value = 0.008503, steps = 88
shifted from previous position = 9.87
rotated from previous position = 14.7 degrees
atoms outside contour = 2569, contour level = 0.0073311
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.74613401 0.59321950 0.30228241 209.86370296
-0.11997346 0.56637890 -0.81536575 282.25496270
-0.65489725 0.57210625 0.49376516 266.21520350
Axis 0.75806648 0.52296970 -0.38966385
Axis point 0.00000000 -280.46538443 365.14298706
Rotation angle (degrees) 66.22543800
Shift along axis 202.96698955
> show #!34 models
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> hide #!1 models
> show #!1 models
> hide #!34 models
> show #!30 models
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009303, steps = 28
shifted from previous position = 0.0341
rotated from previous position = 0.0274 degrees
atoms outside contour = 1174, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79102377 -0.51948810 0.32313081 236.69401192
-0.42077528 -0.07856116 0.90375678 306.92760494
-0.44410536 -0.85085854 -0.28073150 224.06164756
Axis -0.91502074 0.40010879 0.05147811
Axis point 0.00000000 298.35529009 -19.95959041
Rotation angle (degrees) 106.50711717
Shift along axis -82.24122865
> hide #!1 models
> show #!1 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> ui mousemode right select
Drag select of 1 residues
Drag select of 31 residues
> select up
458 atoms, 466 bonds, 53 residues, 1 model selected
> select up
5369 atoms, 5500 bonds, 666 residues, 1 model selected
> select down
458 atoms, 466 bonds, 53 residues, 1 model selected
> delete sel
Drag select of 130 residues, 5 pseudobonds
> delete sel
Drag select of 103 residues, 9 pseudobonds
> select up
1024 atoms, 1036 bonds, 9 pseudobonds, 129 residues, 2 models selected
> delete sel
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2828 atoms
average map value = 0.008232, steps = 88
shifted from previous position = 1.5
rotated from previous position = 2.26 degrees
atoms outside contour = 1434, contour level = 0.0073311
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76973912 0.57262498 0.28213884 209.07872450
-0.11316399 0.55737848 -0.82251027 282.30528869
-0.62824804 0.60119037 0.49383654 267.66031403
Axis 0.78064812 0.49918627 -0.37603401
Axis point 0.00000000 -266.67800857 363.23324447
Rotation angle (degrees) 65.76519291
Shift along axis 203.49045495
> show #!34 models
> show #!30 models
> show #27.2 models
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2828 atoms
average map value = 0.008232, steps = 44
shifted from previous position = 0.0283
rotated from previous position = 0.0435 degrees
atoms outside contour = 1427, contour level = 0.0073311
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76961659 0.57283286 0.28205111 209.09137949
-0.11376863 0.55769249 -0.82221395 282.32528611
-0.62828895 0.60070093 0.49437980 267.68501324
Axis 0.78035887 0.49925118 -0.37654787
Axis point 0.00000000 -267.04771184 363.57213507
Rotation angle (degrees) 65.74210797
Shift along axis 203.32132493
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1407 atoms
average map value = 0.009083, steps = 48
shifted from previous position = 0.00597
rotated from previous position = 0.0186 degrees
atoms outside contour = 717, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.98958692 0.01431371 -0.14322309 -45.81333740
0.02426352 0.96421466 0.26401019 -113.45822597
0.14187677 -0.26473613 0.95382691 -31.20533647
Axis -0.88007902 -0.47453835 0.01656110
Axis point 0.00000000 -165.41785940 239.01187615
Rotation angle (degrees) 17.48145353
Shift along axis 93.64284212
> fitmap #30 inMap #34
Fit molecule 4j87_yeast_alphaCOPI.cif (#30) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2737 atoms
average map value = 0.009304, steps = 28
shifted from previous position = 0.0504
rotated from previous position = 0.047 degrees
atoms outside contour = 1169, contour level = 0.0073311
Position of 4j87_yeast_alphaCOPI.cif (#30) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.79064076 -0.52013247 0.32303159 236.67421339
-0.42073055 -0.07822749 0.90380655 306.89666144
-0.44482918 -0.85049555 -0.28068547 224.01557023
Axis -0.91485786 0.40043472 0.05183749
Axis point 0.00000000 298.39182963 -19.92191304
Rotation angle (degrees) 106.50721587
Shift along axis -82.01878235
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240708_leaf_fitting_v34_labelled.cxs"
> hide #!30 models
> hide #27.2 models
> hide #!1 models
> show #7 models
> hide #7 models
> show #27.1 models
> hide #!34 models
> show #7 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #7 to #27.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3mkq_yeast_alpha_betaprimeCOPI.cif A, chain A (#27.1) with
CopBprime_O55029.pdb, chain A (#7), sequence alignment score = 2455.4
RMSD between 517 pruned atom pairs is 0.958 angstroms; (across all 790 pairs:
3.624)
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 48
shifted from previous position = 0.0194
rotated from previous position = 0.0607 degrees
atoms outside contour = 2945, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99556882 0.00314645 0.09398307 -80.48372282
-0.00470546 0.99985491 0.01637118 -75.53389376
-0.09391792 -0.01674087 0.99543918 -68.55547662
Axis -0.17339992 0.98399275 -0.04111857
Axis point -800.05814897 0.00000000 924.82289501
Rotation angle (degrees) 5.47888119
Shift along axis -57.55002917
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 -0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> show #!34 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 -0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 -0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.89 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13119013 -0.23155876 -0.96393448 237.20355678
0.00439169 -0.97246439 0.23301013 213.62738725
-0.99134750 0.02633533 0.12859467 275.46492911
Axis -0.65639645 0.08706337 0.74937552
Axis point 228.27373609 105.75304677 0.00000000
Rotation angle (degrees) 170.94216411
Shift along axis 69.32622238
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 28
shifted from previous position = 0.0431
rotated from previous position = 0.0479 degrees
atoms outside contour = 2939, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99562004 0.00345097 0.09342818 -80.41290975
-0.00494862 0.99986288 0.01580295 -75.40022926
-0.09336083 -0.01619607 0.99550060 -68.64017862
Axis -0.16868570 0.98467481 -0.04427917
Axis point -807.22349213 0.00000000 926.92051736
Rotation angle (degrees) 5.44257527
Shift along axis -57.64086882
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 28
shifted from previous position = 0.0412
rotated from previous position = 0.0352 degrees
atoms outside contour = 2944, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99557079 0.00346147 0.09395116 -80.51283445
-0.00499735 0.99985762 0.01611732 -75.48425279
-0.09388199 -0.01651544 0.99544634 -68.57582442
Axis -0.17100048 0.98427338 -0.04432547
Axis point -802.39712605 0.00000000 923.77388963
Rotation angle (degrees) 5.47533051
Shift along axis -57.48975145
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.00913, steps = 44
shifted from previous position = 0.0408
rotated from previous position = 0.0274 degrees
atoms outside contour = 2939, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99558674 0.00368020 0.09377362 -80.49497003
-0.00517595 0.99986315 0.01571245 -75.38038534
-0.09370297 -0.01612848 0.99546955 -68.63492522
Axis -0.16726043 0.98481456 -0.04652137
Axis point -805.69492318 0.00000000 923.18001399
Rotation angle (degrees) 5.46189300
Shift along axis -57.57908693
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 44
shifted from previous position = 0.034
rotated from previous position = 0.0358 degrees
atoms outside contour = 2942, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99555643 0.00340933 0.09410514 -80.53037149
-0.00495438 0.99985667 0.01618957 -75.49091907
-0.09403646 -0.01658387 0.99543062 -68.56837507
Axis -0.17144703 0.98422131 -0.04375295
Axis point -800.75273762 0.00000000 922.68257308
Rotation angle (degrees) 5.48464047
Shift along axis -57.49301012
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.00913, steps = 44
shifted from previous position = 0.0336
rotated from previous position = 0.0327 degrees
atoms outside contour = 2940, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99557579 0.00369621 0.09388926 -80.51670044
-0.00519484 0.99986290 0.01572232 -75.38146501
-0.09381827 -0.01614050 0.99545850 -68.62961875
Axis -0.16717103 0.98482376 -0.04664768
Axis point -804.78365522 0.00000000 922.16302415
Rotation angle (degrees) 5.46859046
Shift along axis -57.57598531
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 64
shifted from previous position = 0.00589
rotated from previous position = 0.00894 degrees
atoms outside contour = 2939, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99557361 0.00357088 0.09391721 -80.50555370
-0.00507885 0.99986192 0.01582224 -75.39753821
-0.09384774 -0.01622920 0.99545428 -68.62415739
Axis -0.16809268 0.98472688 -0.04536323
Axis point -803.75002633 0.00000000 922.40898965
Rotation angle (degrees) 5.47080806
Shift along axis -57.60057463
> hide #!34 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #27.1 models
> show #27.1 models
> show #7 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #7 to #27.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3mkq_yeast_alpha_betaprimeCOPI.cif A, chain A (#27.1) with
CopBprime_O55029.pdb, chain A (#7), sequence alignment score = 2455.4
RMSD between 517 pruned atom pairs is 0.958 angstroms; (across all 790 pairs:
3.624)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 5284 atoms
average map value = 0.008583, steps = 48
shifted from previous position = 0.14
rotated from previous position = 0.745 degrees
atoms outside contour = 2530, contour level = 0.0073311
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90665218 0.40362707 0.12274770 209.67691237
-0.23919967 0.73148708 -0.63852185 283.03177820
-0.34751306 0.54955602 0.75975182 275.81749836
Axis 0.83062053 0.32877326 -0.44941927
Axis point 0.00000000 -386.46550217 532.01547934
Rotation angle (degrees) 45.65753367
Shift along axis 143.25752972
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 5284 atoms
average map value = 0.008583, steps = 40
shifted from previous position = 0.0095
rotated from previous position = 0.0126 degrees
atoms outside contour = 2529, contour level = 0.0073311
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90660849 0.40366478 0.12294623 209.68701855
-0.23909291 0.73148131 -0.63856844 283.03757552
-0.34770046 0.54953600 0.75968056 275.82022350
Axis 0.83057060 0.32901595 -0.44933393
Axis point 0.00000000 -386.51434698 531.90852668
Rotation angle (degrees) 45.66236913
Shift along axis 143.34836235
> fitmap #3 inMap #34
Fit molecule CopA_F8WHL2.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 5284 atoms
average map value = 0.008583, steps = 36
shifted from previous position = 0.00112
rotated from previous position = 0.0134 degrees
atoms outside contour = 2529, contour level = 0.0073311
Position of CopA_F8WHL2.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.90666262 0.40360359 0.12274782 209.67968108
-0.23918745 0.73150404 -0.63850700 283.03919042
-0.34749424 0.54955069 0.75976429 275.82218780
Axis 0.83062904 0.32876915 -0.44940655
Axis point 0.00000000 -386.48381822 532.03434149
Rotation angle (degrees) 45.65593678
Shift along axis 143.26428911
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.009129, steps = 28
shifted from previous position = 0.0459
rotated from previous position = 0.0427 degrees
atoms outside contour = 2940, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99552363 0.00341180 0.09445138 -80.59011687
-0.00497571 0.99985432 0.01632724 -75.52022536
-0.09438192 -0.01672411 0.99539558 -68.54190891
Axis -0.17224348 0.98408413 -0.04371059
Axis point -797.71248757 0.00000000 920.18898582
Rotation angle (degrees) 5.50563652
Shift along axis -57.44112491
> show #!34 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 60
shifted from previous position = 0.998
rotated from previous position = 4.91 degrees
atoms outside contour = 3026, contour level = 0.0073311
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13120990 -0.23154697 -0.96393462 237.20289761
0.00437986 -0.97246680 0.23300031 213.62737022
-0.99134493 0.02635005 0.12861142 275.46418453
Axis -0.65638947 0.08706420 0.74938154
Axis point 228.27213575 105.75135926 -0.00000000
Rotation angle (degrees) 170.94315167
Shift along axis 69.32958732
> hide #!34 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #7 models
> hide #27.1 models
> show #27.1 models
> fitmap #27.1 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6538 atoms
average map value = 0.00913, steps = 28
shifted from previous position = 0.0457
rotated from previous position = 0.0619 degrees
atoms outside contour = 2939, contour level = 0.0073311
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99560552 0.00359656 0.09357736 -80.45250014
-0.00508864 0.99986362 0.01571114 -75.37948401
-0.09350809 -0.01611828 0.99548804 -68.64346831
Axis -0.16754757 0.98480336 -0.04571819
Axis point -806.89472186 0.00000000 925.01065336
Rotation angle (degrees) 5.45052511
Shift along axis -57.61609285
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #32.1 models
> show #!4 models
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7211 atoms
average map value = 0.009134, steps = 48
shifted from previous position = 0.016
rotated from previous position = 0.013 degrees
atoms outside contour = 3428, contour level = 0.0073311
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02190054 -0.73060769 0.68244617 220.15974033
-0.01329605 0.68276237 0.73051952 241.08944678
-0.99967174 0.00692493 -0.02466706 272.98068147
Axis -0.36793573 0.85532879 0.36474096
Axis point 254.82558488 0.00000000 -62.21074267
Rotation angle (degrees) 100.48060128
Shift along axis 224.77334454
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 48
shifted from previous position = 0.0114
rotated from previous position = 0.0315 degrees
atoms outside contour = 1320, contour level = 0.0073311
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99554492 -0.07909143 0.05133089 253.49540545
0.06846252 0.98068108 0.18324164 192.96045198
-0.06483207 -0.17891104 0.98172687 287.89487728
Axis -0.88774495 0.28475028 0.36169902
Axis point 0.00000000 1840.70608600 -961.47810858
Rotation angle (degrees) 11.76940835
Shift along axis -65.96242614
> hide #32.1 models
> show #32.1 models
> hide #!4 models
> show #!4 models
> show #!34 models
> hide #!34 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
Drag select of 94 residues
> select up
830 atoms, 842 bonds, 105 residues, 1 model selected
> delete sel
Drag select of 132 residues, 1 pseudobonds
> delete sel
> show #32.1 models
> hide #32.1 models
Drag select of 79 residues, 1 pseudobonds
> select up
728 atoms, 735 bonds, 1 pseudobond, 93 residues, 2 models selected
> delete sel
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
Drag select of 12 residues, 1 pseudobonds
> select clear
[Repeated 1 time(s)]Drag select of 30 residues, 1 pseudobonds
> select up
280 atoms, 278 bonds, 1 pseudobond, 35 residues, 2 models selected
> delete sel
> show #32.1 models
> hide #32.1 models
Drag select of 11 residues
> delete sel
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
Drag select of 18 residues
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> delete sel
> show #32.1 models
> hide #!4 models
> show #!4 models
> show #!34 models
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4053 atoms
average map value = 0.00875, steps = 84
shifted from previous position = 0.663
rotated from previous position = 1.09 degrees
atoms outside contour = 1917, contour level = 0.0073311
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02330996 -0.73054950 0.68246178 220.11377170
-0.03222225 0.68284160 0.72985551 241.56432118
-0.99920887 -0.00497756 -0.03945696 273.35537315
Axis -0.37423079 0.85642978 0.35563935
Axis point 256.52305737 0.00000000 -59.47243657
Rotation angle (degrees) 100.95060483
Shift along axis 221.72545586
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4053 atoms
average map value = 0.00875, steps = 44
shifted from previous position = 0.00769
rotated from previous position = 0.0192 degrees
atoms outside contour = 1917, contour level = 0.0073311
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02322843 -0.73068717 0.68231716 220.11112695
-0.03197079 0.68269515 0.73000356 241.56483053
-0.99921885 -0.00485738 -0.03921858 273.34926672
Axis -0.37423858 0.85634658 0.35583144
Axis point 256.51701092 0.00000000 -59.53984280
Rotation angle (degrees) 100.94554389
Shift along axis 221.75540414
> hide #!34 models
> fitmap #32.1 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2991 atoms
average map value = 0.01065, steps = 44
shifted from previous position = 0.0433
rotated from previous position = 0.0426 degrees
atoms outside contour = 1326, contour level = 0.0073311
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99550918 -0.07964090 0.05117412 253.51946298
0.06906069 0.98072053 0.18280553 192.97867574
-0.06474631 -0.17845047 0.98181635 287.90390194
Axis -0.88651951 0.28446788 0.36491257
Axis point 0.00000000 1843.87837432 -962.01397733
Rotation angle (degrees) 11.75631197
Shift along axis -64.79396291
> show #!34 models
> hide #32.1 models
> show #32.1 models
> hide #!4 models
> show #!4 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!4 models
> hide #!27 models
> show #!26.2 models
> hide #!34 models
> hide #32.1 models
> hide #!32 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> hide #!9 models
> show #!4 models
> hide #!4 models
> show #!9 models
> show #!26.2 models
> ui tool show Matchmaker
> matchmaker #!9 to #26.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B, chain B (#26.2) with
CopG_Q9QZE5, chain A (#9), sequence alignment score = 1225.6
RMSD between 134 pruned atom pairs is 0.962 angstroms; (across all 264 pairs:
3.567)
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> show #!34 models
> hide #!26.2 models
> show #!26.2 models
> hide #!9 models
> show #!9 models
> hide #!34 models
> hide #!9 models
> show #!34 models
> show #!9 models
> hide #!9 models
> hide #!26.2 models
> show #!26.2 models
> hide #!34 models
> show #!9 models
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 4566 atoms
average map value = 0.01074, steps = 80
shifted from previous position = 3.34
rotated from previous position = 5.13 degrees
atoms outside contour = 2028, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49909802 -0.51905420 -0.69389041 274.35179074
0.54047840 -0.43944705 0.71747431 318.90217910
-0.67733615 -0.73312279 0.06121043 295.12418884
Axis -0.80749448 -0.00921515 0.58980314
Axis point 0.00000000 283.39239014 124.73019154
Rotation angle (degrees) 116.07640404
Shift along axis -50.41111464
> hide #!26.2 models
Drag select of 110 residues
> select up
890 atoms, 903 bonds, 113 residues, 1 model selected
> delete sel
Drag select of 91 residues
> delete sel
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 2967 atoms
average map value = 0.01054, steps = 48
shifted from previous position = 0.34
rotated from previous position = 2.65 degrees
atoms outside contour = 1301, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.50694806 -0.52845739 -0.68098197 274.69010864
0.50218549 -0.46103022 0.73161524 318.98755518
-0.70058075 -0.71287020 0.03166526 293.78792105
Axis -0.81398555 0.01104416 0.58078012
Axis point 0.00000000 281.65107335 125.70418936
Rotation angle (degrees) 117.46511421
Shift along axis -49.44464915
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 2967 atoms
average map value = 0.01054, steps = 44
shifted from previous position = 0.0334
rotated from previous position = 0.0167 degrees
atoms outside contour = 1307, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.50719854 -0.52835467 -0.68087516 274.66421831
0.50208682 -0.46096711 0.73172272 318.96544548
-0.70047018 -0.71298713 0.03147807 293.79283152
Axis -0.81408188 0.01104163 0.58064513
Axis point 0.00000000 281.64332366 125.67569448
Rotation angle (degrees) 117.46103343
Shift along axis -49.48788799
> hide #!26.2 models
Drag select of 47 residues
> delete sel
Drag select of 2 pseudobonds
> delete sel
Drag select of 5 residues, 4 pseudobonds
> select clear
Drag select of 3 residues, 3 pseudobonds
> delete sel
Drag select of 1 residues, 1 pseudobonds
> delete sel
> show #!26.2 models
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 2556 atoms
average map value = 0.01067, steps = 44
shifted from previous position = 0.132
rotated from previous position = 1.24 degrees
atoms outside contour = 1127, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.50346645 -0.54606842 -0.66957510 275.34669305
0.49757014 -0.45030989 0.74138044 318.56014835
-0.70636074 -0.70642075 0.04499141 293.43524311
Axis -0.81103737 0.02060678 0.58463129
Axis point 0.00000000 284.08429210 124.79243856
Rotation angle (degrees) 116.80311155
Shift along axis -45.20053501
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 2556 atoms
average map value = 0.01067, steps = 44
shifted from previous position = 0.0204
rotated from previous position = 0.0722 degrees
atoms outside contour = 1122, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.50388998 -0.54672525 -0.66871996 275.37547012
0.49734592 -0.44933645 0.74212114 318.52128539
-0.70621662 -0.70653255 0.04549543 293.46301271
Axis -0.81107915 0.02099381 0.58455956
Axis point 0.00000000 284.26016119 124.66985760
Rotation angle (degrees) 116.74211330
Shift along axis -45.11771772
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
Drag select of 14 residues, 3 pseudobonds
> select up
150 atoms, 148 bonds, 3 pseudobonds, 19 residues, 2 models selected
> select down
111 atoms, 3 pseudobonds, 14 residues, 2 models selected
> select up
150 atoms, 148 bonds, 3 pseudobonds, 19 residues, 2 models selected
> delete sel
Drag select of 1 residues, 2 pseudobonds
> delete sel
Drag select of 1 pseudobonds
Drag select of 1 residues, 2 pseudobonds
> select clear
Drag select of 2 residues, 2 pseudobonds
> delete sel
Drag select of 2 pseudobonds
> delete sel
Drag select of 1 pseudobonds
[Repeated 1 time(s)]
> select up
3 pseudobonds, 1 model selected
> select down
1 pseudobond, 1 model selected
> select down
1 pseudobond, 1 model selected
> select up
3 pseudobonds, 1 model selected
> select down
1 pseudobond, 1 model selected
> select up
3 pseudobonds, 1 model selected
> select down
1 pseudobond, 1 model selected
> select up
3 pseudobonds, 1 model selected
> delete sel
> show #!26.2 models
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 2387 atoms
average map value = 0.01097, steps = 48
shifted from previous position = 0.248
rotated from previous position = 1.1 degrees
atoms outside contour = 1022, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49155273 -0.56119812 -0.66590733 275.57602159
0.49529023 -0.44878681 0.74382658 318.38781306
-0.71628451 -0.69544739 0.05735357 292.72367981
Axis -0.80581155 0.02820485 0.59149998
Axis point 0.00000000 284.91739309 125.39260440
Rotation angle (degrees) 116.73985088
Shift along axis -39.93621102
> hide #!26.2 models
Drag select of 10 residues, 1 pseudobonds
> delete sel
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 2320 atoms
average map value = 0.01101, steps = 44
shifted from previous position = 0.0826
rotated from previous position = 0.368 degrees
atoms outside contour = 997, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.49545404 -0.56085852 -0.66329708 275.65475289
0.49656935 -0.44365201 0.74605078 318.22072220
-0.71270202 -0.69900687 0.05869596 293.01955930
Axis -0.80670507 0.02758037 0.59031030
Axis point 0.00000000 285.62651096 124.66198228
Rotation angle (degrees) 116.40740917
Shift along axis -40.62297843
> show #!26.2 models
> hide #!26.2 models
Drag select of 17 residues, 2 pseudobonds
> delete sel
> show #!26.2 models
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 2198 atoms
average map value = 0.01107, steps = 64
shifted from previous position = 0.0821
rotated from previous position = 0.57 degrees
atoms outside contour = 938, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.48746773 -0.56652448 -0.66439840 275.59439501
0.49867194 -0.44398039 0.74445128 318.28970725
-0.71672973 -0.69421281 0.06608375 292.75462419
Axis -0.80334240 0.02922154 0.59480004
Axis point 0.00000000 285.75896486 125.23483142
Rotation angle (degrees) 116.43706053
Shift along axis -37.96528696
> hide #!26.2 models
Drag select of 3 residues, 1 pseudobonds
> delete sel
Drag select of 3 pseudobonds
> delete sel
[Repeated 2 time(s)]
> hide #!9 models
> show #!9 models
Drag select of 1 pseudobonds
> delete sel
[Repeated 1 time(s)]
> select clear
Drag select of 3 pseudobonds
> delete sel
> ui mousemode right "map eraser"
> ui mousemode right select
Drag select of 1 pseudobonds
> select add #9
2173 atoms, 2202 bonds, 4 pseudobonds, 277 residues, 2 models selected
> select subtract #9
Nothing selected
> select clear
Drag select of 1 pseudobonds
> delete sel
> fitmap #9 inMap #34
Fit molecule CopG_Q9QZE5 (#9) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 2173 atoms
average map value = 0.01105, steps = 36
shifted from previous position = 0.0381
rotated from previous position = 0.188 degrees
atoms outside contour = 934, contour level = 0.0073311
Position of CopG_Q9QZE5 (#9) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.48672193 -0.56899802 -0.66282955 275.67132143
0.49682989 -0.44379152 0.74579430 318.21999902
-0.71851362 -0.69230797 0.06669216 292.62144714
Axis -0.80301721 0.03109325 0.59514416
Axis point 0.00000000 285.90801042 125.25047280
Rotation angle (degrees) 116.43541348
Shift along axis -37.32237979
> show #!26.2 models
> show #!34 models
> select add #9
2173 atoms, 2202 bonds, 4 pseudobonds, 277 residues, 2 models selected
> select subtract #9
Nothing selected
> hide #!9 models
> hide #!34 models
> hide #!26.2 models
> show #!9 models
> hide #!9 models
> show #8 models
> hide #!26 models
> show #32.2 models
> fitmap #8 inMap #34
Fit molecule CopD_Q5XJY5 (#8) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 1462 atoms
average map value = 0.00841, steps = 40
shifted from previous position = 0.0348
rotated from previous position = 0.104 degrees
atoms outside contour = 714, contour level = 0.0073311
Position of CopD_Q5XJY5 (#8) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.07010812 0.98860161 0.13323554 -99.31408813
-0.91255617 0.00961540 0.40883835 163.15937558
0.40289713 -0.15024780 0.90282861 445.76147651
Axis -0.27955371 -0.13483593 -0.95061506
Axis point -59.51477087 162.67491243 0.00000000
Rotation angle (degrees) 90.49985085
Shift along axis -417.98369690
> fitmap #32.2 inMap #34
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1222 atoms
average map value = 0.009669, steps = 44
shifted from previous position = 0.0317
rotated from previous position = 0.0449 degrees
atoms outside contour = 491, contour level = 0.0073311
Position of 5mu7_Thermophila_beta_deltaCOPI.cif B (#32.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.97963550 0.04166777 0.19641305 249.13094960
-0.05652550 0.99589796 0.07065489 194.54481704
-0.19266333 -0.08031839 0.97797229 284.12672109
Axis -0.35213506 0.90749463 -0.22902925
Axis point 1633.48529893 0.00000000 -1141.61503211
Rotation angle (degrees) 12.37847660
Shift along axis 23.74730487
> hide #8 models
> show #8 models
> show #!34 models
> hide #32.2 models
> show #32.1 models
> hide #8 models
> show #!4 models
> hide #!34 models
> hide #32.1 models
> show #32.1 models
> hide #!32 models
> hide #32.1 models
> show #28 models
> hide #!4 models
> show #10 models
> hide #10 models
> show #12 models
> hide #28 models
> show #28 models
> show #!34 models
> hide #12 models
> show #10 models
> hide #10 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #12 models
> show #!26.1 models
> hide #28 models
> hide #!26.1 models
> show #!35 models
> hide #!35 models
> show #!36 models
> show #!37 models
> hide #!36 models
> show #5 models
> hide #5 models
> show #6 models
> hide #!34 models
> hide #6 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!34 models
> hide #!37 models
> hide #!26 models
> view orient
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!34 models
> show #!30 models
> show #27.2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> close #3
> show #!1 models
> show #!34 models
> show #!4 models
> show #8 models
> show #!9 models
> show #!24 models
> show #!26.1 models
> show #!26.2 models
> show #26.3 models
> show #28 models
> show #!29 models
> show #32.1 models
> show #32.2 models
> show #!35 models
> show #!36 models
> show #!37 models
> show #38 models
> hide #38 models
> show #39 models
> hide #39 models
> show #!40 models
> close #39
> close #38
> show #27.1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240708_leaf_fitting_v35_labelled.cxs"
> hide #!4 models
> show #!4 models
> hide #!34 models
> show #!34 models
> hide #!26 models
> hide #!27 models
> hide #!34 models
> hide #!35 models
> hide #!36 models
> hide #!37 models
> hide #!40 models
> hide #32.2 models
> hide #!30 models
> hide #!29 models
> hide #28 models
> show #28 models
> hide #28 models
> hide #!24 models
> hide #!9 models
> hide #8 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!34 models
> volume #34 level 0.00463
> show #!26 models
> show #!27 models
> show #!30 models
> show #28 models
> show #!29 models
> show #!1 models
> show #8 models
> show #!9 models
> show #!35 models
> show #!36 models
> show #!37 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240708_leaf_fitting_v36_labelled.cxs"
——— End of log from Mon Jul 8 16:31:05 2024 ———
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #8 models
> hide #!9 models
> hide #!26 models
> hide #!27 models
> show #!27 models
> hide #27.2 models
> hide #28 models
> hide #!29 models
> hide #!32 models
> hide #32.1 models
> hide #!35 models
> hide #!36 models
> hide #!37 models
> hide #27.1 models
> show #27.2 models
> hide #!34 models
> hide #27.2 models
> hide #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!1 models
> hide #!30 models
> ui mousemode right select
Drag select of 6 residues
> delete sel
> show #!30 models
> hide #!30 models
Drag select of 1 residues
> delete sel
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2771 atoms
average map value = 0.008155, steps = 80
shifted from previous position = 0.211
rotated from previous position = 0.555 degrees
atoms outside contour = 871, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76345177 0.57888387 0.28641728 208.93049254
-0.11441205 0.55766611 -0.82214256 282.30992585
-0.63565027 0.59489661 0.49198248 267.72071042
Axis 0.77550079 0.50461845 -0.37941896
Axis point 0.00000000 -268.97623519 363.55859518
Rotation angle (degrees) 66.01169394
Shift along axis 202.90624492
> show #!30 models
> show #27.2 models
> hide #!30 models
> hide #!1 models
> show #!1 models
> show #!30 models
> hide #27.2 models
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2771 atoms
average map value = 0.008156, steps = 80
shifted from previous position = 0.0143
rotated from previous position = 0.0356 degrees
atoms outside contour = 871, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76333102 0.57877816 0.28695227 208.94720365
-0.11421575 0.55810949 -0.82186894 282.31642752
-0.63583058 0.59458358 0.49212787 267.71075564
Axis 0.77526812 0.50506749 -0.37929693
Axis point 0.00000000 -269.27280295 363.51062044
Rotation angle (degrees) 65.99701789
Shift along axis 203.03709012
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2771 atoms
average map value = 0.008155, steps = 84
shifted from previous position = 0.0375
rotated from previous position = 0.0476 degrees
atoms outside contour = 872, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76340944 0.57903839 0.28621771 208.94170314
-0.11495598 0.55784514 -0.82194521 282.33128471
-0.63560298 0.59457829 0.49242817 267.74785764
Axis 0.77532859 0.50455494 -0.37985509
Axis point 0.00000000 -269.22508204 363.86197383
Rotation angle (degrees) 65.99343122
Shift along axis 202.74473322
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2771 atoms
average map value = 0.008156, steps = 76
shifted from previous position = 0.00939
rotated from previous position = 0.0197 degrees
atoms outside contour = 874, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76335812 0.57894538 0.28654253 208.94383715
-0.11474512 0.55805259 -0.82183384 282.33157319
-0.63570271 0.59447418 0.49242513 267.73980999
Axis 0.77523958 0.50480616 -0.37970295
Axis point 0.00000000 -269.33631433 363.78136540
Rotation angle (degrees) 65.98863033
Shift along axis 202.84265534
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2771 atoms
average map value = 0.008155, steps = 64
shifted from previous position = 0.0263
rotated from previous position = 0.0287 degrees
atoms outside contour = 869, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76334765 0.57904701 0.28636504 208.93346258
-0.11461033 0.55766302 -0.82211704 282.30534689
-0.63573960 0.59474072 0.49205552 267.74112927
Axis 0.77539505 0.50463455 -0.37961360
Axis point 0.00000000 -269.06088199 363.65441165
Rotation angle (degrees) 66.01276541
Shift along axis 202.82883214
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2771 atoms
average map value = 0.008155, steps = 84
shifted from previous position = 0.0277
rotated from previous position = 0.0388 degrees
atoms outside contour = 872, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76328504 0.57889200 0.28684489 208.95713954
-0.11453396 0.55820402 -0.82176045 282.33242854
-0.63582853 0.59438398 0.49237157 267.73728030
Axis 0.77515473 0.50504358 -0.37956044
Axis point -0.00000000 -269.42840638 363.69522541
Rotation angle (degrees) 65.98785262
Shift along axis 202.94181503
> show #27.2 models
> hide #!1 models
> show #!1 models
> hide #27.2 models
> show #27.2 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!30 models
> hide #!34 models
> hide #27.2 models
> ui mousemode right select
Drag select of 14 residues
> delete sel
> show #!34 models
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2662 atoms
average map value = 0.00815, steps = 124
shifted from previous position = 0.121
rotated from previous position = 0.688 degrees
atoms outside contour = 827, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76721005 0.57679881 0.28052073 208.92511024
-0.11147861 0.55061919 -0.82727929 282.31807879
-0.63163381 0.60342492 0.48674130 267.50075303
Axis 0.78136633 0.49816506 -0.37589657
Axis point -0.00000000 -262.54380394 361.43249335
Rotation angle (degrees) 66.27888011
Shift along axis 203.33543503
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2662 atoms
average map value = 0.00815, steps = 104
shifted from previous position = 0.0272
rotated from previous position = 0.0442 degrees
atoms outside contour = 829, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76735078 0.57654760 0.28065217 208.91656123
-0.11083223 0.55034554 -0.82754819 282.29952623
-0.63157660 0.60391444 0.48620813 267.47361378
Axis 0.78165565 0.49812602 -0.37534639
Axis point 0.00000000 -262.19588118 361.08511508
Rotation angle (degrees) 66.29972170
Shift along axis 203.52629268
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2662 atoms
average map value = 0.00815, steps = 96
shifted from previous position = 0.0103
rotated from previous position = 0.0355 degrees
atoms outside contour = 830, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76729951 0.57642489 0.28104414 208.92543386
-0.11082751 0.55084691 -0.82721517 282.31298248
-0.63163971 0.60357438 0.48654830 267.47749914
Axis 0.78143623 0.49846899 -0.37534795
Axis point 0.00000000 -262.53711812 361.15091334
Rotation angle (degrees) 66.27499439
Shift along axis 203.58904116
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2662 atoms
average map value = 0.00815, steps = 76
shifted from previous position = 0.0115
rotated from previous position = 0.0432 degrees
atoms outside contour = 829, contour level = 0.0046305
Position of CopA-F8WHL2.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76729038 0.57673478 0.28043266 208.90991965
-0.11114998 0.55026756 -0.82755743 282.29976135
-0.63159414 0.60380677 0.48631906 267.48105056
Axis 0.78159676 0.49801245 -0.37561963
Axis point -0.00000000 -262.21899930 361.22198079
Rotation angle (degrees) 66.30058043
Shift along axis 203.40097692
> hide #!34 models
Drag select of 1 residues
> delete sel
> show #27.2 models
> show #!34 models
> hide #!34 models
> hide #!1 models
Drag select of 1 residues
Drag select of 3 residues
> delete sel
Drag select of 1 residues
> delete sel
> show #!1 models
Drag select of 1 residues
> select #1/A:651
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 1 residues
Drag select of 3 residues
> show sel atoms
[Repeated 2 time(s)]
> style sel stick
Changed 23 atom styles
> select add #1
2669 atoms, 2707 bonds, 334 residues, 2 models selected
> select subtract #1
16 atoms, 2 residues, 1 model selected
> select add #27.2
1374 atoms, 1381 bonds, 190 residues, 1 model selected
> select subtract #27.2
Nothing selected
> hide #27.2#!1 atoms
> show #!34 models
> hide #!34 models
> hide #27.2 models
> hide #!1 models
> show #!34 models
> show #7 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009017, steps = 44
shifted from previous position = 0.0172
rotated from previous position = 0.071 degrees
atoms outside contour = 2264, contour level = 0.0046305
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13037522 -0.23222210 -0.96388547 237.21265190
0.00507906 -0.97232699 0.23356887 213.62414076
-0.99145171 0.02555596 0.12794681 275.48305004
Axis -0.65667553 0.08702383 0.74913557
Axis point 228.30486617 105.84568006 0.00000000
Rotation angle (degrees) 170.88692890
Shift along axis 69.19279888
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 6695 atoms
average map value = 0.009016, steps = 44
shifted from previous position = 0.00626
rotated from previous position = 0.00774 degrees
atoms outside contour = 2263, contour level = 0.0046305
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.13036153 -0.23228328 -0.96387257 237.21353161
0.00520514 -0.97231549 0.23361396 213.62027007
-0.99145286 0.02543719 0.12796160 275.47804476
Axis -0.65667642 0.08699973 0.74913759
Axis point 228.29425794 105.86016341 0.00000000
Rotation angle (degrees) 170.87970124
Shift along axis 69.18333184
> hide #!34 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v37_labelled.cxs"
> close #2
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopBprime_O55029.pdb"
CopBprime_O55029.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit β' (O55029) [more
info...]
Chain information for CopBprime_O55029.pdb #2
---
Chain | Description | UniProt
A | coatomer subunit β' | COPB2_MOUSE 1-905
> color #2 cyan
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopBprime_O55029.pdb, chain A (#7) with CopBprime_O55029.pdb, chain
A (#2), sequence alignment score = 4630.6
RMSD between 838 pruned atom pairs is 0.000 angstroms; (across all 838 pairs:
0.000)
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> show #!34 models
> hide #2 models
> hide #!34 models
> show #2 models
> hide #7 models
Drag select of 11 residues
> select up
519 atoms, 525 bonds, 67 residues, 1 model selected
> delete sel
> show #7 models
> hide #7 models
> show #7 models
> hide #2 models
> show #2 models
Drag select of 414 residues
> select up
3448 atoms, 3514 bonds, 436 residues, 2 models selected
Drag select of 484 residues
> select up
3988 atoms, 4064 bonds, 500 residues, 2 models selected
> combine sel
Remapping chain ID 'A' in CopBprime_O55029.pdb #7 to 'B'
> select add #2
8689 atoms, 8879 bonds, 1088 residues, 2 models selected
> select subtract #2
1994 atoms, 2032 bonds, 250 residues, 1 model selected
> delete sel
> hide #3 models
> hide #2 models
Drag select of 2 residues, 1 pseudobonds
> delete sel
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #3 models
> hide #3 models
> show #3 models
> show #2 models
> hide #2 models
> hide #3 models
> hide #!7 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!7 models
> hide #!7 models
> show #3 models
> show #!7 models
> hide #!7 models
> hide #3 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> show #!7 models
> show #!34 models
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4686 atoms
average map value = 0.009331, steps = 56
shifted from previous position = 0.857
rotated from previous position = 4.01 degrees
atoms outside contour = 1365, contour level = 0.0046305
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.18382139 -0.18803254 -0.96480747 236.85450936
0.00729281 -0.98176700 0.18994833 212.89973190
-0.98293261 0.02788041 0.18184106 275.49974843
Axis -0.63692579 0.07123166 0.76762725
Axis point 224.08999267 105.52981372 0.00000000
Rotation angle (degrees) 172.69063725
Shift along axis 75.78756851
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4686 atoms
average map value = 0.009331, steps = 48
shifted from previous position = 0.0294
rotated from previous position = 0.0588 degrees
atoms outside contour = 1364, contour level = 0.0046305
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.18351764 -0.18857053 -0.96476029 236.87734116
0.00658726 -0.98164233 0.19061723 212.90804390
-0.98299434 0.02862650 0.18139084 275.47318612
Axis -0.63704804 0.07170759 0.76748148
Axis point 224.13935981 105.44289980 0.00000000
Rotation angle (degrees) 172.69554744
Shift along axis 75.78544446
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4686 atoms
average map value = 0.009331, steps = 56
shifted from previous position = 0.857
rotated from previous position = 4.01 degrees
atoms outside contour = 1365, contour level = 0.0046305
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.18382139 -0.18803254 -0.96480747 236.85450936
0.00729281 -0.98176700 0.18994833 212.89973190
-0.98293261 0.02788041 0.18184106 275.49974843
Axis -0.63692579 0.07123166 0.76762725
Axis point 224.08999267 105.52981372 0.00000000
Rotation angle (degrees) 172.69063725
Shift along axis 75.78756851
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4686 atoms
average map value = 0.009331, steps = 48
shifted from previous position = 0.0294
rotated from previous position = 0.0588 degrees
atoms outside contour = 1364, contour level = 0.0046305
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.18351764 -0.18857053 -0.96476029 236.87734116
0.00658726 -0.98164233 0.19061723 212.90804390
-0.98299434 0.02862650 0.18139084 275.47318612
Axis -0.63704804 0.07170759 0.76748148
Axis point 224.13935981 105.44289980 0.00000000
Rotation angle (degrees) 172.69554744
Shift along axis 75.78544446
> fitmap #7 inMap #34
Fit molecule CopBprime_O55029.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4686 atoms
average map value = 0.009331, steps = 48
shifted from previous position = 0.00591
rotated from previous position = 0.0108 degrees
atoms outside contour = 1364, contour level = 0.0046305
Position of CopBprime_O55029.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.18348706 -0.18866650 -0.96474735 236.88099484
0.00644898 -0.98161951 0.19073949 212.90869913
-0.98300097 0.02877659 0.18133119 275.46732152
Axis -0.63706082 0.07179834 0.76746238
Axis point 224.14561608 105.42520113 0.00000000
Rotation angle (degrees) 172.69695653
Shift along axis 75.78969715
> hide #!34 models
> show #!34 models
> hide #!34 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #3 models
> hide #!7 models
Drag select of 1156 residues
> select up
9356 atoms, 9578 bonds, 1170 residues, 1 model selected
> delete sel
> show #!34 models
> fitmap #3 inMap #34
Fit molecule combination (#3) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 4034 atoms
average map value = 0.009676, steps = 72
shifted from previous position = 1.07
rotated from previous position = 3.24 degrees
atoms outside contour = 1464, contour level = 0.0046305
Position of combination (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.09135641 -0.26647558 -0.95950236 236.85335835
0.03080497 -0.96382670 0.26474354 213.36709311
-0.99534168 -0.00537142 0.09626052 277.10719384
Axis -0.66982079 0.08887299 0.73718498
Axis point 229.97457226 109.33292722 0.00000000
Rotation angle (degrees) 168.36757452
Shift along axis 64.59252983
> fitmap #3 inMap #34
Fit molecule combination (#3) to map relion_locres_filtered_20240326_GT.mrc
(#34) using 4034 atoms
average map value = 0.009675, steps = 48
shifted from previous position = 0.0204
rotated from previous position = 0.0825 degrees
atoms outside contour = 1466, contour level = 0.0046305
Position of combination (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.09042542 -0.26652009 -0.95957818 236.89404424
0.03189874 -0.96380625 0.26468846 213.38303781
-0.99539224 -0.00667477 0.09565424 277.11938100
Axis -0.67013594 0.08844341 0.73695019
Axis point 230.02990386 109.49648079 0.00000000
Rotation angle (degrees) 168.31863565
Shift along axis 64.34428851
> hide #!34 models
> show #!7 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #2
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #3 CopBprime_O55029.pdb
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> rename #3 CopBprime_O55029_solenoid.pdb
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> rename #7 CopBprime_O55029_beta_props.pdb
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> show #!34 models
> hide #!34 models
> hide #!3 models
> hide #!7 models
> show #!1 models
> rename #1 CopA-F8WHL2_E320-V651.pdb
> hide #!1 models
> close #13
> close #14
> close #15
> close #16
> close #17
> close #18
> close #19
> close #20
> close #21
> close #22
> close #23
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!34 models
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2_E320-V651.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2653 atoms
average map value = 0.008168, steps = 80
shifted from previous position = 0.0284
rotated from previous position = 0.0393 degrees
atoms outside contour = 819, contour level = 0.0046305
Position of CopA-F8WHL2_E320-V651.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76766827 0.57618568 0.28052716 208.93708075
-0.11090966 0.55059127 -0.82737434 282.32456434
-0.63117706 0.60403586 0.48657600 267.49371213
Axis 0.78180163 0.49795079 -0.37527486
Axis point 0.00000000 -262.29142513 361.19565696
Rotation angle (degrees) 66.27058784
Shift along axis 203.54742588
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2_E320-V651.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2653 atoms
average map value = 0.008168, steps = 96
shifted from previous position = 0.0317
rotated from previous position = 0.0689 degrees
atoms outside contour = 821, contour level = 0.0046305
Position of CopA-F8WHL2_E320-V651.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76760054 0.57646141 0.28014577 208.91467280
-0.11057666 0.54964981 -0.82804462 282.29207163
-0.63131784 0.60462991 0.48565467 267.45428422
Axis 0.78213018 0.49758908 -0.37506998
Axis point -0.00000000 -261.61679014 360.88280205
Rotation angle (degrees) 66.33098692
Shift along axis 203.54984830
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2_E320-V651.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2653 atoms
average map value = 0.008168, steps = 80
shifted from previous position = 0.00676
rotated from previous position = 0.0138 degrees
atoms outside contour = 821, contour level = 0.0046305
Position of CopA-F8WHL2_E320-V651.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76768046 0.57644333 0.27996392 208.90568347
-0.11076225 0.54965468 -0.82801658 282.29416732
-0.63118811 0.60464272 0.48580732 267.46074649
Axis 0.78216631 0.49744725 -0.37518275
Axis point 0.00000000 -261.62563490 360.97838193
Rotation angle (degrees) 66.32355949
Shift along axis 203.47878638
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2_E320-V651.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2653 atoms
average map value = 0.008168, steps = 80
shifted from previous position = 0.0302
rotated from previous position = 0.0497 degrees
atoms outside contour = 819, contour level = 0.0046305
Position of CopA-F8WHL2_E320-V651.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76758721 0.57639867 0.28031134 208.92856298
-0.11102829 0.55030521 -0.82754873 282.32142277
-0.63125478 0.60409333 0.48640379 267.48878305
Axis 0.78182707 0.49781093 -0.37540739
Axis point -0.00000000 -262.14374413 361.20627789
Rotation angle (degrees) 66.28746428
Shift along axis 203.47143225
> hide #!1 models
> show #27.2 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1374 atoms
average map value = 0.009225, steps = 60
shifted from previous position = 0.0586
rotated from previous position = 0.642 degrees
atoms outside contour = 514, contour level = 0.0046305
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99061919 0.02011670 -0.13516267 -48.16359820
0.01727947 0.96272535 0.26992837 -114.34526161
0.13555460 -0.26973176 0.95334659 -30.33373192
Axis -0.89382876 -0.44838384 -0.00469925
Axis point 0.00000000 -153.28089944 245.53192643
Rotation angle (degrees) 17.57062500
Shift along axis 94.46312279
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1374 atoms
average map value = 0.009225, steps = 48
shifted from previous position = 0.00175
rotated from previous position = 0.0198 degrees
atoms outside contour = 515, contour level = 0.0046305
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99060535 0.01990631 -0.13529518 -48.10906796
0.01748321 0.96279489 0.26966709 -114.30676032
0.13562958 -0.26949906 0.95340174 -30.37812537
Axis -0.89352881 -0.44898790 -0.00401565
Axis point 0.00000000 -153.75246581 245.44309919
Rotation angle (degrees) 17.56010290
Shift along axis 94.43117853
> hide #27.2 models
> show #!30 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1374 atoms
average map value = 0.009229, steps = 60
shifted from previous position = 0.0327
rotated from previous position = 0.0399 degrees
atoms outside contour = 510, contour level = 0.0046305
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99066797 0.01990936 -0.13483544 -48.16065155
0.01742655 0.96265237 0.27017905 -114.38533874
0.13517875 -0.27000745 0.95332192 -30.28651744
Axis -0.89447200 -0.44710507 -0.00411118
Axis point 0.00000000 -153.26991275 246.05491552
Rotation angle (degrees) 17.57526180
Shift along axis 94.34513235
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1374 atoms
average map value = 0.009225, steps = 76
shifted from previous position = 0.0315
rotated from previous position = 0.0318 degrees
atoms outside contour = 515, contour level = 0.0046305
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99069795 0.02037968 -0.13454454 -48.31506305
0.01689558 0.96264976 0.27022208 -114.38942217
0.13502631 -0.26998167 0.95335082 -30.29682417
Axis -0.89476385 -0.44650236 -0.00577088
Axis point 0.00000000 -152.71992024 246.09204308
Rotation angle (degrees) 17.56992189
Shift along axis 94.48055777
> hide #!30 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopA-Q8CIE6.pdb"
CopA-Q8CIE6.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit α (Q8CIE6) [more
info...]
Chain information for CopA-Q8CIE6.pdb #2
---
Chain | Description | UniProt
A | coatomer subunit α | COPA_MOUSE 1-1224
> color #1 #0038ffff
> color #2 #004affff
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA-F8WHL2_E320-V651.pdb, chain A (#1) with CopA-Q8CIE6.pdb, chain
A (#2), sequence alignment score = 4988.1
RMSD between 321 pruned atom pairs is 0.509 angstroms; (across all 323 pairs:
0.621)
> hide #2 models
> show #2 models
> fitmap #2 inMap #34
Fit molecule CopA-Q8CIE6.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 9742 atoms
average map value = 0.005153, steps = 224
shifted from previous position = 7.29
rotated from previous position = 9.89 degrees
atoms outside contour = 5755, contour level = 0.0046305
Position of CopA-Q8CIE6.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.35043779 0.71123122 -0.60937961 201.62294206
0.22926641 -0.56570149 -0.79209768 280.19300043
-0.90809155 -0.41729124 0.03518175 263.45571687
Axis 0.55142524 0.43947298 -0.70907948
Axis point 235.27609784 200.07403859 0.00000000
Rotation angle (degrees) 160.13211482
Shift along axis 47.50618780
> hide #!34 models
> hide #2 models
> show #2 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #!1 models
Drag select of 275 residues
> select up
2492 atoms, 2565 bonds, 306 residues, 1 model selected
> delete sel
Drag select of 11 residues, 1 pseudobonds
> delete sel
Drag select of 1 residues
> delete sel
> select clear
[Repeated 1 time(s)]Drag select of 1 pseudobonds
> delete sel
Drag select of 3 residues
Drag select of 1 pseudobonds
> delete sel
> fitmap #2 inMap #34
Fit molecule CopA-Q8CIE6.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 7152 atoms
average map value = 0.003986, steps = 112
shifted from previous position = 5.7
rotated from previous position = 8.46 degrees
atoms outside contour = 4702, contour level = 0.0046305
Position of CopA-Q8CIE6.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.30646756 0.79102650 -0.52948532 203.77067889
0.27471428 -0.45908197 -0.84485254 282.23864504
-0.91137791 -0.40437707 -0.07661254 261.25682109
Axis 0.56562448 0.49039689 -0.66300818
Axis point 250.43692295 213.54811926 0.00000000
Rotation angle (degrees) 157.08463717
Shift along axis 80.45122939
> show #!34 models
> hide #!34 models
Drag select of 251 residues
> select up
2175 atoms, 2216 bonds, 272 residues, 1 model selected
> delete sel
Drag select of 37 residues, 2 pseudobonds
> select up
939 atoms, 958 bonds, 2 pseudobonds, 127 residues, 2 models selected
> delete sel
> fitmap #2 inMap #34
Fit molecule CopA-Q8CIE6.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4038 atoms
average map value = 0.007489, steps = 224
shifted from previous position = 10.5
rotated from previous position = 31.8 degrees
atoms outside contour = 1662, contour level = 0.0046305
Position of CopA-Q8CIE6.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.09445487 0.80442057 -0.58650305 199.66806763
-0.25064251 -0.58937509 -0.76799436 283.33369896
-0.96346075 0.07446179 0.25729134 274.84434220
Axis 0.60099022 0.26891357 -0.75265945
Axis point 287.34471669 134.75932293 0.00000000
Rotation angle (degrees) 135.50154190
Shift along axis -10.67336194
> show #!34 models
> hide #!34 models
Drag select of 10 residues
> select up
372 atoms, 384 bonds, 48 residues, 1 model selected
> delete sel
> fitmap #2 inMap #34
Fit molecule CopA-Q8CIE6.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 3666 atoms
average map value = 0.00767, steps = 104
shifted from previous position = 0.153
rotated from previous position = 1.3 degrees
atoms outside contour = 1479, contour level = 0.0046305
Position of CopA-Q8CIE6.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.07487981 0.81210513 -0.57868668 199.53827458
-0.24898707 -0.57716149 -0.77774678 283.44604356
-0.96560782 0.08584797 0.24542142 274.88322004
Axis 0.60740961 0.27214109 -0.74631950
Axis point 291.40138479 134.89086090 0.00000000
Rotation angle (degrees) 134.69316763
Shift along axis -6.81192531
> show #27.2 models
> fitmap #27.2 inMap #34
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 1374 atoms
average map value = 0.009228, steps = 64
shifted from previous position = 0.0262
rotated from previous position = 0.036 degrees
atoms outside contour = 512, contour level = 0.0046305
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99063502 0.02023016 -0.13502960 -48.18174625
0.01721852 0.96255674 0.27053291 -114.44046146
0.13544657 -0.27032438 0.95319408 -30.22348955
Axis -0.89438466 -0.44727092 -0.00498018
Axis point 0.00000000 -152.62018173 245.77537926
Rotation angle (degrees) 17.59957350
Shift along axis 94.42942384
> fitmap #4 inMap #34
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 4053 atoms
average map value = 0.00875, steps = 44
shifted from previous position = 0.00377
rotated from previous position = 0.0117 degrees
atoms outside contour = 1354, contour level = 0.0046305
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.02335202 -0.73057438 0.68243370 220.10855531
-0.03197812 0.68281640 0.72988983 241.56842405
-0.99921573 -0.00477854 -0.03930754 273.35150591
Axis -0.37414388 0.85641205 0.35577347
Axis point 256.49039751 0.00000000 -59.50264811
Rotation angle (degrees) 100.94820766
Shift along axis 221.78105418
> hide #27.2 models
Drag select of 123 residues
> select up
1026 atoms, 1036 bonds, 128 residues, 1 model selected
> select up
3658 atoms, 3722 bonds, 458 residues, 1 model selected
> select down
1026 atoms, 1036 bonds, 128 residues, 1 model selected
Drag select of 79 residues
> select up
646 atoms, 653 bonds, 81 residues, 1 model selected
> delete se
Missing or invalid "atoms" argument: invalid atoms specifier
> delete sel
Drag select of 52 residues
> delete sel
Drag select of 2 residues
> delete sel
> show #27.2 models
> fitmap #2 inMap #34
Fit molecule CopA-Q8CIE6.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2593 atoms
average map value = 0.008274, steps = 80
shifted from previous position = 1.58
rotated from previous position = 22.4 degrees
atoms outside contour = 777, contour level = 0.0046305
Position of CopA-Q8CIE6.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.26641990 0.73256583 -0.62639264 199.66098996
0.08848925 -0.62854670 -0.77272162 281.92857678
-0.95978648 -0.26129744 0.10263314 268.24975358
Axis 0.57629484 0.37568257 -0.72577329
Axis point 250.18950057 180.64614574 0.00000000
Rotation angle (degrees) 153.65868773
Shift along axis 26.29074612
> show #!34 models
> hide #!34 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #34
Fit molecule CopA-Q8CIE6.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2593 atoms
average map value = 0.008274, steps = 104
shifted from previous position = 0.0138
rotated from previous position = 0.0479 degrees
atoms outside contour = 775, contour level = 0.0046305
Position of CopA-Q8CIE6.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
-0.26623863 0.73210066 -0.62701325 199.63781715
0.08894234 -0.62905756 -0.77225375 281.92254246
-0.95979490 -0.26137180 0.10236468 268.25573305
Axis 0.57646911 0.37550425 -0.72572717
Axis point 250.15657378 180.66177451 0.00000000
Rotation angle (degrees) 153.69732633
Shift along axis 26.26767435
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2_E320-V651.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2653 atoms
average map value = 0.008168, steps = 104
shifted from previous position = 0.00499
rotated from previous position = 0.0484 degrees
atoms outside contour = 820, contour level = 0.0046305
Position of CopA-F8WHL2_E320-V651.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76783420 0.57630098 0.27983535 208.92325977
-0.11086061 0.54973428 -0.82795057 282.31302208
-0.63098381 0.60470604 0.48599386 267.47771771
Axis 0.78224350 0.49731552 -0.37519646
Axis point 0.00000000 -261.66507065 361.06339025
Rotation angle (degrees) 66.31042451
Shift along axis 203.47081525
> fitmap #1 inMap #34
Fit molecule CopA-F8WHL2_E320-V651.pdb (#1) to map
relion_locres_filtered_20240326_GT.mrc (#34) using 2653 atoms
average map value = 0.008168, steps = 104
shifted from previous position = 0.0303
rotated from previous position = 0.0451 degrees
atoms outside contour = 822, contour level = 0.0046305
Position of CopA-F8WHL2_E320-V651.pdb (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.76755968 0.57631068 0.28056752 208.92584722
-0.11036621 0.55000896 -0.82783419 282.29363072
-0.63140433 0.60444697 0.48576993 267.45684961
Axis 0.78199659 0.49791822 -0.37491171
Axis point 0.00000000 -261.83279019 360.82969852
Rotation angle (degrees) 66.31742467
Shift along axis 203.66573518
> hide #!2 models
> rename #2 CopA-Q8CIE6_E320-V642.pdb
> show #!2 models
> show #!34 models
> hide #!34 models
> show #!34 models
> hide #!1 models
> close #1
> hide #!2 models
> show #!2 models
> hide #!34 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> color #1 #b2b2b2b8 models
> color #1 #b2b2b2a5 models
> color #1 #b2b2b2a6 models
> select add #1
2 models selected
> show #!34 models
> select #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,65.367,0,1,0,76.181,0,0,1,75.337
> fitmap #1 inMap #34
Fit map relion_locres_filtered_20240326_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 247907 points
correlation = 1, correlation about mean = 1, overlap = 26.95
steps = 128, shift = 2.55, angle = 0.976 degrees
Position of relion_locres_filtered_20240326_GT.mrc (#1) relative to
relion_locres_filtered_20240326_GT.mrc (#34) coordinates:
Matrix rotation and translation
0.99999999 -0.00012506 -0.00008620 0.05725254
0.00012506 0.99999999 -0.00002205 -0.01636628
0.00008620 0.00002204 1.00000000 -0.02226246
Axis 0.14360813 -0.56161595 0.81484000
Axis point 134.16098000 458.61542456 0.00000000
Rotation angle (degrees) 0.00879372
Shift along axis -0.00072685
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!34 models
> close #33
> close #34
> fitmap #2 inMap #1
Fit molecule CopA-Q8CIE6_E320-V642.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2593 atoms
average map value = 0.008275, steps = 80
shifted from previous position = 0.0314
rotated from previous position = 0.0382 degrees
atoms outside contour = 799, contour level = 0.0047281
Position of CopA-Q8CIE6_E320-V642.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.26596303 0.73243454 -0.62674022 199.65991761
0.08887658 -0.62875650 -0.77250645 281.94914037
-0.95987740 -0.26116068 0.10212971 268.25628469
Axis 0.57654299 0.37561258 -0.72561241
Axis point 250.24124687 180.68157744 0.00000000
Rotation angle (degrees) 153.67524455
Shift along axis 26.36608210
> fitmap #2 inMap #1
Fit molecule CopA-Q8CIE6_E320-V642.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2593 atoms
average map value = 0.008274, steps = 76
shifted from previous position = 0.0239
rotated from previous position = 0.0376 degrees
atoms outside contour = 796, contour level = 0.0047281
Position of CopA-Q8CIE6_E320-V642.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.26646975 0.73245553 -0.62650042 199.65898109
0.08848498 -0.62866718 -0.77262409 281.93091751
-0.95977304 -0.26131682 0.10270947 268.25264116
Axis 0.57628640 0.37562634 -0.72580910
Axis point 250.17259609 180.64036100 0.00000000
Rotation angle (degrees) 153.66475727
Shift along axis 26.26122582
> fitmap #27.2 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1374 atoms
average map value = 0.009228, steps = 48
shifted from previous position = 0.00494
rotated from previous position = 0.0217 degrees
atoms outside contour = 522, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99064341 0.02019889 -0.13497277 -48.22271731
0.01718831 0.96264614 0.27021654 -114.37202644
0.13538909 -0.27000818 0.95329186 -30.26466585
Axis -0.89425082 -0.44753841 -0.00498351
Axis point 0.00000000 -152.84510082 245.68531982
Rotation angle (degrees) 17.58103461
Shift along axis 94.45990387
> show #!30 models
> fitmap #27.2 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1374 atoms
average map value = 0.009229, steps = 48
shifted from previous position = 0.00899
rotated from previous position = 0.0407 degrees
atoms outside contour = 520, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif B (#27.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99072816 0.02017173 -0.13435328 -48.32702490
0.01709208 0.96255277 0.27055504 -114.41852065
0.13477969 -0.27034287 0.95328336 -30.20567122
Axis -0.89528515 -0.44546438 -0.00509740
Axis point -0.00000000 -152.52705056 246.38057257
Rotation angle (degrees) 17.58265741
Shift along axis 94.38981318
> color #2 #0024ffff
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #27.2 models
> show #27.2 models
> hide #!30 models
> show #!30 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v38_labelled.cxs"
> hide #!30 models
> hide #27.2 models
> hide #!2 models
> show #27.1 models
> show #!1 models
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6538 atoms
average map value = 0.009129, steps = 48
shifted from previous position = 0.00683
rotated from previous position = 0.0266 degrees
atoms outside contour = 2197, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99555627 0.00362167 0.09409890 -80.58908006
-0.00513584 0.99986113 0.01585408 -75.38043922
-0.09402842 -0.01626690 0.99543661 -68.59564412
Axis -0.16812812 0.98469881 -0.04583865
Axis point -802.28218112 0.00000000 921.33841380
Rotation angle (degrees) 5.48155549
Shift along axis -57.53340625
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6538 atoms
average map value = 0.009129, steps = 44
shifted from previous position = 0.0323
rotated from previous position = 0.0101 degrees
atoms outside contour = 2198, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99557143 0.00359514 0.09393932 -80.56899965
-0.00511342 0.99986009 0.01592667 -75.42008740
-0.09386892 -0.01633649 0.99545052 -68.57856091
Axis -0.16913120 0.98453568 -0.04565237
Axis point -803.29062368 0.00000000 923.31930146
Rotation angle (degrees) 5.47313917
Shift along axis -57.49626144
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6538 atoms
average map value = 0.009129, steps = 44
shifted from previous position = 0.0303
rotated from previous position = 0.0146 degrees
atoms outside contour = 2193, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99555366 0.00344087 0.09413328 -80.57178421
-0.00495767 0.99986155 0.01588429 -75.39610791
-0.09406559 -0.01628034 0.99543288 -68.59713070
Axis -0.16830226 0.98475537 -0.04394559
Axis point -800.91827714 0.00000000 921.21427079
Rotation angle (degrees) 5.48333046
Shift along axis -57.67176744
> show #!3 models
> hide #!1 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> fitmap #3 inMap #1
Fit molecule CopBprime_O55029_solenoid.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4034 atoms
average map value = 0.009675, steps = 60
shifted from previous position = 0.0141
rotated from previous position = 0.0255 degrees
atoms outside contour = 1482, contour level = 0.0047281
Position of CopBprime_O55029_solenoid.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.09015386 -0.26641133 -0.95963393 236.89212744
0.03176550 -0.96383663 0.26459383 213.37817753
-0.99542113 -0.00662910 0.09535628 277.14045439
Axis -0.67024420 0.08843708 0.73685249
Axis point 230.08374453 109.47948044 0.00000000
Rotation angle (degrees) 168.32667230
Shift along axis 64.30660495
> fitmap #3 inMap #1
Fit molecule CopBprime_O55029_solenoid.pdb (#3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4034 atoms
average map value = 0.009675, steps = 60
shifted from previous position = 0.0282
rotated from previous position = 0.0175 degrees
atoms outside contour = 1480, contour level = 0.0047281
Position of CopBprime_O55029_solenoid.pdb (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.09041325 -0.26644336 -0.95960064 236.86593363
0.03161617 -0.96382925 0.26463862 213.37297517
-0.99540236 -0.00641206 0.09556685 277.11110769
Axis -0.67015073 0.08851685 0.73692793
Axis point 230.03664950 109.45387438 0.00000000
Rotation angle (degrees) 168.33254007
Shift along axis 64.36213991
> fitmap #7 inMap #1
Fit molecule CopBprime_O55029_beta_props.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4686 atoms
average map value = 0.009331, steps = 48
shifted from previous position = 0.0253
rotated from previous position = 0.0467 degrees
atoms outside contour = 1384, contour level = 0.0047281
Position of CopBprime_O55029_beta_props.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.18358574 -0.18831682 -0.96479689 236.87476151
0.00701091 -0.98170427 0.19028287 212.90846072
-0.98297870 0.02816912 0.18154718 275.48584443
Axis -0.63701813 0.07144452 0.76753084
Axis point 224.12322365 105.49859907 0.00000000
Rotation angle (degrees) 172.68962442
Shift along axis 75.76150644
> fitmap #7 inMap #1
Fit molecule CopBprime_O55029_beta_props.pdb (#7) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4686 atoms
average map value = 0.009331, steps = 44
shifted from previous position = 0.00835
rotated from previous position = 0.0341 degrees
atoms outside contour = 1384, contour level = 0.0047281
Position of CopBprime_O55029_beta_props.pdb (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.18347865 -0.18860756 -0.96476047 236.87355158
0.00656557 -0.98163461 0.19065775 212.91058430
-0.98300177 0.02864742 0.18134731 275.47613721
Axis -0.63706303 0.07172910 0.76746702
Axis point 224.14249023 105.44125947 0.00000000
Rotation angle (degrees) 172.69483148
Shift along axis 75.78735231
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6538 atoms
average map value = 0.009129, steps = 44
shifted from previous position = 0.0113
rotated from previous position = 0.014 degrees
atoms outside contour = 2194, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99555672 0.00366599 0.09409244 -80.59191202
-0.00517297 0.99986215 0.01577705 -75.36752085
-0.09402163 -0.01619369 0.99543844 -68.60347468
Axis -0.16737196 0.98480729 -0.04627338
Axis point -802.66772468 0.00000000 921.00087225
Rotation angle (degrees) 5.48056245
Shift along axis -57.55914293
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6538 atoms
average map value = 0.009129, steps = 40
shifted from previous position = 0.032
rotated from previous position = 0.0219 degrees
atoms outside contour = 2192, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99555535 0.00345103 0.09411503 -80.58052940
-0.00498896 0.99985777 0.01611059 -75.45310217
-0.09404605 -0.01650852 0.99543097 -68.56033750
Axis -0.17064313 0.98434316 -0.04415287
Axis point -800.82402146 0.00000000 922.61688892
Rotation angle (degrees) 5.48452907
Shift along axis -57.49409541
> hide #27.1 models
> hide #!7 models
> hide #!3 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopA-Q8CIE6.pdb"
CopA-Q8CIE6.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit α (Q8CIE6) [more
info...]
Chain information for CopA-Q8CIE6.pdb #13
---
Chain | Description | UniProt
A | coatomer subunit α | COPA_MOUSE 1-1224
> color #13 #0038ffff
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #13 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA-Q8CIE6_E320-V642.pdb, chain A (#2) with CopA-Q8CIE6.pdb, chain
A (#13), sequence alignment score = 5036.7
RMSD between 324 pruned atom pairs is 0.000 angstroms; (across all 324 pairs:
0.000)
> combine #13
[Repeated 1 time(s)]
> hide #15 models
> hide #14 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #13 models
> show #13 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right select
Drag select of 311 residues
> select up
3114 atoms, 3179 bonds, 399 residues, 1 model selected
> delete sel
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 297 residues
> select up
2613 atoms, 2687 bonds, 321 residues, 1 model selected
> delete sel
Drag select of 3 residues
> select up
37 atoms, 37 bonds, 4 residues, 1 model selected
> delete sel
> fitmap #13 inMap #1
Fit molecule CopA-Q8CIE6.pdb (#13) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3978 atoms
average map value = 0.007481, steps = 228
shifted from previous position = 5.68
rotated from previous position = 21.7 degrees
atoms outside contour = 1678, contour level = 0.0047281
Position of CopA-Q8CIE6.pdb (#13) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.09946351 0.80564030 -0.58399547 199.48908893
-0.24922291 -0.58836882 -0.76922693 283.37506930
-0.96332494 0.06903504 0.25930525 274.83807073
Axis 0.59886391 0.27099730 -0.75360631
Axis point 286.50297224 135.30530391 0.00000000
Rotation angle (degrees) 135.58287597
Shift along axis -10.85900981
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!1 models
> hide #!2 models
> show #!13 models
Drag select of 204 residues
> select up
1878 atoms, 1912 bonds, 233 residues, 1 model selected
Drag select of 70 residues
Drag select of 226 residues
> select up
2021 atoms, 2057 bonds, 254 residues, 1 model selected
> select clear
Drag select of 254 residues
Drag select of 238 residues
Drag select of 262 residues
> select up
2188 atoms, 2230 bonds, 274 residues, 1 model selected
> select down
2088 atoms, 262 residues, 1 model selected
Drag select of 71 residues
> select clear
Drag select of 228 residues
> select up
1999 atoms, 2036 bonds, 251 residues, 1 model selected
> delete sel
Drag select of 15 residues, 1 pseudobonds
> delete sel
> show #!1 models
> fitmap #13 inMap #1
Fit molecule CopA-Q8CIE6.pdb (#13) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1865 atoms
average map value = 0.00897, steps = 56
shifted from previous position = 0.674
rotated from previous position = 3.69 degrees
atoms outside contour = 684, contour level = 0.0047281
Position of CopA-Q8CIE6.pdb (#13) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.13654802 0.80145366 -0.58225997 199.09573463
-0.29788921 -0.59378120 -0.74745295 281.94987931
-0.94478392 0.07138574 0.31982404 271.93620355
Axis 0.57749602 0.25567446 -0.77532504
Axis point 278.04684340 128.75122066 0.00000000
Rotation angle (degrees) 134.84995391
Shift along axis -23.77456835
> fitmap #13 inMap #1
Fit molecule CopA-Q8CIE6.pdb (#13) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1865 atoms
average map value = 0.00897, steps = 48
shifted from previous position = 0.0041
rotated from previous position = 0.0587 degrees
atoms outside contour = 683, contour level = 0.0047281
Position of CopA-Q8CIE6.pdb (#13) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.13748732 0.80118616 -0.58240705 199.09730314
-0.29755557 -0.59424011 -0.74722110 281.94423583
-0.94475284 0.07056504 0.32009788 271.93191939
Axis 0.57720938 0.25575071 -0.77551331
Axis point 277.87079304 128.81627672 0.00000000
Rotation angle (degrees) 134.89540566
Shift along axis -23.85855294
> hide #!1 models
Drag select of 12 residues
> select up
372 atoms, 384 bonds, 48 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #13 inMap #1
Fit molecule CopA-Q8CIE6.pdb (#13) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1493 atoms
average map value = 0.009858, steps = 64
shifted from previous position = 0.412
rotated from previous position = 2.61 degrees
atoms outside contour = 506, contour level = 0.0047281
Position of CopA-Q8CIE6.pdb (#13) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.09655165 0.81642437 -0.56932331 198.81758171
-0.30234192 -0.56902489 -0.76472220 282.29081333
-0.94829697 0.09829511 0.30177960 272.22690948
Axis 0.58993851 0.25905756 -0.76476254
Axis point 285.98011714 127.74194415 0.00000000
Rotation angle (degrees) 132.99217470
Shift along axis -17.76922692
> rename #13 CopA-Q8CIE6_solenoid.pdb
> hide #!1 models
> show #!1 models
> hide #!13 models
> show #!13 models
> hide #!1 models
> show #14 models
> hide #!13 models
Drag select of 535 residues
> select up
4425 atoms, 4514 bonds, 565 residues, 1 model selected
> delete sel
Drag select of 2 residues
> delete sel
> fitmap #14 inMap #1
Fit molecule copy of CopA-Q8CIE6.pdb (#14) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5301 atoms
average map value = 0.008461, steps = 68
shifted from previous position = 3.21
rotated from previous position = 8.56 degrees
atoms outside contour = 1732, contour level = 0.0047281
Position of copy of CopA-Q8CIE6.pdb (#14) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.33497523 0.69483088 -0.63639739 200.55601777
0.21403454 -0.60164836 -0.76955082 281.25327405
-0.91759512 -0.39399149 0.05281949 264.17163778
Axis 0.55905496 0.41858895 -0.71571003
Axis point 235.37583132 196.39849704 0.00000000
Rotation angle (degrees) 160.37347442
Shift along axis 40.78105937
> show #!1 models
> hide #!1 models
Drag select of 50 residues
> select up
487 atoms, 495 bonds, 60 residues, 1 model selected
Drag select of 66 residues
Drag select of 58 residues
> select up
538 atoms, 548 bonds, 66 residues, 1 model selected
> delete sel
> fitmap #14 inMap #1
Fit molecule copy of CopA-Q8CIE6.pdb (#14) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008718, steps = 44
shifted from previous position = 0.272
rotated from previous position = 0.784 degrees
atoms outside contour = 1499, contour level = 0.0047281
Position of copy of CopA-Q8CIE6.pdb (#14) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.34429351 0.69720481 -0.62878251 201.11062000
0.21642490 -0.59275352 -0.77575996 281.02073780
-0.91357662 -0.40317331 0.05318871 263.97597983
Axis 0.55475542 0.42403849 -0.71584760
Axis point 234.64506404 197.20196587 0.00000000
Rotation angle (degrees) 160.37809947
Shift along axis 41.76424549
> show #!1 models
> hide #!1 models
> show #!30 models
> hide #!30 models
> show #27.2 models
> hide #27.2 models
> show #!2 models
> hide #!2 models
> show #27.2 models
> hide #27.2 models
> show #!30 models
> fitmap #14 inMap #1
Fit molecule copy of CopA-Q8CIE6.pdb (#14) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008718, steps = 28
shifted from previous position = 0.0214
rotated from previous position = 0.012 degrees
atoms outside contour = 1498, contour level = 0.0047281
Position of copy of CopA-Q8CIE6.pdb (#14) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.34444666 0.69707488 -0.62884267 201.10502206
0.21646045 -0.59281472 -0.77570329 281.00582538
-0.91351047 -0.40330797 0.05330391 263.96548545
Axis 0.55470027 0.42402602 -0.71589772
Axis point 234.60444415 197.19298857 0.00000000
Rotation angle (degrees) 160.38655922
Shift along axis 41.73450133
> fitmap #14 inMap #1
Fit molecule copy of CopA-Q8CIE6.pdb (#14) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008718, steps = 40
shifted from previous position = 0.0258
rotated from previous position = 0.0246 degrees
atoms outside contour = 1501, contour level = 0.0047281
Position of copy of CopA-Q8CIE6.pdb (#14) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.34410034 0.69730151 -0.62878101 201.10848078
0.21633810 -0.59277765 -0.77576574 281.02540295
-0.91366995 -0.40297054 0.05312211 263.97796969
Axis 0.55482862 0.42399832 -0.71581466
Axis point 234.67905251 197.19172890 0.00000000
Rotation angle (degrees) 160.36936225
Shift along axis 41.77574043
> hide #!14 models
> show #!14 models
> show #!1 models
> close #15
> rename #14 CopA-Q8CIE6_beta_props.pdb
> show #!13 models
> hide #!13 models
> hide #!14 models
> hide #!30 models
> hide #!1 models
> show #!4 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #!4 models
> show #!4 models
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4053 atoms
average map value = 0.00875, steps = 60
shifted from previous position = 0.023
rotated from previous position = 0.0058 degrees
atoms outside contour = 1377, contour level = 0.0047281
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02339990 -0.73051856 0.68249182 220.12357711
-0.03191624 0.68287664 0.72983618 241.57823865
-0.99921659 -0.00470448 -0.03929465 273.35256704
Axis -0.37407791 0.85643995 0.35577567
Axis point 256.48319067 0.00000000 -59.50468413
Rotation angle (degrees) 100.94747093
Shift along axis 221.80608061
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4053 atoms
average map value = 0.00875, steps = 64
shifted from previous position = 0.00896
rotated from previous position = 0.0162 degrees
atoms outside contour = 1374, contour level = 0.0047281
Position of CopB_Q9JIF7.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02354741 -0.73035997 0.68265645 220.12625836
-0.03198603 0.68304660 0.72967406 241.57922012
-0.99921089 -0.00465353 -0.03944530 273.35505958
Axis -0.37397413 0.85653171 0.35566386
Axis point 256.45874274 0.00000000 -59.45008610
Rotation angle (degrees) 100.95121196
Shift along axis 221.82125205
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2991 atoms
average map value = 0.01065, steps = 44
shifted from previous position = 0.0361
rotated from previous position = 0.0316 degrees
atoms outside contour = 1091, contour level = 0.0047281
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99551010 -0.07940155 0.05152702 253.49799044
0.06873037 0.98065549 0.18327835 192.94826820
-0.06508284 -0.17891398 0.98170974 287.90534252
Axis -0.88703328 0.28558535 0.36278502
Axis point 0.00000000 1839.78826465 -960.34310326
Rotation angle (degrees) 11.78029424
Shift along axis -65.31021219
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2991 atoms
average map value = 0.01065, steps = 60
shifted from previous position = 0.0121
rotated from previous position = 0.0265 degrees
atoms outside contour = 1092, contour level = 0.0047281
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99552361 -0.07944603 0.05119636 253.49390279
0.06881249 0.98059002 0.18359751 192.95535330
-0.06478873 -0.17925271 0.98166740 287.92411424
Axis -0.88766221 0.28374126 0.36269367
Axis point 0.00000000 1837.48799202 -958.46116796
Rotation angle (degrees) 11.79351762
Shift along axis -65.83930804
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2991 atoms
average map value = 0.01065, steps = 76
shifted from previous position = 0.0193
rotated from previous position = 0.025 degrees
atoms outside contour = 1088, contour level = 0.0047281
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99551654 -0.07955168 0.05116976 253.50960352
0.06894836 0.98065708 0.18318793 192.96250485
-0.06475290 -0.17883854 0.98174530 287.91044751
Axis -0.88708136 0.28404783 0.36387289
Axis point 0.00000000 1840.79041662 -960.25690300
Rotation angle (degrees) 11.77417540
Shift along axis -65.31025602
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2991 atoms
average map value = 0.01065, steps = 60
shifted from previous position = 0.0129
rotated from previous position = 0.0138 degrees
atoms outside contour = 1089, contour level = 0.0047281
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99552608 -0.07947362 0.05110542 253.51297695
0.06886907 0.98062310 0.18339952 192.96033883
-0.06469058 -0.17905942 0.98170915 287.90881591
Axis -0.88750914 0.28353557 0.36322871
Axis point 0.00000000 1839.18692996 -959.39691372
Rotation angle (degrees) 11.78267869
Shift along axis -65.70721611
> fitmap #32.1 inMap #1
Fit molecule 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2991 atoms
average map value = 0.01065, steps = 60
shifted from previous position = 0.0205
rotated from previous position = 0.0186 degrees
atoms outside contour = 1092, contour level = 0.0047281
Position of 5mu7_Thermophila_beta_deltaCOPI.cif A (#32.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99552600 -0.07933918 0.05131543 253.49679161
0.06868605 0.98059953 0.18359410 192.94992631
-0.06488609 -0.17924805 0.98166182 287.91648514
Axis -0.88770813 0.28429178 0.36214978
Axis point 0.00000000 1837.50194689 -958.84713846
Rotation angle (degrees) 11.79263263
Shift along axis -65.90819220
> hide #32.1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #32.1 models
> hide #32.1 models
> show #!4 models
> rename #4 CopB_Q9JIF7_P395-L953.pdb
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!3 models
> show #!7 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopB_ Q9JIF7.pdb"
CopB_ Q9JIF7.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit β (Q9JIF7) [more
info...]
Chain information for CopB_ Q9JIF7.pdb #15
---
Chain | Description | UniProt
A | coatomer subunit β | COPB_MOUSE 1-953
> color #15 #076000ff
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopB_ Q9JIF7.pdb"
CopB_ Q9JIF7.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit β (Q9JIF7) [more
info...]
Chain information for CopB_ Q9JIF7.pdb #16
---
Chain | Description | UniProt
A | coatomer subunit β | COPB_MOUSE 1-953
> color #16 #076000ff
> hide #!3 models
> hide #!7 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #15 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_Q9JIF7_P395-L953.pdb, chain A (#4) with CopB_ Q9JIF7.pdb,
chain A (#15), sequence alignment score = 4184.9
RMSD between 418 pruned atom pairs is 0.845 angstroms; (across all 520 pairs:
2.356)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #16 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA-Q8CIE6_E320-V642.pdb, chain A (#2) with CopB_ Q9JIF7.pdb,
chain A (#16), sequence alignment score = 5
Fewer than 3 residues aligned; cannot match CopA-Q8CIE6_E320-V642.pdb, chain A
with CopB_ Q9JIF7.pdb, chain A
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #16 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_Q9JIF7_P395-L953.pdb, chain A (#4) with CopB_ Q9JIF7.pdb,
chain A (#16), sequence alignment score = 4184.9
RMSD between 418 pruned atom pairs is 0.845 angstroms; (across all 520 pairs:
2.356)
> hide #15 models
> show #15 models
> hide #15 models
> hide #16 models
> show #!4 models
> show #15 models
> show #16 models
> hide #16 models
> hide #15 models
> show #16 models
> hide #!4 models
> show #!1 models
> hide #16 models
> show #16 models
> hide #16 models
> hide #!1 models
> show #15 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #15 models
> show #15 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
Drag select of 91 residues
> select up
886 atoms, 896 bonds, 116 residues, 1 model selected
Drag select of 42 residues
Drag select of 58 residues
> select up
562 atoms, 567 bonds, 73 residues, 1 model selected
> delete sel
Drag select of 34 residues, 1 pseudobonds
> select up
376 atoms, 382 bonds, 1 pseudobond, 48 residues, 2 models selected
> delete sel
> show #!1 models
> fitmap #15 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#15) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6563 atoms
average map value = 0.007851, steps = 132
shifted from previous position = 8.19
rotated from previous position = 7.85 degrees
atoms outside contour = 3176, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#15) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.01844824 -0.74284748 0.66920646 220.14509666
-0.03147128 0.66942014 0.74221710 241.70022532
-0.99933439 -0.00736819 -0.03572798 272.50039049
Axis -0.38192670 0.85015048 0.36245850
Axis point 257.63491425 0.00000000 -62.53223112
Rotation angle (degrees) 101.09159635
Shift along axis 220.17235598
> hide #!1 models
Drag select of 24 residues
> select up
303 atoms, 304 bonds, 40 residues, 1 model selected
> select up
6563 atoms, 6664 bonds, 832 residues, 1 model selected
> select down
303 atoms, 304 bonds, 40 residues, 1 model selected
Drag select of 33 residues
> select up
424 atoms, 427 bonds, 54 residues, 1 model selected
Drag select of 6 residues
Drag select of 93 residues
> select up
943 atoms, 955 bonds, 123 residues, 1 model selected
Drag select of 108 residues
> select down
828 atoms, 108 residues, 1 model selected
> select up
984 atoms, 997 bonds, 130 residues, 1 model selected
> select up
6563 atoms, 6664 bonds, 832 residues, 1 model selected
> select down
984 atoms, 997 bonds, 130 residues, 1 model selected
> select clear
Drag select of 114 residues
> select up
930 atoms, 945 bonds, 122 residues, 1 model selected
> delete sel
Drag select of 3 residues
> delete sel
> show #!1 models
> fitmap #15 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#15) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5609 atoms
average map value = 0.008594, steps = 72
shifted from previous position = 0.0768
rotated from previous position = 0.628 degrees
atoms outside contour = 2493, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#15) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02232557 -0.74737698 0.66402501 220.08242939
-0.02402614 0.66439983 0.74699104 241.71444367
-0.99946201 0.00072304 -0.03278969 272.56997046
Axis -0.38046477 0.84808436 0.36878107
Axis point 256.54257924 0.00000000 -63.53916094
Rotation angle (degrees) 101.26562109
Shift along axis 221.77927269
> fitmap #15 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#15) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5609 atoms
average map value = 0.008594, steps = 60
shifted from previous position = 0.00441
rotated from previous position = 0.00916 degrees
atoms outside contour = 2491, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#15) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02228893 -0.74731749 0.66409320 220.07875194
-0.02389765 0.66446668 0.74693569 241.71413304
-0.99946591 0.00077814 -0.03266938 272.56807915
Axis -0.38039983 0.84810184 0.36880787
Axis point 256.53065659 0.00000000 -63.55295808
Rotation angle (degrees) 101.25908391
Shift along axis 221.80553434
> fitmap #15 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#15) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5609 atoms
average map value = 0.008594, steps = 76
shifted from previous position = 0.0166
rotated from previous position = 0.00886 degrees
atoms outside contour = 2488, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#15) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02232063 -0.74736321 0.66404068 220.06468865
-0.02403359 0.66441532 0.74697702 241.70565054
-0.99946194 0.00071372 -0.03279199 272.57067260
Axis -0.38046168 0.84809074 0.36876958
Axis point 256.53287602 0.00000000 -63.52597982
Rotation angle (degrees) 101.26509137
Shift along axis 221.77791678
> fitmap #15 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#15) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5609 atoms
average map value = 0.008594, steps = 76
shifted from previous position = 0.0078
rotated from previous position = 0.0159 degrees
atoms outside contour = 2491, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#15) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02247122 -0.74746006 0.66392658 220.06921073
-0.02421650 0.66430637 0.74706801 241.70092821
-0.99945415 0.00070955 -0.03302864 272.57488700
Axis -0.38052938 0.84807136 0.36874429
Axis point 256.53348528 0.00000000 -63.48963462
Rotation angle (degrees) 101.27958588
Shift along axis 221.74727038
> hide #!1 models
Drag select of 11 residues
> select up
163 atoms, 166 bonds, 22 residues, 1 model selected
> delete sel
> fitmap #15 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#15) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5446 atoms
average map value = 0.008714, steps = 76
shifted from previous position = 0.0618
rotated from previous position = 0.525 degrees
atoms outside contour = 2382, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#15) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02596350 -0.75079113 0.66002923 220.02712084
-0.01759900 0.66049277 0.75062612 241.71169737
-0.99950796 0.00787303 -0.03036188 272.65278835
Axis -0.37887103 0.84651355 0.37399407
Axis point 255.53355241 0.00000000 -64.28644925
Rotation angle (degrees) 101.41513659
Shift along axis 223.22085069
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> show #!1 models
> hide #32.1 models
> show #32.1 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #32.1 models
> show #!15 models
> hide #!1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!15 to #32.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5mu7_Thermophila_beta_deltaCOPI.cif A, chain A (#32.1) with CopB_
Q9JIF7.pdb, chain A (#15), sequence alignment score = 1250.8
RMSD between 252 pruned atom pairs is 1.196 angstroms; (across all 369 pairs:
1.979)
> show #!1 models
> hide #!1 models
> hide #32.1 models
> show #!1 models
> hide #!1 models
> show #32.1 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 201 residues
> select up
1960 atoms, 1982 bonds, 249 residues, 1 model selected
Drag select of 34 residues
> select up
356 atoms, 359 bonds, 46 residues, 1 model selected
> delete sel
Drag select of 250 residues
> select up
2072 atoms, 2098 bonds, 264 residues, 1 model selected
> delete sel
Drag select of 3 residues
> delete sel
> fitmap #15 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#15) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2995 atoms
average map value = 0.01087, steps = 52
shifted from previous position = 0.203
rotated from previous position = 2.56 degrees
atoms outside contour = 1018, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#15) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02724952 -0.68722196 0.72593625 220.50900449
0.02502038 0.72550951 0.68775717 239.42442791
-0.99931549 0.03690425 -0.00257523 273.99104548
Axis -0.32926029 0.87278841 0.36031661
Axis point 248.43699619 0.00000000 -58.82961491
Rotation angle (degrees) 98.75198425
Shift along axis 235.08553176
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> rename #15 "CopB_ Q9JIF7_G23-F394.pdb"
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #16 models
> hide #!15 models
Drag select of 73 residues
> select up
781 atoms, 794 bonds, 99 residues, 1 model selected
> delete sel
Drag select of 92 residues
> select up
903 atoms, 922 bonds, 110 residues, 1 model selected
> delete sel
Drag select of 3 residues
> delete sel
Drag select of 44 residues
> select up
364 atoms, 369 bonds, 45 residues, 1 model selected
> delete sel
Drag select of 91 residues
> select up
726 atoms, 731 bonds, 94 residues, 1 model selected
> select up
5427 atoms, 5504 bonds, 696 residues, 1 model selected
> select clear
Drag select of 62 residues
> select up
562 atoms, 568 bonds, 73 residues, 1 model selected
> delete sel
Drag select of 24 residues
> select clear
Drag select of 20 residues
> select up
174 atoms, 174 bonds, 22 residues, 1 model selected
> delete sel
Drag select of 36 residues
> select up
446 atoms, 451 bonds, 53 residues, 1 model selected
> select clear
Drag select of 19 residues
> select up
337 atoms, 339 bonds, 41 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #16 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#16) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4354 atoms
average map value = 0.007983, steps = 64
shifted from previous position = 1.62
rotated from previous position = 2.08 degrees
atoms outside contour = 1739, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#16) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.03640664 -0.65956348 0.75076665 218.50269376
0.00387517 0.75116587 0.66010212 248.03049444
-0.99932954 0.02694145 -0.02479150 272.25066764
Axis -0.32045400 0.88575516 0.33577824
Axis point 246.48105337 0.00000000 -53.68695182
Rotation angle (degrees) 98.91773215
Shift along axis 241.09007696
> hide #!1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v39_labelled.cxs"
——— End of log from Tue Jul 9 17:02:08 2024 ———
opened ChimeraX session
> show #!1 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #16 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#16) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4354 atoms
average map value = 0.007983, steps = 60
shifted from previous position = 0.00721
rotated from previous position = 0.02 degrees
atoms outside contour = 1737, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#16) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.03643722 -0.65930467 0.75099247 218.49884823
0.00383116 0.75139382 0.65984290 248.02662965
-0.99932860 0.02692002 -0.02485280 272.24992976
Axis -0.32033020 0.88585940 0.33562135
Axis point 246.46803886 0.00000000 -53.63717478
Rotation angle (degrees) 98.91378636
Shift along axis 241.09783052
> fitmap #16 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#16) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4354 atoms
average map value = 0.007982, steps = 44
shifted from previous position = 0.0305
rotated from previous position = 0.0254 degrees
atoms outside contour = 1741, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#16) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.03647715 -0.65947997 0.75083659 218.52782150
0.00419660 0.75122890 0.66002843 248.04323495
-0.99932568 0.02722691 -0.02463511 272.24790496
Axis -0.32026844 0.88577813 0.33589468
Axis point 246.44552444 0.00000000 -53.71596676
Rotation angle (degrees) 98.91341394
Shift along axis 241.17032964
> hide #!1 models
> show #!4 models
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7_P395-L953.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4053 atoms
average map value = 0.00875, steps = 48
shifted from previous position = 0.0121
rotated from previous position = 0.014 degrees
atoms outside contour = 1375, contour level = 0.0047281
Position of CopB_Q9JIF7_P395-L953.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02337695 -0.73046668 0.68254813 220.14244287
-0.03207702 0.68293123 0.72977805 241.57330662
-0.99921198 -0.00483413 -0.03939604 273.35713550
Axis -0.37411521 0.85646829 0.35566821
Axis point 256.51140605 0.00000000 -59.48371440
Rotation angle (degrees) 100.94816697
Shift along axis 221.76568322
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7_P395-L953.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4053 atoms
average map value = 0.00875, steps = 48
shifted from previous position = 0.00579
rotated from previous position = 0.0174 degrees
atoms outside contour = 1371, contour level = 0.0047281
Position of CopB_Q9JIF7_P395-L953.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02355850 -0.73044234 0.68256793 220.13580643
-0.03183473 0.68295929 0.72976239 241.57756739
-0.99921546 -0.00453726 -0.03934293 273.34929776
Axis -0.37395975 0.85648862 0.35578272
Axis point 256.45009066 0.00000000 -59.48589705
Rotation angle (degrees) 100.95109604
Shift along axis 221.83946375
> fitmap #4 inMap #1
Fit molecule CopB_Q9JIF7_P395-L953.pdb (#4) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4053 atoms
average map value = 0.00875, steps = 40
shifted from previous position = 0.00772
rotated from previous position = 0.0109 degrees
atoms outside contour = 1373, contour level = 0.0047281
Position of CopB_Q9JIF7_P395-L953.pdb (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.02354235 -0.73041659 0.68259604 220.12769576
-0.03202010 0.68298589 0.72972939 241.57433729
-0.99920992 -0.00467725 -0.03946710 273.35408889
Axis -0.37401724 0.85650699 0.35567806
Axis point 256.46580478 0.00000000 -59.45365642
Rotation angle (degrees) 100.95347164
Shift along axis 221.80460690
> fitmap #16 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#16) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4354 atoms
average map value = 0.007983, steps = 48
shifted from previous position = 0.0411
rotated from previous position = 0.0515 degrees
atoms outside contour = 1736, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#16) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.03638626 -0.65899236 0.75126900 218.48669982
0.00360782 0.75167529 0.65952349 248.02017180
-0.99933129 0.02670804 -0.02497312 272.25136210
Axis -0.32027043 0.88598580 0.33534460
Axis point 246.48102243 0.00000000 -53.56712757
Rotation angle (degrees) 98.90763551
Shift along axis 241.06554695
> fitmap #16 inMap #1
Fit molecule CopB_ Q9JIF7.pdb (#16) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4354 atoms
average map value = 0.007983, steps = 44
shifted from previous position = 0.0131
rotated from previous position = 0.0397 degrees
atoms outside contour = 1740, contour level = 0.0047281
Position of CopB_ Q9JIF7.pdb (#16) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.03637895 -0.65951364 0.75081178 218.49894110
0.00358828 0.75121805 0.66004437 248.02561118
-0.99933162 0.02670584 -0.02496200 272.25349195
Axis -0.32054633 0.88578543 0.33561022
Axis point 246.51297715 0.00000000 -53.64753499
Rotation angle (degrees) 98.92036028
Shift along axis 241.02949485
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> hide #!16 models
> show #!16 models
> rename #16 "CopB_ Q9JIF7_.pdb"
> rename #16 "CopB_ Q9JIF7_F394-L953.pdb"
> hide #!16 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v40_labelled.cxs"
> show #!3 models
> show #!7 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #!3 models
> hide #!7 models
> show #!3 models
> hide #27.1 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> rename #7 CopBprime_O55029_beta_props_M1-S586.pdb
> rename #3 CopBprime_O55029_solenoid_L587-E838.pdb
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v40_labelled.cxs"
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopBprime_O55029.pdb"
CopBprime_O55029.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit β' (O55029) [more
info...]
Chain information for CopBprime_O55029.pdb #17
---
Chain | Description | UniProt
A | coatomer subunit β' | COPB2_MOUSE 1-905
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #17 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopBprime_O55029_solenoid_L587-E838.pdb, chain A (#3) with
CopBprime_O55029.pdb, chain A (#17), sequence alignment score = 3580.9
RMSD between 253 pruned atom pairs is 0.000 angstroms; (across all 253 pairs:
0.000)
> color #17 cyan
> close #17
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v40_labelled.cxs"
> show #!30 models
> show #!2 models
> show #27.2 models
> hide #!2 models
> hide #27.2 models
> hide #!30 models
> hide #!32 models
> show #!13 models
> show #!14 models
> show #!1 models
> fitmap #13 inMap #1
Fit molecule CopA-Q8CIE6_solenoid.pdb (#13) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1493 atoms
average map value = 0.009856, steps = 40
shifted from previous position = 0.04
rotated from previous position = 0.256 degrees
atoms outside contour = 504, contour level = 0.0047281
Position of CopA-Q8CIE6_solenoid.pdb (#13) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.09214279 0.81710559 -0.56907658 198.83642817
-0.30256058 -0.56746131 -0.76579681 282.30024669
-0.94866580 0.10161748 0.29951141 272.32967343
Axis 0.59155130 0.25886880 -0.76357973
Axis point 286.85143345 127.57854798 0.00000000
Rotation angle (degrees) 132.84726465
Shift along axis -17.24474722
> fitmap #14 inMap #1
Fit molecule CopA-Q8CIE6_beta_props.pdb (#14) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008718, steps = 28
shifted from previous position = 0.024
rotated from previous position = 0.0248 degrees
atoms outside contour = 1497, contour level = 0.0047281
Position of CopA-Q8CIE6_beta_props.pdb (#14) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.34442107 0.69704982 -0.62888447 201.10586095
0.21648780 -0.59284749 -0.77567060 281.00648441
-0.91351363 -0.40330312 0.05328639 263.96649003
Axis 0.55471611 0.42401227 -0.71589359
Axis point 234.60558972 197.19377182 0.00000000
Rotation angle (degrees) 160.38866792
Shift along axis 41.73494188
> hide #!13 models
> hide #!1 models
> rename #14 CopA-Q8CIE6_beta_props_M1-T591.pdb
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!1 models
> hide #!1 models
> rename #13 CopA-Q8CIE6_solenoid_I592-T777.pdb
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopA-Q8CIE6.pdb"
CopA-Q8CIE6.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit α (Q8CIE6) [more
info...]
Chain information for CopA-Q8CIE6.pdb #17
---
Chain | Description | UniProt
A | coatomer subunit α | COPA_MOUSE 1-1224
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #17 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA-Q8CIE6_solenoid_I592-T777.pdb, chain A (#13) with
CopA-Q8CIE6.pdb, chain A (#17), sequence alignment score = 4842.3
RMSD between 186 pruned atom pairs is 0.000 angstroms; (across all 186 pairs:
0.000)
> show #!14 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> hide #17 models
> show #17 models
> show #!1 models
> show #!3 models
> hide #17 models
> hide #!3 models
> show #17 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> ui mousemode right select
Drag select of 324 residues
> select up
2945 atoms, 3023 bonds, 360 residues, 1 model selected
> delete sel
> hide #!13 models
> show #!13 models
> hide #!17 models
> show #!17 models
> hide #!13 models
> show #!13 models
> hide #!13 models
Drag select of 220 residues, 4 pseudobonds
> select up
1806 atoms, 1835 bonds, 4 pseudobonds, 229 residues, 2 models selected
> delete sel
> hide #!17 models
> show #!17 models
> show #!13 models
> hide #!17 models
> show #!17 models
Drag select of 2 residues
> delete sel
> hide #!13 models
> show #!13 models
Drag select of 299 residues
> select up
3058 atoms, 3120 bonds, 391 residues, 1 model selected
> delete sel
Drag select of 6 residues
Drag select of 8 residues
> delete sel
Drag select of 12 residues
> delete sel
> color #17 #004affff
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
Drag select of 5 residues
> delete sel
Drag select of 5 residues
> delete sel
Drag select of 3 residues
> delete sel
Drag select of 3 residues
> delete sel
> show #!1 models
> fitmap #17 inMap #1
Fit molecule CopA-Q8CIE6.pdb (#17) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1653 atoms
average map value = 0.009453, steps = 48
shifted from previous position = 0.0862
rotated from previous position = 1.38 degrees
atoms outside contour = 577, contour level = 0.0047281
Position of CopA-Q8CIE6.pdb (#17) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.06845807 0.82084445 -0.56703428 198.78096995
-0.30358441 -0.55855363 -0.77191602 282.52342968
-0.95034204 0.11929889 0.28743308 272.74817735
Axis 0.60010334 0.25810191 -0.75713895
Axis point 291.53210163 126.85447772 0.00000000
Rotation angle (degrees) 132.05080567
Shift along axis -14.29930723
> fitmap #17 inMap #1
Fit molecule CopA-Q8CIE6.pdb (#17) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1653 atoms
average map value = 0.009453, steps = 40
shifted from previous position = 0.00991
rotated from previous position = 0.0527 degrees
atoms outside contour = 577, contour level = 0.0047281
Position of CopA-Q8CIE6.pdb (#17) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.06755042 0.82094493 -0.56699768 198.78818114
-0.30351587 -0.55826991 -0.77214819 282.52608291
-0.95042888 0.11993386 0.28688118 272.77368705
Axis 0.60045412 0.25808483 -0.75686661
Axis point 291.71815224 126.83502087 0.00000000
Rotation angle (degrees) 132.02613965
Shift along axis -14.17441757
> hide #!1 models
Drag select of 3 residues
> delete sel
> show #!1 models
> hide #!1 models
Drag select of 12 residues
> select clear
> fitmap #17 inMap #1
Fit molecule CopA-Q8CIE6.pdb (#17) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1629 atoms
average map value = 0.009463, steps = 44
shifted from previous position = 0.132
rotated from previous position = 1.12 degrees
atoms outside contour = 562, contour level = 0.0047281
Position of CopA-Q8CIE6.pdb (#17) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.08657160 0.81843121 -0.56804551 198.83570444
-0.29956180 -0.56518406 -0.76865448 282.36669779
-0.95014109 0.10362109 0.29409961 272.49652777
Axis 0.59395260 0.26017771 -0.76126728
Axis point 288.02467807 127.91892222 0.00000000
Rotation angle (degrees) 132.75212810
Shift along axis -15.87818803
> fitmap #17 inMap #1
Fit molecule CopA-Q8CIE6.pdb (#17) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1629 atoms
average map value = 0.009463, steps = 44
shifted from previous position = 0.0381
rotated from previous position = 0.104 degrees
atoms outside contour = 563, contour level = 0.0047281
Position of CopA-Q8CIE6.pdb (#17) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.08837560 0.81836583 -0.56786189 198.80999445
-0.29937497 -0.56555704 -0.76845290 282.38827482
-0.95003388 0.10209115 0.29497969 272.44395498
Axis 0.59325832 0.26044255 -0.76171795
Axis point 287.67565023 128.03192381 0.00000000
Rotation angle (degrees) 132.80274633
Shift along axis -16.03384414
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 3 residues
> delete sel
> show #!1 models
> show #!3 models
> hide #!3 models
> rename #17 CopA-Q8CIE6_solecoid_I592-.pdb
> hide #!1 models
> rename #17 CopA-Q8CIE6_solecoid_I592-N791.pdb
> hide #!17 models
> close #13
> rename #17 CopA-Q8CIE6_solenoid_I592-N791.pdb
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!27 models
> show #!27 models
> show #27.1 models
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6538 atoms
average map value = 0.009129, steps = 28
shifted from previous position = 0.0407
rotated from previous position = 0.0452 degrees
atoms outside contour = 2197, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99559484 0.00374324 0.09368509 -80.52958620
-0.00521737 0.99986633 0.01549493 -75.31400016
-0.09361457 -0.01591546 0.99548130 -68.64550567
Axis -0.16520792 0.98513204 -0.04712972
Axis point -806.87142651 0.00000000 923.30838386
Rotation angle (degrees) 5.45495891
Shift along axis -57.65486622
> fitmap #27.1 inMap #1
Fit molecule 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6538 atoms
average map value = 0.009129, steps = 28
shifted from previous position = 0.0471
rotated from previous position = 0.0446 degrees
atoms outside contour = 2199, contour level = 0.0047281
Position of 3mkq_yeast_alpha_betaprimeCOPI.cif A (#27.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99555306 0.00346629 0.09413872 -80.58795937
-0.00500218 0.99985813 0.01608414 -75.45401159
-0.09406962 -0.01648351 0.99542915 -68.55921561
Axis -0.17033920 0.98438951 -0.04429282
Axis point -800.70772442 0.00000000 922.29669395
Rotation angle (degrees) 5.48565168
Shift along axis -57.51216813
> hide #!1 models
> hide #27.1 models
> show #!7 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> hide #!7 models
> hide #!3 models
> show #32.1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #32.1 models
> hide #!4 models
> show #!15 models
> show #!16 models
> hide #!15 models
> show #!15 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopB_ Q9JIF7.pdb"
CopB_ Q9JIF7.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit β (Q9JIF7) [more
info...]
Chain information for CopB_ Q9JIF7.pdb #13
---
Chain | Description | UniProt
A | coatomer subunit β | COPB_MOUSE 1-953
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopB_ Q9JIF7.pdb"
CopB_ Q9JIF7.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit β (Q9JIF7) [more
info...]
Chain information for CopB_ Q9JIF7.pdb #18
---
Chain | Description | UniProt
A | coatomer subunit β | COPB_MOUSE 1-953
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #18 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_Q9JIF7_P395-L953.pdb, chain A (#4) with CopB_ Q9JIF7.pdb,
chain A (#18), sequence alignment score = 4184.9
RMSD between 418 pruned atom pairs is 0.845 angstroms; (across all 520 pairs:
2.356)
> hide #!16 models
> hide #!15 models
> hide #13 models
> close #13
> show #!1 models
> hide #!1 models
> show #!4 models
> close #18
> show #!1 models
> hide #!4 models
> hide #!1 models
> hide #!27 models
> show #!27 models
> show #32.2 models
> color #32.2 #b55c00ff
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #8 to #32.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5mu7_Thermophila_beta_deltaCOPI.cif B, chain B (#32.2) with
CopD_Q5XJY5, chain A (#8), sequence alignment score = 518
RMSD between 138 pruned atom pairs is 0.707 angstroms; (across all 150 pairs:
1.098)
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #!1 models
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map relion_locres_filtered_20240326_GT.mrc
(#1) using 1462 atoms
average map value = 0.00841, steps = 84
shifted from previous position = 1.47
rotated from previous position = 5.16 degrees
atoms outside contour = 557, contour level = 0.0047281
Position of CopD_Q5XJY5 (#8) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.07154755 0.98848917 0.13330464 -99.08181251
-0.91244029 0.01087778 0.40906527 162.75356743
0.40290653 -0.15090014 0.90271562 445.95259972
Axis -0.27999043 -0.13480467 -0.95049096
Axis point -59.66961351 162.60931329 0.00000000
Rotation angle (degrees) 90.42568446
Shift along axis -418.07189440
> fitmap #8 inMap #1
Fit molecule CopD_Q5XJY5 (#8) to map relion_locres_filtered_20240326_GT.mrc
(#1) using 1462 atoms
average map value = 0.00841, steps = 84
shifted from previous position = 1.47
rotated from previous position = 5.16 degrees
atoms outside contour = 557, contour level = 0.0047281
Position of CopD_Q5XJY5 (#8) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.07154755 0.98848917 0.13330464 -99.08181251
-0.91244029 0.01087778 0.40906527 162.75356743
0.40290653 -0.15090014 0.90271562 445.95259972
Axis -0.27999043 -0.13480467 -0.95049096
Axis point -59.66961351 162.60931329 0.00000000
Rotation angle (degrees) 90.42568446
Shift along axis -418.07189440
> hide #!1 models
> hide #8 models
> show #32.1 models
> show #8 models
> show #!1 models
> hide #!1 models
> hide #32.1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_v41_labelled.cxs"
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopD_Q5XJY5.pdb"
CopD_Q5XJY5.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit δ (Q5XJY5) [more
info...]
Chain information for CopD_Q5XJY5.pdb #13
---
Chain | Description | UniProt
A | coatomer subunit δ | COPD_MOUSE 1-511
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #13 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopD_Q5XJY5, chain A (#8) with CopD_Q5XJY5.pdb, chain A (#13),
sequence alignment score = 2127.5
RMSD between 179 pruned atom pairs is 0.000 angstroms; (across all 179 pairs:
0.000)
> hide #8 models
> hide #32.2 models
> close #13
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.1 models
> hide #26.3 models
> show #!9 models
> show #!29 models
> hide #!29 models
> hide #!1 models
> hide #!9 models
> fitmap #26.2 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2069 atoms
average map value = 0.01291, steps = 56
shifted from previous position = 0.0251
rotated from previous position = 0.051 degrees
atoms outside contour = 608, contour level = 0.0047281
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.26733622 0.21032158 -0.94037023 331.60663228
0.69674895 0.71631482 -0.03786782 310.04890379
0.66563672 -0.66532541 -0.33803823 215.93057949
Axis -0.35023598 -0.89644530 0.27151535
Axis point -0.95000729 0.00000000 228.97636103
Rotation angle (degrees) 116.39326055
Shift along axis -335.45398968
> fitmap #26.2 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2069 atoms
average map value = 0.01291, steps = 36
shifted from previous position = 0.00374
rotated from previous position = 0.0122 degrees
atoms outside contour = 609, contour level = 0.0047281
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.26717041 0.21033229 -0.94041496 331.60392234
0.69686519 0.71620571 -0.03779244 310.03972167
0.66558160 -0.66543948 -0.33792223 215.92559862
Axis -0.35032496 -0.89639662 0.27156126
Axis point -0.98873363 0.00000000 228.98410216
Rotation angle (degrees) 116.38773736
Shift along axis -335.45066247
> fitmap #26.2 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2069 atoms
average map value = 0.01291, steps = 28
shifted from previous position = 0.0326
rotated from previous position = 0.0234 degrees
atoms outside contour = 610, contour level = 0.0047281
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.26697217 0.21065641 -0.94039871 331.59657938
0.69706188 0.71602994 -0.03749454 310.03682210
0.66545517 -0.66552610 -0.33800062 215.90836829
Axis -0.35054501 -0.89633087 0.27149434
Axis point -1.03095250 0.00000000 228.93362673
Rotation angle (degrees) 116.38952549
Shift along axis -335.51719967
> fitmap #26.2 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2069 atoms
average map value = 0.01291, steps = 28
shifted from previous position = 0.00445
rotated from previous position = 0.0137 degrees
atoms outside contour = 610, contour level = 0.0047281
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.26679252 0.21056017 -0.94047124 331.58927289
0.69714625 0.71594888 -0.03747386 310.03464837
0.66543884 -0.66564375 -0.33780104 215.89715592
Axis -0.35059328 -0.89628824 0.27157273
Axis point -1.07395213 0.00000000 228.95451697
Rotation angle (degrees) 116.37999043
Shift along axis -335.50160010
> fitmap #26.2 inMap #1
Fit molecule 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2069 atoms
average map value = 0.01291, steps = 28
shifted from previous position = 0.0267
rotated from previous position = 0.0146 degrees
atoms outside contour = 611, contour level = 0.0047281
Position of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B (#26.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.26667615 0.21041952 -0.94053572 331.59520251
0.69725196 0.71584216 -0.03754595 310.01061083
0.66537473 -0.66580299 -0.33761345 215.89823911
Axis -0.35062278 -0.89623952 0.27169540
Axis point -1.10328148 0.00000000 228.99319129
Rotation angle (degrees) 116.37368341
Shift along axis -335.45003587
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!26.2 models
Drag select of 2 pseudobonds
> delete sel
> select add #9
2173 atoms, 2202 bonds, 4 pseudobonds, 277 residues, 2 models selected
> select subtract #9
Nothing selected
Drag select of 1 pseudobonds
> delete sel
[Repeated 1 time(s)]
> show #!26.2 models
> hide #!9 models
> select add #9
2173 atoms, 2202 bonds, 4 pseudobonds, 277 residues, 2 models selected
> show #!9 models
> select subtract #9
Nothing selected
> hide #!26.2 models
> show #!26.2 models
> rename #8 CopD_Q5XJY5_M1-R175
> hide #!9 models
> show #!9 models
> hide #!26.2 models
> rename #9 CopG_Q9QZE5_L311-T583
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopG1_ Q9QZE5.pdb"
CopG1_ Q9QZE5.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit γ-1 (Q9QZE5) [more
info...]
Chain information for CopG1_ Q9QZE5.pdb #13
---
Chain | Description | UniProt
A | coatomer subunit γ-1 | COPG1_MOUSE 1-874
> color #13 #24fa00ff
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #13 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopG_Q9QZE5_L311-T583, chain A (#9) with CopG1_ Q9QZE5.pdb, chain A
(#13), sequence alignment score = 3547.2
RMSD between 276 pruned atom pairs is 0.730 angstroms; (across all 277 pairs:
2.377)
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #13 models
> show #13 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!1 models
> show #!1 models
> hide #13 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> show #!29 models
> hide #!29 models
> show #!29 models
> show #13 models
> hide #!1 models
> hide #!9 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #13 to #29
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B, chain B (#29)
with CopG1_ Q9QZE5.pdb, chain A (#13), sequence alignment score = 1223.2
RMSD between 214 pruned atom pairs is 0.825 angstroms; (across all 264 pairs:
2.836)
> show #!1 models
> show #!7 models
> hide #!7 models
> hide #13 models
> show #13 models
> hide #13 models
> hide #!26.2 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!17 models
> hide #!17 models
> show #!26.2 models
> show #13 models
> hide #!26.2 models
> hide #13 models
> show #!15 models
> hide #!15 models
> show #!17 models
> hide #!17 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> show #!9 models
> show #13 models
> show #8 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #5 models
> show #6 models
> show #!7 models
> hide #13 models
> hide #!9 models
> hide #!26.2 models
> show #!25.6 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!25.6 to #29
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B, chain B (#29)
with 5nzr_COPI_coat_leaf_2017.cif G, chain G (#25.6), sequence alignment score
= 1180.9
RMSD between 127 pruned atom pairs is 1.367 angstroms; (across all 263 pairs:
3.108)
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #5 models
> hide #6 models
> hide #!7 models
> hide #8 models
> show #13 models
> hide #!1 models
> hide #13 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!29 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #!25.6 models
> hide #13 models
> show #!9 models
> show #13 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #13 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopG_Q9QZE5_L311-T583, chain A (#9) with CopG1_ Q9QZE5.pdb, chain A
(#13), sequence alignment score = 3547.2
RMSD between 276 pruned atom pairs is 0.730 angstroms; (across all 277 pairs:
2.377)
> hide #!9 models
> show #!9 models
> hide #!9 models
Drag select of 140 residues
> select up
1252 atoms, 1269 bonds, 161 residues, 1 model selected
> delete sel
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
Drag select of 129 residues, 1 pseudobonds
> delete sel
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
Drag select of 52 residues
> select up
437 atoms, 438 bonds, 56 residues, 1 model selected
> select down
413 atoms, 52 residues, 1 model selected
> select up
437 atoms, 438 bonds, 56 residues, 1 model selected
Drag select of 68 residues, 1 pseudobonds
> select up
580 atoms, 584 bonds, 1 pseudobond, 77 residues, 2 models selected
> delete sel
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
Drag select of 101 residues
> select clear
Drag select of 193 residues
> select down
1544 atoms, 193 residues, 1 model selected
> select up
1595 atoms, 1619 bonds, 200 residues, 1 model selected
> select down
1544 atoms, 193 residues, 1 model selected
Drag select of 165 residues
> select up
1436 atoms, 1456 bonds, 180 residues, 1 model selected
> delete sel
> select clear
[Repeated 2 time(s)]
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
Drag select of 3 residues
> delete sel
Drag select of 17 residues
> select clear
Drag select of 8 residues
> select up
103 atoms, 104 bonds, 13 residues, 1 model selected
> delete sel
Drag select of 1 residues
Drag select of 2 residues
[Repeated 1 time(s)]
> select up
98 atoms, 99 bonds, 12 residues, 1 model selected
> delete sel
> show #!9 models
> hide #!9 models
> show #!1 models
> select add #13
2328 atoms, 2373 bonds, 299 residues, 1 model selected
Drag select of 1 relion_locres_filtered_20240326_GT.mrc
Drag select of 1 relion_locres_filtered_20240326_GT.mrc , 3 residues
> select subtract #1
27 atoms, 3 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.26248,-0.32251,-0.90944,345.14,0.81049,-0.43779,0.38917,383.4,-0.52366,-0.83924,0.14648,353.45
> view matrix models
> #13,0.26248,-0.32251,-0.90944,352.18,0.81049,-0.43779,0.38917,384.15,-0.52366,-0.83924,0.14648,347.38
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.20094,-0.82826,0.52308,353.56,0.46419,-0.38971,-0.7954,372.84,0.86264,0.40263,0.30616,383.21
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view matrix models
> #13,-0.6819,-0.58472,0.43944,345.73,-0.64001,0.18612,-0.74548,367.96,0.35411,-0.7896,-0.50114,354.56
> view matrix models
> #13,-0.66738,-0.63667,0.38634,344.81,-0.58717,0.13074,-0.79884,367.46,0.45808,-0.75997,-0.46109,356.52
> fitmap #13 inMap #1
Fit molecule CopG1_ Q9QZE5.pdb (#13) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2328 atoms
average map value = 0.005846, steps = 152
shifted from previous position = 18.7
rotated from previous position = 34.7 degrees
atoms outside contour = 1035, contour level = 0.0047281
Position of CopG1_ Q9QZE5.pdb (#13) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.46400453 -0.87604818 0.13129885 283.29510646
-0.79478126 0.34625888 -0.49842507 304.63145454
0.39118098 -0.33562535 -0.85693236 272.46239451
Axis 0.51316106 -0.81917459 0.25616151
Axis point 223.36083300 0.00000000 198.52241567
Rotation angle (degrees) 170.87294058
Shift along axis -34.37594886
> select add #13
2328 atoms, 2373 bonds, 299 residues, 1 model selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!13 to #25.6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif G, chain G (#25.6) with CopG1_
Q9QZE5.pdb, chain A (#13), sequence alignment score = 3073
RMSD between 123 pruned atom pairs is 1.312 angstroms; (across all 269 pairs:
3.600)
> select subtract #13
Nothing selected
> hide #!13 models
> show #!13 models
> fitmap #13 inMap #1
Fit molecule CopG1_ Q9QZE5.pdb (#13) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2328 atoms
average map value = 0.004732, steps = 72
shifted from previous position = 2.67
rotated from previous position = 6.72 degrees
atoms outside contour = 1293, contour level = 0.0047281
Position of CopG1_ Q9QZE5.pdb (#13) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.18707219 0.85236259 -0.48834620 272.23506983
0.06514904 -0.48526289 -0.87193780 156.24354137
-0.98018346 -0.19493060 0.03524859 290.05062704
Axis 0.58927078 0.42809784 -0.68519499
Axis point 294.03599204 109.85965168 0.00000000
Rotation angle (degrees) 144.93923178
Shift along axis 28.56645803
> hide #!13 models
> show #!13 models
> hide #!1 models
> show #!25.6 models
> show #!29 models
> hide #!29 models
> hide #!25.6 models
> show #!26.2 models
> hide #!26.2 models
> show #!1 models
> ui mousemode right select
> hide #!1 models
Drag select of 8 residues
> select up
215 atoms, 218 bonds, 30 residues, 1 model selected
Drag select of 14 residues
> select up
238 atoms, 241 bonds, 33 residues, 1 model selected
> delete sel
> fitmap #13 inMap #1
Fit molecule CopG1_ Q9QZE5.pdb (#13) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2090 atoms
average map value = 0.005123, steps = 36
shifted from previous position = 0.196
rotated from previous position = 0.651 degrees
atoms outside contour = 1054, contour level = 0.0047281
Position of CopG1_ Q9QZE5.pdb (#13) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.19744764 0.85137415 -0.48597993 272.26620708
0.06847691 -0.48255036 -0.87318731 156.25250448
-0.97791889 -0.20568718 0.03697896 289.87675959
Axis 0.58532639 0.43137797 -0.68651734
Axis point 292.60102451 110.83100436 0.00000000
Rotation angle (degrees) 145.23618902
Shift along axis 27.76306241
> show #!1 models
> rename #13 "CopG1_ Q9QZE5_R609-G874.pdb"
> hide #!13 models
> show #!13 models
> hide #!13 models
> combine #9
> hide #!18 models
> show #!18 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!1 models
> hide #!18 models
> show #!18 models
> show #!25.6 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!18 to #25.6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif G, chain G (#25.6) with copy of
CopG_Q9QZE5_L311-T583, chain A (#18), sequence alignment score = 3090.4
RMSD between 60 pruned atom pairs is 1.358 angstroms; (across all 242 pairs:
4.811)
> hide #!25.6 models
> show #!1 models
> show #!29 models
> show #!13 models
> hide #!29 models
> hide #!18 models
> hide #!13 models
> show #!26.2 models
> show #!9 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!25.6 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopG_Q9QZE5_L311-T583, chain A (#9) with
5nzr_COPI_coat_leaf_2017.cif G, chain G (#25.6), sequence alignment score =
3090.4
RMSD between 60 pruned atom pairs is 1.358 angstroms; (across all 242 pairs:
4.811)
> show #!25.6 models
> combine #13
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!19 to #25.6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5nzr_COPI_coat_leaf_2017.cif G, chain G (#25.6) with copy of CopG1_
Q9QZE5_R609-G874.pdb, chain A (#19), sequence alignment score = 3065.8
RMSD between 122 pruned atom pairs is 1.308 angstroms; (across all 266 pairs:
3.294)
> hide #!25.6 models
> fitmap #19 inMap #1
Fit molecule copy of CopG1_ Q9QZE5_R609-G874.pdb (#19) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2090 atoms
average map value = 0.005022, steps = 344
shifted from previous position = 25.9
rotated from previous position = 56.5 degrees
atoms outside contour = 1255, contour level = 0.0047281
Position of copy of CopG1_ Q9QZE5_R609-G874.pdb (#19) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.55193647 -0.74723442 -0.37014437 274.69126079
0.63814190 -0.66421874 0.38934353 305.66395297
-0.53678771 -0.02131174 0.84344814 288.65866085
Axis -0.28232731 0.11456803 0.95245234
Axis point 116.95421290 212.51516264 0.00000000
Rotation angle (degrees) 133.34214802
Shift along axis 232.40009025
> hide #!26.2 models
> show #!26.2 models
> show #!29 models
> show #!18 models
> show #!13 models
> hide #!1 models
> hide #!9 models
> hide #!26.2 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/CopG1_ Q9QZE5.pdb"
CopG1_ Q9QZE5.pdb title:
Alphafold monomer V2.0 prediction for coatomer subunit γ-1 (Q9QZE5) [more
info...]
Chain information for CopG1_ Q9QZE5.pdb #20
---
Chain | Description | UniProt
A | coatomer subunit γ-1 | COPG1_MOUSE 1-874
> color #20 #38fb00ff
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #20 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopG_Q9QZE5_L311-T583, chain A (#9) with CopG1_ Q9QZE5.pdb, chain A
(#20), sequence alignment score = 3547.2
RMSD between 276 pruned atom pairs is 0.730 angstroms; (across all 277 pairs:
2.377)
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> hide #!18 models
> hide #!19 models
> hide #!13 models
> hide #!29 models
> show #!19 models
> hide #20 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!9 models
> show #20 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #20 to #26.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B, chain B (#26.2) with
CopG1_ Q9QZE5.pdb, chain A (#20), sequence alignment score = 1223.2
RMSD between 214 pruned atom pairs is 0.825 angstroms; (across all 264 pairs:
2.836)
> show #!26.2 models
> hide #!26.2 models
Drag select of 487 residues
> select up
3979 atoms, 4051 bonds, 507 residues, 1 model selected
> delete sel
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> hide #!20 models
> show #!20 models
Drag select of 14 residues
> select up
129 atoms, 129 bonds, 16 residues, 1 model selected
> delete sel
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> show #!1 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!26.2 models
> hide #!20 models
> show #!29 models
> hide #!29 models
> show #!26.2 models
> hide #!1 models
> show #!20 models
> show #!9 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!9 models
> hide #!9 models
> hide #!20 models
> show #!9 models
> show #!1 models
> hide #!1 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!20 models
Drag select of 24 residues
> select up
197 atoms, 196 bonds, 26 residues, 1 model selected
> delete sel
Drag select of 7 residues
> delete sel
> fitmap #20 inMap #1
Fit molecule CopG1_ Q9QZE5.pdb (#20) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2482 atoms
average map value = 0.01112, steps = 52
shifted from previous position = 0.772
rotated from previous position = 5.6 degrees
atoms outside contour = 865, contour level = 0.0047281
Position of CopG1_ Q9QZE5.pdb (#20) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55710873 -0.07627004 -0.82692971 263.00523089
0.76700327 -0.33445249 0.54758334 289.99057464
-0.31833291 -0.93932125 -0.12782703 276.73132173
Axis -0.83372741 -0.28517707 0.47283470
Axis point 0.00000000 231.68438433 124.14950695
Rotation angle (degrees) 116.90968153
Shift along axis -171.12516145
> show #!1 models
> hide #!1 models
Drag select of 15 residues
> select up
180 atoms, 182 bonds, 23 residues, 1 model selected
> delete sel
> fitmap #20 inMap #1
Fit molecule CopG1_ Q9QZE5.pdb (#20) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2302 atoms
average map value = 0.01162, steps = 48
shifted from previous position = 0.0621
rotated from previous position = 0.185 degrees
atoms outside contour = 743, contour level = 0.0047281
Position of CopG1_ Q9QZE5.pdb (#20) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55964495 -0.07618951 -0.82522281 262.95431078
0.76574603 -0.33324062 0.55007609 290.10442387
-0.31690778 -0.93975840 -0.12815461 276.70475087
Axis -0.83455979 -0.28474256 0.47162658
Axis point 0.00000000 232.00364407 123.73056407
Rotation angle (degrees) 116.79984588
Shift along axis -171.55485435
> fitmap #20 inMap #1
Fit molecule CopG1_ Q9QZE5.pdb (#20) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2302 atoms
average map value = 0.01162, steps = 40
shifted from previous position = 0.0116
rotated from previous position = 0.00964 degrees
atoms outside contour = 745, contour level = 0.0047281
Position of CopG1_ Q9QZE5.pdb (#20) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55953483 -0.07626531 -0.82529048 262.96525640
0.76582416 -0.33317606 0.55000643 290.09547063
-0.31691344 -0.93977514 -0.12801779 276.71363286
Axis -0.83450860 -0.28476994 0.47170063
Axis point 0.00000000 232.00972021 123.74632857
Rotation angle (degrees) 116.79691707
Shift along axis -171.53124161
> show #!1 models
> hide #!1 models
> show #!9 models
> show #!1 models
> hide #!1 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> rename #20 "CopG1_ Q9QZE5_K24-.pdb"
> rename #20 "CopG1_ Q9QZE5_K24-H318.pdb"
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_v42_labelled.cxs"
> combine #20
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!21 to #29
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B, chain B (#29)
with copy of CopG1_ Q9QZE5_K24-H318.pdb, chain A (#21), sequence alignment
score = 1214.8
RMSD between 214 pruned atom pairs is 0.839 angstroms; (across all 260 pairs:
2.778)
> hide #!20 models
> show #!29 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!21 models
> hide #!29 models
> show #!18 models
> show #!21 models
> show #!1 models
> hide #!21 models
> hide #!18 models
> hide #!1 models
> show #!1 models
> show #10 models
> show #12 models
> show #26.3 models
> show #28 models
> hide #!1 models
> hide #26.3 models
> show #26.3 models
> hide #26.3 models
> hide #28 models
> show #28 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #12 models
> show #12 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #32.1 models
> hide #32.1 models
> show #!40 models
> hide #!40 models
> show #!29 models
> show #!18 models
> hide #!18 models
> show #!21 models
> hide #!29 models
> hide #28 models
> show #28 models
> hide #!21 models
> hide #28 models
> show #28 models
> hide #!1 models
> hide #12 models
> show #12 models
> hide #10 models
> show #!1 models
> hide #!1 models
Drag select of 17 residues
> select up
200 atoms, 202 bonds, 25 residues, 1 model selected
> select clear
Drag select of 24 residues
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> delete sel
> show #!1 models
> hide #!1 models
> hide #28 models
> rename #12 "copy of CopZ1_P61924_M1-V153.pdb"
> hide #12 models
> show #12 models
> show #10 models
Drag select of 23 residues
> delete sel
Drag select of 1 residues
> delete sel
> rename #10 CopZ1_P61924_M1-V153.pdb
> hide #10 models
> show #26.3 models
> show #10 models
> hide #10 models
> hide #12 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_v42_labelled.cxs"
> hide #26.3 models
> show #!24 models
> show #11 models
> hide #11 models
> show #11 models
> show #!1 models
> hide #!1 models
Drag select of 20 residues
> select up
174 atoms, 173 bonds, 23 residues, 1 model selected
> delete sel
Drag select of 16 residues
> select up
281 atoms, 280 bonds, 38 residues, 1 model selected
> select down
100 atoms, 16 residues, 1 model selected
Drag select of 4 residues
Drag select of 8 residues
> delete sel
Drag select of 11 residues
> delete sel
Drag select of 3 residues
Drag select of 5 residues
> delete sel
> select clear
Drag select of 6 residues
> delete sel
Drag select of 1 residues
> delete sel
> show #!1 models
> select #11/A:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> hide #!1 models
> hide #!24 models
> rename #11 "Golph3_ Q9CRA5_K56-K298.pdb"
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_v42_labelled.cxs"
> hide #11 models
> show #!40 models
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!4 models
> hide #!4 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!40 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_Q9JIF7_P395-L953.pdb, chain A (#4) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 4110.5
RMSD between 179 pruned atom pairs is 1.370 angstroms; (across all 520 pairs:
5.457)
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #40.1 models
> show #40.1 models
> hide #!40 models
> show #!40 models
> hide #40.1 models
> show #40.1 models
> hide #40.2 models
> show #40.2 models
> hide #40.1 models
> show #40.1 models
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> show #!4 models
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.45175,0.88042,0.14417,282.18,0.88959,0.45675,-0.0017694,344.15,-0.067408,0.12745,-0.98955,350.14
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.48319,0.8755,0.0039949,280.87,0.85474,0.47271,-0.21439,341.94,-0.18959,-0.10018,-0.97674,352.43
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.48319,0.8755,0.0039949,278.81,0.85474,0.47271,-0.21439,341.94,-0.18959,-0.10018,-0.97674,350.53
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 200
shifted from previous position = 8.42
rotated from previous position = 12.5 degrees
atoms outside contour = 24977, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52028952 0.84088907 0.14901137 220.07158255
0.84302980 0.53359831 -0.06762847 260.64421830
-0.13638026 0.09043464 -0.98652015 268.86282147
Axis 0.48448953 0.87477245 0.00656169
Axis point 50.37234045 0.00000000 130.77427705
Rotation angle (degrees) 170.61176661
Shift along axis 336.39095332
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005222, steps = 64
shifted from previous position = 0.0384
rotated from previous position = 0.0256 degrees
atoms outside contour = 24974, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52062312 0.84070985 0.14885742 220.03596019
0.84281462 0.53392261 -0.06775084 260.63448528
-0.13643714 0.09018656 -0.98653500 268.85402522
Axis 0.48432100 0.87486657 0.00645437
Axis point 50.38436969 0.00000000 130.78499451
Rotation angle (degrees) 170.61600734
Shift along axis 336.32371732
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 104
shifted from previous position = 0.0365
rotated from previous position = 0.0151 degrees
atoms outside contour = 24982, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52041410 0.84082219 0.14895373 220.07025505
0.84294218 0.53372423 -0.06772691 260.64629599
-0.13644650 0.09031335 -0.98652210 268.85494797
Axis 0.48442493 0.87480870 0.00649820
Axis point 50.38369375 0.00000000 130.77854463
Rotation angle (degrees) 170.61187337
Shift along axis 336.37023767
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005222, steps = 48
shifted from previous position = 0.0459
rotated from previous position = 0.0282 degrees
atoms outside contour = 24966, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52081360 0.84060651 0.14877464 220.02590390
0.84270437 0.53409979 -0.06772571 260.63740010
-0.13639118 0.09010057 -0.98654921 268.85096863
Axis 0.48422748 0.87491846 0.00643644
Axis point 50.38967324 0.00000000 130.78640422
Rotation angle (degrees) 170.62084158
Shift along axis 336.30950487
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005222, steps = 48
shifted from previous position = 0.0366
rotated from previous position = 0.0134 degrees
atoms outside contour = 24967, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52067236 0.84069681 0.14875876 220.05486438
0.84276997 0.53397284 -0.06791016 260.65467963
-0.13652500 0.09001047 -0.98653892 268.83774949
Axis 0.48429600 0.87488112 0.00635777
Axis point 50.39301899 0.00000000 130.79007829
Rotation angle (degrees) 170.61652318
Shift along axis 336.32275464
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 44
shifted from previous position = 0.0138
rotated from previous position = 0.018 degrees
atoms outside contour = 24974, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52048878 0.84078702 0.14889135 220.06131970
0.84289793 0.53379198 -0.06774370 260.65567170
-0.13643503 0.09024038 -0.98653037 268.84933649
Axis 0.48438915 0.87482870 0.00647220
Axis point 50.37990075 0.00000000 130.78014813
Rotation angle (degrees) 170.61454145
Shift along axis 336.36442614
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> view matrix models
> #40,-0.53175,0.83455,0.14409,280.1,0.83762,0.54337,-0.055977,340.95,-0.12501,0.090928,-0.98798,350.27
> view matrix models
> #40,-0.53175,0.83455,0.14409,281.03,0.83762,0.54337,-0.055977,340.26,-0.12501,0.090928,-0.98798,350.34
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.41151,0.87987,0.23768,281.72,0.86546,0.459,-0.20074,339.93,-0.28572,0.12309,-0.95037,349.89
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.41151,0.87987,0.23768,280.57,0.86546,0.459,-0.20074,340.91,-0.28572,0.12309,-0.95037,350.32
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.61633,0.72128,0.31606,282.47,0.75468,0.65564,-0.024568,340.07,-0.22494,0.22338,-0.94842,349.41
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.61633,0.72128,0.31606,282.55,0.75468,0.65564,-0.024568,340.73,-0.22494,0.22338,-0.94842,347.75
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!40 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_Q9JIF7_P395-L953.pdb, chain A (#4) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 4110.5
RMSD between 179 pruned atom pairs is 1.370 angstroms; (across all 520 pairs:
5.457)
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.31935,0.83114,0.45521,287.02,0.88268,0.43568,-0.17625,341.17,-0.34481,0.34552,-0.87277,346.76
> view matrix models
> #40,-0.44367,0.86607,0.23039,284.23,0.80522,0.49809,-0.32175,338.94,-0.39341,0.042765,-0.91837,349.54
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.44367,0.86607,0.23039,282.32,0.80522,0.49809,-0.32175,339.86,-0.39341,0.042765,-0.91837,348.1
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 164
shifted from previous position = 4.58
rotated from previous position = 16.7 degrees
atoms outside contour = 24975, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52048952 0.84078158 0.14891953 220.04518033
0.84289479 0.53379676 -0.06774517 260.61986334
-0.13645165 0.09026284 -0.98652602 268.86066498
Axis 0.48438709 0.87482980 0.00647824
Axis point 50.38454975 0.00000000 130.78449689
Rotation angle (degrees) 170.61306625
Shift along axis 336.32681054
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 64
shifted from previous position = 0.0314
rotated from previous position = 0.0123 degrees
atoms outside contour = 24976, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52035216 0.84085379 0.14899177 220.06715093
0.84299036 0.53365933 -0.06763871 260.64221906
-0.13638511 0.09040267 -0.98652242 268.86235387
Axis 0.48445775 0.87479014 0.00654940
Axis point 50.37588260 0.00000000 130.77563938
Rotation angle (degrees) 170.61244765
Shift along axis 336.38136726
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 44
shifted from previous position = 0.00595
rotated from previous position = 0.00214 degrees
atoms outside contour = 24974, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52032365 0.84086898 0.14900562 220.06753255
0.84300489 0.53363422 -0.06765573 260.63688843
-0.13640410 0.09040958 -0.98651916 268.86496746
Axis 0.48447124 0.87478269 0.00654655
Axis point 50.37676888 0.00000000 130.77712244
Rotation angle (degrees) 170.61127680
Shift along axis 336.37716843
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 48
shifted from previous position = 0.0189
rotated from previous position = 0.00916 degrees
atoms outside contour = 24967, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52027091 0.84090187 0.14900419 220.05680972
0.84301710 0.53359531 -0.06781028 260.63941243
-0.13652973 0.09033336 -0.98650876 268.84978446
Axis 0.48449382 0.87477068 0.00648028
Axis point 50.37255935 0.00000000 130.77855079
Rotation angle (degrees) 170.60702404
Shift along axis 336.35810393
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 80
shifted from previous position = 0.0104
rotated from previous position = 0.00932 degrees
atoms outside contour = 24970, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52038816 0.84083756 0.14895765 220.05287043
0.84296038 0.53369740 -0.06771195 260.64877964
-0.13643306 0.09032890 -0.98652254 268.84767937
Axis 0.48443866 0.87480103 0.00650702
Axis point 50.37095373 0.00000000 130.77458825
Rotation angle (degrees) 170.61210637
Shift along axis 336.36733609
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005222, steps = 60
shifted from previous position = 0.012
rotated from previous position = 0.0197 degrees
atoms outside contour = 24967, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52065246 0.84069698 0.14882751 220.04216754
0.84279516 0.53395016 -0.06777583 260.64388132
-0.13644540 0.09014345 -0.98653780 268.84741201
Axis 0.48430666 0.87487465 0.00643470
Axis point 50.38648022 0.00000000 130.78444062
Rotation angle (degrees) 170.61681330
Shift along axis 336.32856452
> view matrix models
> #40,-0.53191,0.83446,0.14403,279.19,0.83752,0.54353,-0.05601,338.7,-0.12502,0.090833,-0.98799,349.49
> view matrix models
> #40,-0.53191,0.83446,0.14403,281.55,0.83752,0.54353,-0.05601,343.34,-0.12502,0.090833,-0.98799,350.66
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.53273,0.81883,0.21381,282.36,0.8282,0.55639,-0.067245,343.07,-0.17402,0.14125,-0.97456,350.1
> view matrix models
> #40,-0.59069,0.78688,0.17862,282.23,0.75978,0.61694,-0.20523,340.96,-0.27169,0.01448,-0.96228,351.34
> view matrix models
> #40,-0.60784,0.77483,0.17371,282.27,0.75759,0.63141,-0.16548,341.16,-0.2379,0.031016,-0.97079,351.17
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.60784,0.77483,0.17371,283.1,0.75759,0.63141,-0.16548,341.45,-0.2379,0.031016,-0.97079,350.66
> hide #!4 models
> select subtract #40
2 models selected
> show #!1 models
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
> view matrix models
> #40,-0.60784,0.77483,0.17371,282.46,0.75759,0.63141,-0.16548,341.97,-0.2379,0.031016,-0.97079,350.98
> select subtract #40
2 models selected
> hide #!1 models
> show #!15 models
> hide #!15 models
> show #!16 models
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 144
shifted from previous position = 8
rotated from previous position = 9.35 degrees
atoms outside contour = 24973, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52035327 0.84085371 0.14898840 220.06435873
0.84298688 0.53366200 -0.06766092 260.64248984
-0.13640238 0.09038768 -0.98652140 268.85959648
Axis 0.48445666 0.87479082 0.00653869
Axis point 50.37526868 0.00000000 130.77574819
Rotation angle (degrees) 170.61199384
Shift along axis 336.37729411
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 48
shifted from previous position = 0.0189
rotated from previous position = 0.0144 degrees
atoms outside contour = 24978, contour level = 0.0047281
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52020195 0.84092692 0.14910355 220.06127059
0.84308960 0.53351511 -0.06753935 260.63173968
-0.13634465 0.09057354 -0.98651234 268.87432330
Axis 0.48453259 0.87474811 0.00662749
Axis point 50.36493224 0.00000000 130.77083377
Rotation angle (degrees) 170.60962523
Shift along axis 336.39593915
> show #!1 models
> hide #!1 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!40 models
> show #!40 models
> show #!1 models
> hide #!1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_v43_labelled.cxs"
> hide #!40 models
> close #11
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/GOLPH3-Q9H4A6-human.pdb"
GOLPH3-Q9H4A6-human.pdb title:
Alphafold monomer V2.0 prediction for golgi phosphoprotein 3 (Q9H4A6) [more
info...]
Chain information for GOLPH3-Q9H4A6-human.pdb #11
---
Chain | Description | UniProt
A | golgi phosphoprotein 3 | GOLP3_HUMAN 1-298
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #11 to #24
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3kn1_Golph3_xtal.cif, chain A (#24) with GOLPH3-Q9H4A6-human.pdb,
chain A (#11), sequence alignment score = 1244.7
RMSD between 221 pruned atom pairs is 0.675 angstroms; (across all 239 pairs:
1.219)
> color #11 #b21effff
> show #!24 models
> ui mousemode right select
Drag select of 30 residues
> delete sel
> show #!1 models
> hide #!1 models
Drag select of 13 residues
> delete sel
> show #!1 models
> hide #!1 models
Drag select of 2 residues
> select up
147 atoms, 146 bonds, 18 residues, 1 model selected
> select down
19 atoms, 2 residues, 1 model selected
> delete sel
> show #!1 models
> hide #!1 models
Drag select of 1 residues
> delete sel
> show #!1 models
> hide #!1 models
> hide #11 models
> show #11 models
> hide #!24 models
> show #!24 models
> show #!1 models
> hide #!1 models
> rename #11 GOLPH3-Q9H4A6-human_Q47-.pdb
> rename #11 GOLPH3-Q9H4A6-human_Q47-K298.pdb
> show #!1 models
> hide #11 models
> show #11 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #11 models
> hide #!24 models
> show #11 models
> hide #11 models
> close #5
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/Arf1-P84077-human.pdb"
Arf1-P84077-human.pdb title:
Alphafold monomer V2.0 prediction for adp-ribosylation factor 1 (P84077) [more
info...]
Chain information for Arf1-P84077-human.pdb #5
---
Chain | Description | UniProt
A | adp-ribosylation factor 1 | ARF1_HUMAN 1-181
> color #5 #ff269dff
> close #6
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/Arf1-P84077-human.pdb"
Arf1-P84077-human.pdb title:
Alphafold monomer V2.0 prediction for adp-ribosylation factor 1 (P84077) [more
info...]
Chain information for Arf1-P84077-human.pdb #6
---
Chain | Description | UniProt
A | adp-ribosylation factor 1 | ARF1_HUMAN 1-181
> color #6 #ff15a8ff
> show #!26.1 models
> hide #!26.1 models
> show #!26.1 models
> show #!35 models
> show #!36 models
> show #!37 models
> hide #6 models
> hide #5 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #5 to #26.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#26.1) with
Arf1-P84077-human.pdb, chain A (#5), sequence alignment score = 714.3
RMSD between 158 pruned atom pairs is 0.857 angstroms; (across all 159 pairs:
0.877)
> show #5 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #6 to #35
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#35)
with Arf1-P84077-human.pdb, chain A (#6), sequence alignment score = 714.3
RMSD between 158 pruned atom pairs is 0.857 angstroms; (across all 159 pairs:
0.877)
> hide #5 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/Arf1-P84077-human.pdb"
Arf1-P84077-human.pdb title:
Alphafold monomer V2.0 prediction for adp-ribosylation factor 1 (P84077) [more
info...]
Chain information for Arf1-P84077-human.pdb #22
---
Chain | Description | UniProt
A | adp-ribosylation factor 1 | ARF1_HUMAN 1-181
> color #22 #ff15a8ff
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold/Arf1-P84077-human.pdb"
Arf1-P84077-human.pdb title:
Alphafold monomer V2.0 prediction for adp-ribosylation factor 1 (P84077) [more
info...]
Chain information for Arf1-P84077-human.pdb #23
---
Chain | Description | UniProt
A | adp-ribosylation factor 1 | ARF1_HUMAN 1-181
> color #23 #ff00b2ff
> select add #22
1457 atoms, 1483 bonds, 181 residues, 1 model selected
> select subtract #22
Nothing selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #22 to #36
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#36)
with Arf1-P84077-human.pdb, chain A (#22), sequence alignment score = 714.3
RMSD between 158 pruned atom pairs is 0.857 angstroms; (across all 159 pairs:
0.877)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #23 to #37
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#37)
with Arf1-P84077-human.pdb, chain A (#23), sequence alignment score = 714.3
RMSD between 158 pruned atom pairs is 0.857 angstroms; (across all 159 pairs:
0.877)
> hide #22 models
> hide #23 models
> hide #!26.1 models
> hide #!35 models
> hide #!36 models
> hide #!37 models
> show #!26.1 models
> show #5 models
> hide #!1 models
> show #!1 models
> ui tool show "Side View"
> volume #1 level 0.004728
> hide #!1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #5 models
> show #!1 models
> hide #5 models
> hide #!26.1 models
> show #6 models
> show #!35 models
> hide #!35 models
> show #!36 models
> hide #6 models
> show #22 models
> hide #22 models
> show #23 models
> hide #!36 models
> show #!37 models
> hide #!37 models
> show #5 models
> hide #23 models
> fitmap #5 inMap #1
Fit molecule Arf1-P84077-human.pdb (#5) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.008207, steps = 56
shifted from previous position = 1.94
rotated from previous position = 3.57 degrees
atoms outside contour = 426, contour level = 0.0047281
Position of Arf1-P84077-human.pdb (#5) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.18942851 0.67637478 -0.71178227 323.61574599
0.98186050 0.12444879 -0.14304705 261.78874814
-0.00817297 -0.72596809 -0.68767982 255.09048932
Axis -0.60505182 -0.73032205 0.31708359
Axis point -8.53082974 0.00000000 208.70218842
Rotation angle (degrees) 151.20274669
Shift along axis -306.10938398
> hide #!25 models
> hide #!26 models
> hide #!27 models
> hide #!32 models
> hide #5 models
> show #!30 models
> show #!2 models
> show #27.2 models
> show #27.1 models
> show #32.2 models
> show #32.1 models
> show #!4 models
> show #!26.1 models
> show #!35 models
> show #!36 models
> show #!37 models
> show #!40 models
> show #28 models
> show #26.3 models
> show #!29 models
> show #!26.2 models
> show #!24 models
> show #!18 models
> show #!19 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!13 models
> show #!9 models
> volume #1 level 0.004557
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> show #!16 models
> hide #!4 models
> hide #!16 models
> show #!4 models
> volume #1 level 0.004045
> view orient
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_xtal_alphafold_fitting.cxs"
> hide #!1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #!25.2 models
> hide #!25.2 models
> show #!25.2 models
> hide #!25.2 models
> show #25.3 models
> hide #25.3 models
> show #25.3 models
> hide #25.3 models
> show #!25.6 models
> hide #!25.6 models
> show #!25.6 models
> hide #!25.6 models
> show #!1 models
> view orient
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_xtal_alphafold_fitting.cxs"
> hide #!2 models
> hide #!4 models
> hide #!9 models
> show #!9 models
> show #!3 models
> show #!7 models
> show #5 models
> show #6 models
> show #!15 models
> show #!16 models
> show #11 models
> show #10 models
> show #12 models
> hide #!24 models
> hide #!26.1 models
> show #23 models
> show #22 models
> hide #!26.2 models
> hide #26.3 models
> hide #27.1 models
> hide #27.2 models
> hide #28 models
> hide #!29 models
> hide #!30 models
> hide #32.1 models
> hide #32.2 models
> hide #!35 models
> hide #!36 models
> hide #!37 models
> show #!14 models
> show #!17 models
> show #!20 models
> show #!21 models
> hide #!13 models
> show #!13 models
> hide #!21 models
> show #!21 models
> hide #!9 models
> show #!9 models
> color #5 #ff00b2ff
> color #22 #ff3cb7ff
> color #26.1 #ff00bcff
> color #35 #ff00c6ff
> color #36 #fe00cfff
> color #37 #fd00d7ff
> view orient
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"
> hide #!1 models
> show #25.1 models
> hide #25.1 models
> show #!25.2 models
> hide #!25.2 models
> show #25.3 models
> hide #25.3 models
> show #25.3 models
> hide #25.3 models
> show #!25.6 models
> hide #!25.6 models
> close #25
> show #!1 models
> view orient
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"
——— End of log from Wed Jul 10 16:07:37 2024 ———
opened ChimeraX session
> show #8 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"
——— End of log from Wed Jul 10 16:36:09 2024 ———
opened ChimeraX session
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/fold_2024_06_04_12_31_model_0.cif"
Chain information for fold_2024_06_04_12_31_model_0.cif #25
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G H | .
> select add #25
39611 atoms, 40368 bonds, 5006 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #25,1,0,0,374.94,0,1,0,307.54,0,0,1,48.791
> view matrix models #25,1,0,0,363.27,0,1,0,224.54,0,0,1,363.61
> view matrix models #25,1,0,0,182.77,0,1,0,315.74,0,0,1,357.5
> color #25/A blue
> color #25/H deep pink
> color #25/G deep pink
> color #25/F yellow
> color #25/B dark green
> color #25/C cyan
> color #25/D chocolate
> color #25/E lime green
> color #25/C cyan
> select subtract #25
Nothing selected
> select #25/A
9742 atoms, 9961 bonds, 1224 residues, 1 model selected
> cartoon hide sel
> select #25/B
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> cartoon hide sel
> select #25/C
7214 atoms, 7373 bonds, 905 residues, 1 model selected
> cartoon hide sel
> select #25/H
1445 atoms, 1472 bonds, 181 residues, 1 model selected
> cartoon hide sel
> select #25/G
1445 atoms, 1472 bonds, 181 residues, 1 model selected
> cartoon hide sel
> select #25/F
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> cartoon hide sel
> select #25/D
4014 atoms, 4083 bonds, 511 residues, 1 model selected
> cartoon hide sel
> select #25/E
6830 atoms, 6947 bonds, 874 residues, 1 model selected
> cartoon hide sel
> select #25/B
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3.cxs"
> select add #25
39611 atoms, 40368 bonds, 5006 residues, 1 model selected
> select subtract #25
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #25 models
> show #25 models
> hide #25 models
> show #25 models
> select #25/B
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> cartoon sel
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #25 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_Q9JIF7_P395-L953.pdb, chain A (#4) with
fold_2024_06_04_12_31_model_0.cif, chain B (#25), sequence alignment score =
4122.5
RMSD between 165 pruned atom pairs is 1.015 angstroms; (across all 520 pairs:
5.012)
> select add #25
39611 atoms, 40368 bonds, 5006 residues, 1 model selected
> select subtract #25
Nothing selected
> select add #25
39611 atoms, 40368 bonds, 5006 residues, 1 model selected
> select subtract #25
Nothing selected
> hide #!3 models
> hide #5 models
> hide #6 models
> hide #!7 models
> hide #8 models
> hide #!9 models
> hide #10 models
> show #!4 models
> hide #11 models
> hide #12 models
> hide #!14 models
> hide #!13 models
> hide #!4 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #23 models
> hide #22 models
> hide #!1 models
> hide #!40 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #25 models
> show #25 models
> show #!1 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!1 models
> show #!1 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> volume #1 level 0.003845
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #25 to #15
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopB_ Q9JIF7_G23-F394.pdb, chain A (#15) with
fold_2024_06_04_12_31_model_0.cif, chain B (#25), sequence alignment score =
3974.9
RMSD between 223 pruned atom pairs is 0.851 angstroms; (across all 372 pairs:
3.614)
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #25 models
> show #25 models
> hide #!1 models
> show #!1 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!1 models
> show #!16 models
> show #!1 models
> show #!13 models
> hide #!13 models
> show #!18 models
> hide #!18 models
> hide #!16 models
> show #!16 models
> hide #!1 models
> hide #!16 models
> show #!1 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!7 models
> hide #!1 models
> hide #!7 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!1 models
> hide #!1 models
> show #!17 models
> show #!14 models
> show #!7 models
> show #!3 models
> show #5 models
> show #6 models
> show #8 models
> show #!1 models
> hide #!1 models
> hide #8 models
> show #8 models
> show #11 models
> show #10 models
> show #!9 models
> show #!18 models
> show #!19 models
> show #!13 models
> show #!20 models
> show #!21 models
> show #22 models
> show #23 models
> hide #!21 models
> hide #!20 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #22 models
> hide #23 models
> hide #!14 models
> hide #!13 models
> hide #11 models
> hide #10 models
> hide #!9 models
> hide #8 models
> hide #!7 models
> hide #6 models
> hide #5 models
> hide #!3 models
> select #25/D
4014 atoms, 4083 bonds, 511 residues, 1 model selected
> cartoon sel
> select add #25
39611 atoms, 40368 bonds, 5006 residues, 1 model selected
> select subtract #25
Nothing selected
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #!1 models
> volume #1 level 0.005446
> volume #1 level 0.004645
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v2.cxs"
——— End of log from Wed Jul 10 17:31:38 2024 ———
opened ChimeraX session
> split #25 chains
Split fold_2024_06_04_12_31_model_0.cif (#25) into 8 models
Chain information for fold_2024_06_04_12_31_model_0.cif A #25.1
---
Chain | Description
A | No description available
Chain information for fold_2024_06_04_12_31_model_0.cif B #25.2
---
Chain | Description
B | No description available
Chain information for fold_2024_06_04_12_31_model_0.cif C #25.3
---
Chain | Description
C | No description available
Chain information for fold_2024_06_04_12_31_model_0.cif D #25.4
---
Chain | Description
D | No description available
Chain information for fold_2024_06_04_12_31_model_0.cif E #25.5
---
Chain | Description
E | No description available
Chain information for fold_2024_06_04_12_31_model_0.cif F #25.6
---
Chain | Description
F | No description available
Chain information for fold_2024_06_04_12_31_model_0.cif G #25.7
---
Chain | Description
G | No description available
Chain information for fold_2024_06_04_12_31_model_0.cif H #25.8
---
Chain | Description
H | No description available
> hide #!1 models
> hide #!15 models
> hide #25.1 models
> show #25.1 models
> hide #25.1 models
> show #25.1 models
> select add #25.1
9742 atoms, 9961 bonds, 1224 residues, 1 model selected
> cartoon sel
> select subtract #25.1
Nothing selected
> select add #25.2
7501 atoms, 7619 bonds, 953 residues, 1 model selected
> select subtract #25.2
Nothing selected
> select add #25.3
7214 atoms, 7373 bonds, 905 residues, 1 model selected
> cartoon sel
> select subtract #25.3
Nothing selected
> select add #25.4
4014 atoms, 4083 bonds, 511 residues, 1 model selected
> select subtract #25.4
Nothing selected
> select add #25.5
6830 atoms, 6947 bonds, 874 residues, 1 model selected
> cartoon sel
> select subtract #25.5
Nothing selected
> select add #25.6
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> cartoon sel
> select subtract #25.6
Nothing selected
> select add #25.7
1445 atoms, 1472 bonds, 181 residues, 1 model selected
> cartoon sel
> select subtract #25.7
Nothing selected
> select add #25.8
1445 atoms, 1472 bonds, 181 residues, 1 model selected
> cartoon sel
> select subtract #25.8
Nothing selected
> hide #25.8 models
> show #25.8 models
> select add #26
4503 atoms, 4577 bonds, 5 pseudobonds, 565 residues, 6 models selected
> cartoon #25#!26-27,32
> select subtract #26
Nothing selected
> hide #!26 models
> show #!26 models
> show #!26.1 models
> hide #!26.1 models
> show #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #25 2024_06_04_12_31_AF3_model_0.cif
> rename #25.1 "2024_06_04_12_31_model_0_CopA.cif A"
> rename #25.2 "2024_06_04_12_31_model_0_CopB.cif B"
> rename #25.3 "2024_06_04_12_31_model_0_CopBprime.cif C"
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v3.cxs"
> show #!16 models
> hide #!16 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #25.2 inMap #1
Fit molecule 2024_06_04_12_31_model_0_CopB.cif B (#25.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7501 atoms
average map value = 0.008543, steps = 92
shifted from previous position = 4.83
rotated from previous position = 8.42 degrees
atoms outside contour = 3060, contour level = 0.0046452
Position of 2024_06_04_12_31_model_0_CopB.cif B (#25.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.81836991 -0.03043632 0.57388528 219.84667924
0.54622648 0.35157960 -0.76028180 252.72686731
-0.17862618 0.93566309 0.30434729 262.25133331
Axis 0.87287250 0.38730419 0.29679803
Axis point 0.00000000 -34.12525913 174.24483479
Rotation angle (degrees) 76.28170258
Shift along axis 367.61597236
> show #!16 models
> hide #!1 models
> hide #!16 models
> show #!1 models
> fitmap #25.3 inMap #1
Fit molecule 2024_06_04_12_31_model_0_CopBprime.cif C (#25.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7214 atoms
average map value = 0.008369, steps = 160
shifted from previous position = 6.47
rotated from previous position = 12.7 degrees
atoms outside contour = 2796, contour level = 0.0046452
Position of 2024_06_04_12_31_model_0_CopBprime.cif C (#25.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.84345587 0.00482068 0.53717683 223.29518155
0.47339236 0.46600929 -0.74748579 248.12832786
-0.25393278 0.88476670 0.39077620 257.93229712
Axis 0.87127387 0.42228340 0.25011710
Axis point 0.00000000 -68.12363713 175.06688149
Rotation angle (degrees) 69.50530340
Shift along axis 363.84501176
> fitmap #25.4 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif D (#25.4) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4014 atoms
average map value = 0.004982, steps = 256
shifted from previous position = 4.02
rotated from previous position = 10.1 degrees
atoms outside contour = 2765, contour level = 0.0046452
Position of fold_2024_06_04_12_31_model_0.cif D (#25.4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.80534835 0.02456211 0.59229278 219.83833435
0.54486002 0.36295360 -0.75590492 251.11971251
-0.23354142 0.93148343 0.27892117 259.71968287
Axis 0.86561293 0.42364448 0.26690750
Axis point 0.00000000 -45.73336002 165.62858715
Rotation angle (degrees) 77.07875382
Shift along axis 366.00151472
> hide #25.8 models
> show #25.8 models
> hide #25.7 models
> show #25.7 models
> hide #25.7 models
> show #25.7 models
> fitmap #25.7 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif G (#25.7) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1445 atoms
average map value = 0.007837, steps = 72
shifted from previous position = 6.15
rotated from previous position = 14.8 degrees
atoms outside contour = 505, contour level = 0.0046452
Position of fold_2024_06_04_12_31_model_0.cif G (#25.7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.83207671 0.08557782 0.54801896 221.29669356
0.47205720 0.40949785 -0.78068784 251.64545733
-0.29122215 0.90828847 0.30033600 256.11679191
Axis 0.87730649 0.43592777 0.20074934
Axis point 0.00000000 -68.21876802 175.56477609
Rotation angle (degrees) 74.27888041
Shift along axis 355.25954487
> hide #25.3 models
> show #!3 models
> show #!7 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v4.cxs"
——— End of log from Wed Jul 10 18:08:13 2024 ———
opened ChimeraX session
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604 /fold_2024_06_04_12_31
> (1)/fold_2024_06_04_12_31_summary_confidences_0.json"
Failed opening file /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/COPI-Golph3 dataset/Structure files/alphafold 3 /GT 20240604
/fold_2024_06_04_12_31 (1)/fold_2024_06_04_12_31_summary_confidences_0.json:
expected str, bytes or os.PathLike object, not NoneType
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604 /fold_2024_06_04_12_31
> (1)/fold_2024_06_04_12_31_summary_confidences_0.json"
Failed opening file /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/COPI-Golph3 dataset/Structure files/alphafold 3 /GT 20240604
/fold_2024_06_04_12_31 (1)/fold_2024_06_04_12_31_summary_confidences_0.json:
expected str, bytes or os.PathLike object, not NoneType
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #25.1 inMap #1
Fit molecule 2024_06_04_12_31_model_0_CopA.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 9742 atoms
average map value = 0.005669, steps = 116
shifted from previous position = 9.72
rotated from previous position = 11.3 degrees
atoms outside contour = 5635, contour level = 0.0046452
Position of 2024_06_04_12_31_model_0_CopA.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.75553140 0.04537000 0.65353950 219.16243552
0.61538755 0.29295285 -0.73176279 259.39055669
-0.22465634 0.95504984 0.19341494 257.39821799
Axis 0.84964385 0.44234533 0.28711660
Axis point -0.00000000 -26.88413277 153.85341339
Rotation angle (degrees) 83.05309036
Shift along axis 374.85351736
> show #25.3 models
> fitmap #25.3 inMap #1
Fit molecule 2024_06_04_12_31_model_0_CopBprime.cif C (#25.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7214 atoms
average map value = 0.008368, steps = 48
shifted from previous position = 0.0306
rotated from previous position = 0.0358 degrees
atoms outside contour = 2792, contour level = 0.0046452
Position of 2024_06_04_12_31_model_0_CopBprime.cif C (#25.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.84321152 0.00513755 0.53755738 223.25372064
0.47367936 0.46575275 -0.74746387 248.14694008
-0.25420896 0.88489998 0.39029453 257.93051862
Axis 0.87116267 0.42255119 0.25005218
Axis point 0.00000000 -68.10469645 174.97857555
Rotation angle (degrees) 69.53535083
Shift along axis 363.84118025
> fitmap #25.5 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif E (#25.5) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6830 atoms
average map value = 0.00533, steps = 144
shifted from previous position = 18.8
rotated from previous position = 32.2 degrees
atoms outside contour = 3946, contour level = 0.0046452
Position of fold_2024_06_04_12_31_model_0.cif E (#25.5) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.92680175 -0.00991127 0.37542014 203.02780080
0.37483013 -0.03749334 -0.92633505 259.56425147
0.02325691 0.99924773 -0.03103385 251.03464453
Axis 0.96521787 0.17652538 0.19285553
Axis point 0.00000000 17.09180671 205.76151029
Rotation angle (degrees) 94.06354038
Shift along axis 290.19915859
> fitmap #25.6 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif F (#25.6) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.006566, steps = 156
shifted from previous position = 14.5
rotated from previous position = 50.9 degrees
atoms outside contour = 670, contour level = 0.0046452
Position of fold_2024_06_04_12_31_model_0.cif F (#25.6) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.91730136 0.38762874 0.09111629 227.23819734
-0.16863333 0.58545743 -0.79297062 293.42586081
-0.36072292 0.71202778 0.60240802 274.50516754
Axis 0.90286439 0.27106310 -0.33370748
Axis point 0.00000000 -237.05848562 427.95408374
Rotation angle (degrees) 56.45557375
Shift along axis 193.09777338
> volume #1 level 0.007361
> select add #25.8
1445 atoms, 1472 bonds, 181 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #25.8,0.74055,-0.13166,0.65898,273.87,0.65555,0.35719,-0.66533,308.82,-0.14779,0.92471,0.35082,357.56
> view matrix models
> #25.8,0.74055,-0.13166,0.65898,290.35,0.65555,0.35719,-0.66533,310.7,-0.14779,0.92471,0.35082,354.71
> fitmap #25.6 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif F (#25.6) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.006567, steps = 28
shifted from previous position = 0.0442
rotated from previous position = 0.0449 degrees
atoms outside contour = 875, contour level = 0.0073613
Position of fold_2024_06_04_12_31_model_0.cif F (#25.6) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.91700642 0.38823271 0.09151274 227.23927269
-0.16874008 0.58547245 -0.79293682 293.39526347
-0.36142220 0.71168629 0.60239241 274.54257906
Axis 0.90253319 0.27168852 -0.33409458
Axis point 0.00000000 -237.32869351 427.92431869
Rotation angle (degrees) 56.46573103
Shift along axis 193.07992175
> fitmap #25.8 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif H (#25.8) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1445 atoms
average map value = 0.008109, steps = 468
shifted from previous position = 13.3
rotated from previous position = 60.9 degrees
atoms outside contour = 833, contour level = 0.0073613
Position of fold_2024_06_04_12_31_model_0.cif H (#25.8) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.12575643 -0.88575141 0.44679946 228.82969252
0.99073145 0.08881934 -0.10277317 179.18096389
0.05134705 0.45558267 0.88871138 240.16932217
Axis 0.27955096 0.19799041 0.93949511
Axis point 14.33554481 141.59673741 0.00000000
Rotation angle (degrees) 87.03972432
Shift along axis 325.08357550
> view matrix models
> #25.8,0.11366,-0.88418,0.45312,290.07,0.99167,0.073124,-0.10606,260.62,0.060642,0.4614,0.88512,318.11
> view matrix models
> #25.8,0.11366,-0.88418,0.45312,294.87,0.99167,0.073124,-0.10606,262.05,0.060642,0.4614,0.88512,317.92
> ui mousemode right "rotate selected models"
> view matrix models
> #25.8,-0.66494,-0.24529,-0.70547,392.21,-0.019471,-0.93852,0.34468,260.9,-0.74664,0.24292,0.61928,357.82
> ui mousemode right "translate selected models"
> view matrix models
> #25.8,-0.66494,-0.24529,-0.70547,406.09,-0.019471,-0.93852,0.34468,256.15,-0.74664,0.24292,0.61928,359.03
> fitmap #25.8 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif H (#25.8) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1445 atoms
average map value = 0.01011, steps = 148
shifted from previous position = 4.47
rotated from previous position = 45.9 degrees
atoms outside contour = 599, contour level = 0.0073613
Position of fold_2024_06_04_12_31_model_0.cif H (#25.8) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.98716163 -0.15525535 -0.03751933 340.31636141
0.09860749 -0.77717312 0.62151308 169.78952644
-0.12565225 0.60983417 0.78250483 262.93874124
Axis -0.04341926 0.32765622 0.94379880
Axis point 173.51910029 51.88093325 0.00000000
Rotation angle (degrees) 172.27087505
Shift along axis 289.01757907
> select subtract #25.8
Nothing selected
> fitmap #25.7 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif G (#25.7) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1445 atoms
average map value = 0.007837, steps = 60
shifted from previous position = 0.0106
rotated from previous position = 0.0255 degrees
atoms outside contour = 805, contour level = 0.0073613
Position of fold_2024_06_04_12_31_model_0.cif G (#25.7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.83215962 0.08563418 0.54788425 221.30652905
0.47179779 0.40985808 -0.78065563 251.64999561
-0.29140559 0.90812067 0.30066533 256.11008960
Axis 0.87730176 0.43600237 0.20060799
Axis point 0.00000000 -68.32153315 175.59524077
Rotation angle (degrees) 74.25588981
Shift along axis 355.25032939
> fitmap #25.7 inMap #1
Fit molecule fold_2024_06_04_12_31_model_0.cif G (#25.7) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1445 atoms
average map value = 0.007837, steps = 48
shifted from previous position = 0.026
rotated from previous position = 0.0382 degrees
atoms outside contour = 804, contour level = 0.0073613
Position of fold_2024_06_04_12_31_model_0.cif G (#25.7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.83221936 0.08509556 0.54787744 221.30074730
0.47184021 0.41022785 -0.78043573 251.66017447
-0.29116620 0.90800433 0.30124805 256.12289313
Axis 0.87725727 0.43593915 0.20093965
Axis point 0.00000000 -68.30458057 175.60720654
Rotation angle (degrees) 74.22575907
Shift along axis 355.31145663
> select add #25.5
6830 atoms, 6947 bonds, 874 residues, 1 model selected
> select add #25
39611 atoms, 40368 bonds, 5006 residues, 9 models selected
> select subtract #25
Nothing selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #25.5 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopG_Q9QZE5_L311-T583, chain A (#9) with
fold_2024_06_04_12_31_model_0.cif E, chain E (#25.5), sequence alignment score
= 3514.8
RMSD between 175 pruned atom pairs is 0.803 angstroms; (across all 277 pairs:
3.261)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #25.6 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopZ1_P61924_M1-V153.pdb, chain A (#10) with
fold_2024_06_04_12_31_model_0.cif F, chain F (#25.6), sequence alignment score
= 834
RMSD between 140 pruned atom pairs is 0.442 angstroms; (across all 153 pairs:
2.101)
> hide #25.8 models
> hide #25.7 models
> hide #25.6 models
> hide #25.5 models
> hide #25.4 models
> hide #25.3 models
> hide #25.2 models
> hide #!7 models
> hide #!3 models
> hide #!1 models
> hide #25.1 models
> show #25.1 models
> combine #25.1
> hide #33 models
> show #!1 models
> hide #!1 models
> ui mousemode right select
Drag select of 373 residues
> select up
3070 atoms, 3133 bonds, 393 residues, 1 model selected
> delete sel
Drag select of 16 residues, 2 pseudobonds
> select up
416 atoms, 427 bonds, 2 pseudobonds, 54 residues, 2 models selected
> delete sel
> show #!1 models
> fitmap #25.1 inMap #1
Fit molecule 2024_06_04_12_31_model_0_CopA.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6256 atoms
average map value = 0.008111, steps = 48
shifted from previous position = 0.31
rotated from previous position = 0.572 degrees
atoms outside contour = 3215, contour level = 0.0073613
Position of 2024_06_04_12_31_model_0_CopA.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.76006059 0.04278394 0.64844231 218.74194091
0.60950045 0.29920371 -0.73415689 259.35375027
-0.22542647 0.95322960 0.20133612 257.86149366
Axis 0.85094793 0.44069147 0.28579477
Axis point -0.00000000 -28.07039157 155.48469352
Rotation angle (degrees) 82.51305906
Shift along axis 374.12845394
> fitmap #25.1 inMap #1
Fit molecule 2024_06_04_12_31_model_0_CopA.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 6256 atoms
average map value = 0.008111, steps = 44
shifted from previous position = 0.0292
rotated from previous position = 0.00608 degrees
atoms outside contour = 3212, contour level = 0.0073613
Position of 2024_06_04_12_31_model_0_CopA.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.76009501 0.04286795 0.64839642 218.76025174
0.60943303 0.29922890 -0.73420259 259.36442844
-0.22549271 0.95321792 0.20131725 257.87889146
Axis 0.85096738 0.44070292 0.28571918
Axis point 0.00000000 -28.09786587 155.50118606
Rotation angle (degrees) 82.51188250
Shift along axis 374.14144497
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #33
> select clear
Drag select of 153 residues
> select up
1269 atoms, 1286 bonds, 160 residues, 1 model selected
> select down
1219 atoms, 153 residues, 1 model selected
> select up
1269 atoms, 1286 bonds, 160 residues, 1 model selected
> select clear
Drag select of 164 residues
> select down
1309 atoms, 164 residues, 1 model selected
> select clear
Drag select of 57 residues
Drag select of 120 residues
> select up
1073 atoms, 1086 bonds, 133 residues, 1 model selected
Drag select of 161 residues
Drag select of 157 residues
[Repeated 1 time(s)]
> combine sel
> hide #!33 models
> delete sel
> fitmap #25.1 inMap #1
Fit molecule 2024_06_04_12_31_model_0_CopA.cif A (#25.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5009 atoms
average map value = 0.008583, steps = 68
shifted from previous position = 0.841
rotated from previous position = 2.63 degrees
atoms outside contour = 2386, contour level = 0.0073613
Position of 2024_06_04_12_31_model_0_CopA.cif A (#25.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.72960486 0.04624134 0.68230381 220.93350354
0.64220662 0.29658780 -0.70682836 260.25489256
-0.23504768 0.95388543 0.18669540 256.90234719
Axis 0.83510136 0.46129651 0.29968524
Axis point 0.00000000 -25.87166094 144.93945606
Rotation angle (degrees) 83.88963054
Shift along axis 381.54638528
> show #!1 models
> show #!33 models
> hide #!1 models
> hide #!25.1 models
> show #!25.1 models
> hide #!25.1 models
Drag select of 605 residues
> delete sel
Drag select of 11 residues, 1 pseudobonds
Drag select of 12 residues
> select up
139 atoms, 140 bonds, 17 residues, 1 model selected
> select clear
Drag select of 14 residues, 1 pseudobonds
> delete sel
> select clear
[Repeated 1 time(s)]
> fitmap #33 inMap #1
Fit molecule copy of 2024_06_04_12_31_model_0_CopA.cif A (#33) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1255 atoms
average map value = 0.01015, steps = 68
shifted from previous position = 6.46
rotated from previous position = 7.67 degrees
atoms outside contour = 557, contour level = 0.0073613
Position of copy of 2024_06_04_12_31_model_0_CopA.cif A (#33) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.83497221 0.02462714 0.54974076 216.64059216
0.51007972 0.34023297 -0.78997481 253.86750709
-0.20649476 0.94001863 0.27152327 263.80669951
Axis 0.88741727 0.38791850 0.24901771
Axis point 0.00000000 -44.20380174 183.25726602
Rotation angle (degrees) 77.09329231
Shift along axis 356.42304552
> show #!1 models
> show #!25.1 models
> hide #!1 models
> rename #25.1 "2024_06_04_12_31_model_0_CopA_M1-L620.cif A"
> rename #33 "2024_06_04_12_31_model_0_CopA_L620-.cif A"
> rename #33 "2024_06_04_12_31_model_0_CopA_L620-T777.cif A"
> show #!17 models
> show #!14 models
> hide #!17 models
> hide #!14 models
> hide #!25.1 models
> hide #!33 models
> show #25.2 models
> show #!16 models
> show #!15 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v5.cxs"
——— End of log from Fri Jul 12 14:16:12 2024 ———
opened ChimeraX session
> show #!1 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> hide #!16 models
> show #!25.1 models
> show #25.3 models
> show #25.4 models
> show #25.5 models
> show #25.6 models
> show #25.7 models
> show #25.8 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240711_leaf_fitting_alphafold_only_withAF3_v6.cxs"
> show #!30 models
> hide #!30 models
> show #27.2 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240711_leaf_fitting_alphafold_only_withAF3_v6.cxs"
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3
> /fold_20240711_copi_golph3/fold_20240711_copi_golph3_full_data_0.json"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 129, in open
structs = [m for m in session.models.list(type = AtomicStructure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 130, in
if hasattr(m, 'filename') and dirname(m.filename) == dirname(path)]
^^^^^^^^^^^^^^^^^^^
File "", line 152, in dirname
TypeError: expected str, bytes or os.PathLike object, not NoneType
TypeError: expected str, bytes or os.PathLike object, not NoneType
File "", line 152, in dirname
See log for complete Python traceback.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3
> /fold_20240711_copi_golph3/fold_20240711_copi_golph3_model_0.cif"
Chain information for fold_20240711_copi_golph3_model_0.cif #34
---
Chain | Description
A | .
B C | .
D | .
E | .
F | .
G | .
H | .
I | .
> select add #34
35468 atoms, 36117 bonds, 4477 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models #34,1,0,0,383.59,0,1,0,259.53,0,0,1,227.72
> view matrix models #34,1,0,0,320.11,0,1,0,310.5,0,0,1,342.85
> select subtract #34
Nothing selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #34 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopA-Q8CIE6_E320-V642.pdb, chain A (#2) with
fold_20240711_copi_golph3_model_0.cif, chain D (#34), sequence alignment score
= 3817.3
RMSD between 298 pruned atom pairs is 0.587 angstroms; (across all 324 pairs:
1.078)
> hide #!25 models
> hide #27.2 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #34 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif (#34) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 35468 atoms
average map value = 0.00656, steps = 116
shifted from previous position = 6.74
rotated from previous position = 3.63 degrees
atoms outside contour = 22252, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif (#34) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58546173 0.33589766 0.73783964 228.27558541
-0.09809695 -0.87408690 0.47576158 252.58695297
0.80474316 -0.35092001 -0.47879389 262.95256421
Axis -0.88313937 -0.07147266 -0.46363403
Axis point 0.00000000 131.76923686 39.45816280
Rotation angle (degrees) 152.09313163
Shift along axis -341.56597663
> split chains #34
Expected a keyword
> split #34 chains
Split fold_20240711_copi_golph3_model_0.cif (#34) into 9 models
Chain information for fold_20240711_copi_golph3_model_0.cif A #34.1
---
Chain | Description
A | No description available
Chain information for fold_20240711_copi_golph3_model_0.cif B #34.2
---
Chain | Description
B | No description available
Chain information for fold_20240711_copi_golph3_model_0.cif C #34.3
---
Chain | Description
C | No description available
Chain information for fold_20240711_copi_golph3_model_0.cif D #34.4
---
Chain | Description
D | No description available
Chain information for fold_20240711_copi_golph3_model_0.cif E #34.5
---
Chain | Description
E | No description available
Chain information for fold_20240711_copi_golph3_model_0.cif F #34.6
---
Chain | Description
F | No description available
Chain information for fold_20240711_copi_golph3_model_0.cif G #34.7
---
Chain | Description
G | No description available
Chain information for fold_20240711_copi_golph3_model_0.cif H #34.8
---
Chain | Description
H | No description available
Chain information for fold_20240711_copi_golph3_model_0.cif I #34.9
---
Chain | Description
I | No description available
> hide #34.1 models
> hide #34.2 models
> hide #34.3 models
> hide #34.4 models
> hide #34.5 models
> hide #34.6 models
> hide #34.7 models
> hide #34.8 models
> hide #34.9 models
> show #34.1 models
> color #34.1 #b21effff
> fitmap #34.1 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif A (#34.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2371 atoms
average map value = 0.00748, steps = 68
shifted from previous position = 6.3
rotated from previous position = 8.74 degrees
atoms outside contour = 1259, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif A (#34.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.52771432 0.46260878 0.71239786 230.68377417
0.01556661 -0.84381163 0.53641367 257.97236074
0.84927927 -0.27198355 -0.45249273 263.23110022
Axis -0.86565399 -0.14657638 -0.47870506
Axis point -0.00000000 122.22516554 38.53470155
Rotation angle (degrees) 152.16489046
Shift along axis -363.51504457
> hide #34.1 models
> show #34.2 models
> color #34.2 #ff009eff
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 80
shifted from previous position = 6.24
rotated from previous position = 5.68 degrees
atoms outside contour = 834, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64416681 0.35711118 0.67640278 226.66433422
-0.02970052 -0.87197447 0.48864957 253.33862049
0.76430818 -0.33486135 -0.55109063 256.83042733
Axis -0.90092929 -0.09616940 -0.42317592
Axis point 0.00000000 129.89043181 45.52689960
Rotation angle (degrees) 152.80410812
Shift along axis -337.25641452
> hide #34.2 models
> show #34.3 models
> color #34.3 #ff00a9ff
> fitmap #34.3 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif C (#34.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007717, steps = 120
shifted from previous position = 16.1
rotated from previous position = 2.93 degrees
atoms outside contour = 821, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif C (#34.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55724589 0.30890177 0.77075075 216.26500571
-0.12170943 -0.88781537 0.44381380 253.82096759
0.82137923 -0.34112105 -0.45713520 251.42339780
Axis -0.87533713 -0.05645945 -0.48020542
Axis point 0.00000000 132.87199639 34.54285231
Rotation angle (degrees) 153.36139527
Shift along axis -324.37025870
> hide #34.3 models
> show #34.3 models
> hide #34.3 models
> show #34.4 models
> color #34.4 #0024ffff
> fitmap #34.4 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif D (#34.4) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7166 atoms
average map value = 0.007568, steps = 68
shifted from previous position = 3.39
rotated from previous position = 1.98 degrees
atoms outside contour = 3864, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif D (#34.4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.56992681 0.36183288 0.73774006 227.91110670
-0.07205669 -0.87235986 0.48352467 256.55796769
0.81852994 -0.32873278 -0.47110879 263.77891615
Axis -0.87866866 -0.08739536 -0.46936494
Axis point 0.00000000 131.04482198 39.47393179
Rotation angle (degrees) 152.47024536
Shift along axis -346.48889708
> fitmap #34.4 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif D (#34.4) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7166 atoms
average map value = 0.007567, steps = 44
shifted from previous position = 0.0262
rotated from previous position = 0.00836 degrees
atoms outside contour = 3859, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif D (#34.4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.56999916 0.36178137 0.73770943 227.93094964
-0.07197947 -0.87240559 0.48345366 256.54968376
0.81848635 -0.32866811 -0.47122963 263.79414942
Axis -0.87869372 -0.08739844 -0.46931745
Axis point 0.00000000 131.03935522 39.49351975
Rotation angle (degrees) 152.47608536
Shift along axis -346.50673304
> hide #34.4 models
> show #34.5 models
> fitmap #34.5 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif E (#34.5) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7501 atoms
average map value = 0.008391, steps = 104
shifted from previous position = 1.23
rotated from previous position = 1.02 degrees
atoms outside contour = 4038, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif E (#34.5) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58719953 0.35086370 0.72944594 227.28064832
-0.08423493 -0.86979043 0.48617805 251.90546793
0.80504732 -0.34692835 -0.48118555 262.65301991
Axis -0.88354151 -0.08017819 -0.46143890
Axis point 0.00000000 130.49029375 40.15321991
Rotation angle (degrees) 151.87098420
Shift along axis -342.20753257
> fitmap #34.5 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif E (#34.5) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7501 atoms
average map value = 0.008391, steps = 76
shifted from previous position = 0.0209
rotated from previous position = 0.00496 degrees
atoms outside contour = 4035, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif E (#34.5) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58722470 0.35088756 0.72941420 227.26576357
-0.08415396 -0.86980219 0.48617103 251.91606564
0.80503743 -0.34687473 -0.48124075 262.66279930
Axis -0.88355045 -0.08020801 -0.46141659
Axis point 0.00000000 130.49372789 40.16867906
Rotation angle (degrees) 151.87352378
Shift along axis -342.20342816
> fitmap #34.5 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif E (#34.5) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7501 atoms
average map value = 0.008391, steps = 80
shifted from previous position = 0.011
rotated from previous position = 0.0181 degrees
atoms outside contour = 4035, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif E (#34.5) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58741011 0.35090953 0.72925432 227.26213947
-0.08392848 -0.86983144 0.48615767 251.91860141
0.80492569 -0.34677914 -0.48149648 262.64949044
Axis -0.88360949 -0.08027493 -0.46129189
Axis point 0.00000000 130.48784527 40.19498052
Rotation angle (degrees) 151.87957518
Shift along axis -342.19181048
> fitmap #34.5 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif E (#34.5) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7501 atoms
average map value = 0.008392, steps = 96
shifted from previous position = 0.0102
rotated from previous position = 0.00763 degrees
atoms outside contour = 4036, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif E (#34.5) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58750289 0.35083317 0.72921632 227.26656106
-0.08398670 -0.86983061 0.48614910 251.92182627
0.80485191 -0.34685847 -0.48156267 262.64059694
Axis -0.88363648 -0.08023260 -0.46124755
Axis point 0.00000000 130.49742196 40.19320920
Rotation angle (degrees) 151.87790907
Shift along axis -342.17569793
> color #34.5 #0a6f00ff
> show #32.1 models
> hide #32.1 models
> show #32.1 models
> hide #32.1 models
> hide #34.5 models
> show #34.6 models
> color #34.6 cyan
> fitmap #34.6 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif F (#34.6) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7214 atoms
average map value = 0.008416, steps = 88
shifted from previous position = 2.83
rotated from previous position = 5.13 degrees
atoms outside contour = 3516, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif F (#34.6) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58316797 0.35661943 0.72988883 229.42465943
-0.01511797 -0.89356886 0.44867152 249.28076519
0.81221092 -0.27268529 -0.51570938 258.75772005
Axis -0.88437088 -0.10092544 -0.45574357
Axis point 0.00000000 123.73222530 44.42705025
Rotation angle (degrees) 155.93102330
Shift along axis -345.98242545
> hide #34.6 models
> show #34.7 models
> fitmap #34.7 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif G (#34.7) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2130 atoms
average map value = 0.007774, steps = 60
shifted from previous position = 3.19
rotated from previous position = 3.76 degrees
atoms outside contour = 1200, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif G (#34.7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60590881 0.38239877 0.69759995 225.80992915
-0.05307526 -0.85551020 0.51505855 251.49460333
0.79376163 -0.34910382 -0.49806526 260.96610639
Axis -0.88864344 -0.09888587 -0.44781069
Axis point 0.00000000 128.89841076 41.81263691
Rotation angle (degrees) 150.90719891
Shift along axis -342.39718752
> fitmap #34.7 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif G (#34.7) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2130 atoms
average map value = 0.007775, steps = 44
shifted from previous position = 0.0414
rotated from previous position = 0.0326 degrees
atoms outside contour = 1203, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif G (#34.7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60610451 0.38203307 0.69763032 225.82071776
-0.05295935 -0.85576756 0.51464279 251.53576995
0.79361996 -0.34887336 -0.49845235 260.95147721
Axis -0.88871636 -0.09879093 -0.44768692
Axis point 0.00000000 128.92145471 41.84455385
Rotation angle (degrees) 150.93364992
Shift along axis -342.36458246
> color #34.7 #bf6300ff
> hide #34.7 models
> show #34.8 models
> fitmap #34.8 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif H (#34.8) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4752 atoms
average map value = 0.007743, steps = 128
shifted from previous position = 7.22
rotated from previous position = 9.05 degrees
atoms outside contour = 2924, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif H (#34.8) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60711318 0.39430654 0.68988111 230.62646417
-0.16058066 -0.78940106 0.59250301 257.81976511
0.77822069 -0.47049795 -0.41593778 262.55156168
Axis -0.88409384 -0.07347169 -0.46149756
Axis point 0.00000000 138.94204460 27.13554287
Rotation angle (degrees) 143.04546715
Shift along axis -344.00479526
> color #34.8 #24fa00ff
> hide #34.8 models
> color #34.9 #eff0f0ff
> color #34.9 #fffa00ff
> show #34.9 models
> fitmap #34.9 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif I (#34.9) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.007202, steps = 180
shifted from previous position = 14.7
rotated from previous position = 20.8 degrees
atoms outside contour = 883, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif I (#34.9) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.74653717 0.33711316 0.57361745 245.26298776
0.15110497 -0.92551307 0.34726481 263.21012299
0.64795798 -0.17256964 -0.74186938 278.68417065
Axis -0.93311848 -0.13344349 -0.33389029
Axis point 0.00000000 126.20926941 79.04979370
Rotation angle (degrees) 163.82650418
Shift along axis -357.03304509
> hide #!1 models
> show #10 models
> hide #10 models
> show #10 models
> hide #34.9 models
> show #34.9 models
> select add #34.9
1420 atoms, 1441 bonds, 177 residues, 1 model selected
> view matrix models
> #34.9,0.74828,0.34766,0.56499,301.82,0.15396,-0.91943,0.36186,343.01,0.64527,-0.18378,-0.74152,352.83
> ui mousemode right "rotate selected models"
> view matrix models
> #34.9,0.37364,0.83003,0.41405,310.38,0.82373,-0.091695,-0.55951,370.79,-0.42645,0.55013,-0.71799,360.84
> view matrix models
> #34.9,-0.78088,0.59563,0.18825,341.65,0.61218,0.66973,0.42035,317.47,0.12429,0.44349,-0.88762,361.96
> view matrix models
> #34.9,-0.35045,0.13998,0.92606,302.58,-0.5316,0.78433,-0.31973,370.91,-0.77109,-0.60434,-0.20046,351.51
> view matrix models
> #34.9,0.10437,0.19584,0.97507,292.62,-0.42105,0.89692,-0.13507,358.86,-0.90101,-0.39645,0.17607,332.6
> fitmap #34.9 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif I (#34.9) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.007558, steps = 172
shifted from previous position = 5.84
rotated from previous position = 30.3 degrees
atoms outside contour = 803, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif I (#34.9) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.26830525 0.10951105 0.95708913 240.47366535
-0.09219807 0.98603763 -0.13866968 276.40976195
-0.95891177 -0.12544757 -0.25446237 278.46557109
Axis 0.00686280 0.99448069 -0.10469506
Axis point 235.50650213 0.00000000 62.60461133
Rotation angle (degrees) 105.56699787
Shift along axis 247.38052555
> view matrix models
> #34.9,0.71072,-0.27814,0.64615,307.37,0.22556,-0.77992,-0.58383,387.44,0.66633,0.56068,-0.49157,335.49
> view matrix models
> #34.9,0.32684,-0.94017,0.096226,347.28,0.89604,0.2759,-0.34783,355,0.30047,0.19991,0.93261,273.29
> view matrix models
> #34.9,-0.062416,-0.94261,-0.32802,374.51,0.92237,0.071062,-0.37971,358.21,0.38123,-0.32626,0.865,280.61
> color #34.9 #73fdffff
> view matrix models
> #34.9,-0.87509,-0.19817,0.44153,341.08,0.23219,0.62855,0.7423,307.09,-0.42462,0.7521,-0.50403,350.92
> view matrix models
> #34.9,-0.45011,0.72378,0.52301,321.45,0.70663,0.64679,-0.28695,351.21,-0.54596,0.24041,-0.80257,372.75
> view matrix models
> #34.9,-0.6968,0.27512,0.6624,322.65,0.50668,0.84247,0.18309,328.8,-0.50768,0.4632,-0.72643,366.17
> fitmap #34.9 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif I (#34.9) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.007908, steps = 88
shifted from previous position = 2.18
rotated from previous position = 14 degrees
atoms outside contour = 732, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif I (#34.9) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.67161254 0.33110185 0.66280324 259.75065098
0.40793397 0.91203340 -0.04224840 265.74184674
-0.61848723 0.24200541 -0.74760077 294.34280962
Axis 0.21621363 0.97459545 0.05844127
Axis point 153.26883916 0.00000000 103.06975835
Rotation angle (degrees) 138.90231543
Shift along axis 332.35419188
> view matrix models
> #34.9,-0.3835,-0.29515,0.87511,313.33,-0.093113,0.95509,0.28132,333.04,-0.91884,0.0264,-0.39375,360.07
> fitmap #34.9 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif I (#34.9) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.007916, steps = 232
shifted from previous position = 7.32
rotated from previous position = 23.5 degrees
atoms outside contour = 740, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif I (#34.9) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.17303343 -0.17503221 0.96923843 241.59813206
0.25142938 0.94362700 0.21529357 259.75433651
-0.95228287 0.28094801 -0.11927077 273.76469403
Axis 0.03333776 0.97570281 0.21654705
Axis point 204.14769021 0.00000000 8.83996268
Rotation angle (degrees) 100.04017117
Shift along axis 320.78031311
> view matrix models
> #34.9,-0.95748,-0.19083,-0.21639,375.58,0.28844,-0.6501,-0.70297,397.03,-0.0065236,-0.73549,0.6775,306.16
> view matrix models
> #34.9,-0.90104,-0.29832,-0.31485,380.71,0.43099,-0.5344,-0.72709,394.92,0.048654,-0.79084,0.61009,309.24
> view matrix models
> #34.9,-0.88531,-0.33626,-0.32118,381.16,0.45673,-0.49906,-0.73643,394.65,0.087344,-0.79867,0.5954,309.46
> ui mousemode right "translate selected models"
> view matrix models
> #34.9,-0.88531,-0.33626,-0.32118,372.76,0.45673,-0.49906,-0.73643,381.8,0.087344,-0.79867,0.5954,309.71
> fitmap #34.9 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif I (#34.9) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.007313, steps = 212
shifted from previous position = 10
rotated from previous position = 15.2 degrees
atoms outside contour = 862, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif I (#34.9) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.77843807 -0.55264862 -0.29768046 310.77651000
0.54683725 -0.36417671 -0.75388614 313.10382630
0.30822585 -0.74963644 0.58569788 232.63476634
Axis 0.00338515 -0.48264302 0.87581063
Axis point 86.62936034 283.23574831 0.00000000
Rotation angle (degrees) 141.11964909
Shift along axis 53.67864989
> view matrix models
> #34.9,-0.78344,-0.55233,-0.28489,371.74,0.53391,-0.36355,-0.7634,381.48,0.31807,-0.75018,0.57971,303.13
> ui mousemode right "rotate selected models"
> view matrix models
> #34.9,-0.62244,-0.50088,0.6014,324.37,-0.021401,0.77901,0.62665,309.13,-0.78238,0.37718,-0.4956,362.76
> view matrix models
> #34.9,-0.76847,-0.46048,0.44431,334.08,-0.21176,0.83825,0.50249,317.67,-0.60383,0.29206,-0.74168,373.19
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui mousemode right "translate selected models"
> view matrix models
> #34.9,-0.76847,-0.46048,0.44431,340.36,-0.21176,0.83825,0.50249,331.15,-0.60383,0.29206,-0.74168,369.61
> view matrix models
> #34.9,-0.76847,-0.46048,0.44431,336.23,-0.21176,0.83825,0.50249,331.27,-0.60383,0.29206,-0.74168,369.31
> ui mousemode right "rotate selected models"
> view matrix models
> #34.9,-0.48926,-0.34807,0.79967,313.05,0.28899,0.80041,0.5252,322.84,-0.82287,0.48805,-0.29102,348.16
> ui mousemode right "translate selected models"
> view matrix models
> #34.9,-0.48926,-0.34807,0.79967,317.57,0.28899,0.80041,0.5252,328.11,-0.82287,0.48805,-0.29102,351.95
> view matrix models
> #34.9,-0.48926,-0.34807,0.79967,319.73,0.28899,0.80041,0.5252,325.65,-0.82287,0.48805,-0.29102,352.6
> fitmap #34.9 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif I (#34.9) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.007916, steps = 120
shifted from previous position = 3.53
rotated from previous position = 23.8 degrees
atoms outside contour = 739, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif I (#34.9) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.17363841 -0.17473580 0.96918372 241.60893560
0.25146371 0.94364305 0.21518312 259.77002142
-0.95216369 0.28107859 -0.11991297 273.77647355
Axis 0.03346386 0.97572269 0.21643797
Axis point 204.09647485 0.00000000 8.93729259
Rotation angle (degrees) 100.07599094
Shift along axis 320.80429641
> select subtract #34.9
Nothing selected
> show #!1 models
> hide #34.9 models
> show #34.9 models
> hide #34.9 models
> show #34.9 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color #34.9 #fffa00ff
> hide #34.9 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #34.9 & sel to #10 & sel
No 'to' model specified
> ui tool show Matchmaker
> matchmaker #34.9 & sel to #10
No molecules/chains to match specified
> ui tool show Matchmaker
> show #34.8 models
> show #34.6 models
> show #34.7 models
> show #34.5 models
> show #34.4 models
> show #34.3 models
> show #34.2 models
> show #34.1 models
> ui tool show Matchmaker
> matchmaker #34.9 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CopZ1_P61924_M1-V153.pdb, chain A (#10) with
fold_20240711_copi_golph3_model_0.cif I, chain I (#34.9), sequence alignment
score = 834
RMSD between 144 pruned atom pairs is 0.487 angstroms; (across all 153 pairs:
1.639)
> show #34.9 models
> hide #34.9 models
> show #34.9 models
> hide #!1 models
> hide #10 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #34.2 models
> show #34.2 models
> ui tool show Matchmaker
> matchmaker #34.2 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Arf1-P84077-human.pdb, chain A (#6) with
fold_20240711_copi_golph3_model_0.cif B, chain B (#34.2), sequence alignment
score = 902.5
RMSD between 160 pruned atom pairs is 0.730 angstroms; (across all 181 pairs:
6.148)
> hide #34.3 models
> show #34.3 models
> hide #6 models
> show #22 models
> hide #22 models
> show #22 models
> hide #22 models
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> show #23 models
> hide #23 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #34.3 to #23
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Arf1-P84077-human.pdb, chain A (#23) with
fold_20240711_copi_golph3_model_0.cif C, chain C (#34.3), sequence alignment
score = 902.5
RMSD between 157 pruned atom pairs is 0.695 angstroms; (across all 181 pairs:
6.432)
> hide #34.3 models
> show #34.3 models
> show #!1 models
> fitmap #34.3 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif C (#34.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.01001, steps = 68
shifted from previous position = 0.227
rotated from previous position = 2.22 degrees
atoms outside contour = 623, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif C (#34.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.54968172 0.35481834 -0.75627637 335.66728281
0.52670407 0.84989962 0.01592060 166.85451496
0.64840792 -0.38958258 -0.65405855 271.13399774
Axis -0.27545663 -0.95419623 0.11676126
Axis point 75.48007854 0.00000000 209.04048356
Rotation angle (degrees) 132.60345266
Shift along axis -220.01578155
> fitmap #34.3 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif C (#34.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.01001, steps = 84
shifted from previous position = 0.0284
rotated from previous position = 0.0625 degrees
atoms outside contour = 624, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif C (#34.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.54962853 0.35489903 -0.75627717 335.67547785
0.52746175 0.84944131 0.01528258 166.85707183
0.64783684 -0.39050754 -0.65407285 271.22274561
Axis -0.27572382 -0.95405890 0.11725188
Axis point 75.43029175 0.00000000 209.10692899
Rotation angle (degrees) 132.61977887
Shift along axis -219.94382110
> hide #!1 models
> show #!1 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> hide #34.1 models
> show #34.1 models
> hide #34.5 models
> show #34.5 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3
> /fold_20240711_copi_golph3/20240711_leaf_fitting_alphafold_withGolph3AF3_v1.cxs"
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3
> /fold_20240711_copi_golph3/20240711_leaf_fitting_alphafold_withGolph3AF3_v2.cxs"
——— End of log from Sat Jul 13 09:14:12 2024 ———
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #34.1 models
> show #34.1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #34.1 models
> hide #34.2 models
> show #34.2 models
> hide #34.2 models
> show #34.2 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 64
shifted from previous position = 0.248
rotated from previous position = 2.71 degrees
atoms outside contour = 834, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64432560 0.35698285 0.67631928 226.65167399
-0.03018417 -0.87180479 0.48892261 253.33060500
0.76415537 -0.33543949 -0.55095092 256.82984099
Axis -0.90096298 -0.09599795 -0.42314311
Axis point 0.00000000 129.93033443 45.49616360
Rotation angle (degrees) 152.77477596
Shift along axis -337.19976560
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 48
shifted from previous position = 0.0361
rotated from previous position = 0.046 degrees
atoms outside contour = 835, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64411089 0.35714951 0.67643580 226.66372194
-0.02956162 -0.87202532 0.48856725 253.34453506
0.76436070 -0.33468803 -0.55112308 256.83246742
Axis -0.90091671 -0.09621926 -0.42319136
Axis point 0.00000000 129.88083392 45.53649969
Rotation angle (degrees) 152.81283600
Shift along axis -337.27104026
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 48
shifted from previous position = 0.0337
rotated from previous position = 0.0592 degrees
atoms outside contour = 833, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64471671 0.35650419 0.67619903 226.68116161
-0.03020175 -0.87201891 0.48853954 253.32157186
0.76382473 -0.33539200 -0.55143811 256.79928251
Axis -0.90108643 -0.09583118 -0.42291799
Axis point 0.00000000 129.94286445 45.52854398
Rotation angle (degrees) 152.79420692
Shift along axis -337.14046055
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 60
shifted from previous position = 0.00222
rotated from previous position = 0.0189 degrees
atoms outside contour = 834, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64456528 0.35676967 0.67620337 226.66616982
-0.03015048 -0.87189761 0.48875914 253.32836692
0.76395454 -0.33542503 -0.55123816 256.81153638
Axis -0.90103727 -0.09593375 -0.42299948
Axis point 0.00000000 129.93692500 45.51545932
Rotation angle (degrees) 152.78356795
Shift along axis -337.16855269
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 60
shifted from previous position = 0.0325
rotated from previous position = 0.0426 degrees
atoms outside contour = 833, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64429202 0.35689581 0.67639720 226.67538323
-0.02964787 -0.87211347 0.48840464 253.33933408
0.76420469 -0.33472894 -0.55131455 256.81639486
Axis -0.90097264 -0.09611094 -0.42309691
Axis point 0.00000000 129.89157565 45.54507875
Rotation angle (degrees) 152.81901251
Shift along axis -337.23522198
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 60
shifted from previous position = 0.0297
rotated from previous position = 0.0339 degrees
atoms outside contour = 833, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64458822 0.35669011 0.67622348 226.67106189
-0.03003524 -0.87199842 0.48858637 253.33241227
0.76393973 -0.33524755 -0.55136663 256.80741557
Axis -0.90104970 -0.09593767 -0.42297210
Axis point 0.00000000 129.93127775 45.53111558
Rotation angle (degrees) 152.79649635
Shift along axis -337.16838500
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 48
shifted from previous position = 0.0372
rotated from previous position = 0.0454 degrees
atoms outside contour = 833, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64422597 0.35682412 0.67649793 226.68001862
-0.02956760 -0.87222125 0.48821701 253.33910120
0.76426348 -0.33452450 -0.55135714 256.81707073
Axis -0.90095922 -0.09610938 -0.42312583
Axis point 0.00000000 129.88181796 45.55489965
Rotation angle (degrees) 152.83258813
Shift along axis -337.24365378
> hide #34.2 models
> show #34.2 models
> hide #34.2 models
> hide #34.3 models
> show #34.3 models
> fitmap #34.3 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif C (#34.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.01001, steps = 48
shifted from previous position = 0.0376
rotated from previous position = 0.0533 degrees
atoms outside contour = 623, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif C (#34.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.54976862 0.35490996 -0.75617021 335.66204339
0.52683519 0.84981999 0.01583258 166.86602425
0.64822770 -0.38967282 -0.65418342 271.14642081
Axis -0.27550830 -0.95417543 0.11680936
Axis point 75.48209689 0.00000000 209.03180877
Rotation angle (degrees) 132.61479508
Shift along axis -220.02469949
> fitmap #34.3 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif C (#34.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.01001, steps = 48
shifted from previous position = 0.0359
rotated from previous position = 0.0719 degrees
atoms outside contour = 625, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif C (#34.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.54966200 0.35546795 -0.75598559 335.64620514
0.52641333 0.85005967 0.01695742 166.82818569
0.64866068 -0.38864005 -0.65436857 271.11571830
Axis -0.27554310 -0.95424807 0.11613194
Axis point 75.51025450 0.00000000 208.94253072
Rotation angle (degrees) 132.60852240
Shift along axis -220.19527612
> fitmap #34.3 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif C (#34.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.01001, steps = 48
shifted from previous position = 0.0259
rotated from previous position = 0.0904 degrees
atoms outside contour = 624, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif C (#34.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.54960161 0.35507513 -0.75621407 335.66385777
0.52722425 0.84958042 0.01573838 166.84432392
0.64805298 -0.39004456 -0.65413499 271.19599798
Axis -0.27570103 -0.95410091 0.11696324
Axis point 75.44482347 0.00000000 209.06469932
Rotation angle (degrees) 132.61573417
Shift along axis -220.00922798
> hide #34.3 models
> show #34.3 models
> hide #34.3 models
> show #34.2 models
> show #34.3 models
> hide #34.4 models
> show #34.4 models
> combine #34.4
> hide #38 models
> show #38 models
> combine #34.4
> hide #34.4 models
> hide #34.9 models
> hide #34.8 models
> hide #34.7 models
> hide #34.6 models
> hide #34.5 models
> hide #34.3 models
> hide #34.2 models
> hide #39 models
> hide #!34 models
> show #!34 models
> hide #!1 models
> hide #38 models
> show #38 models
> ui mousemode right select
> show #!1 models
> hide #!1 models
Drag select of 119 residues
> select clear
Drag select of 302 residues
> select up
2380 atoms, 2423 bonds, 306 residues, 1 model selected
> delete sel
Drag select of 2 residues
> delete sel
> select #38/D:592
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> show #!1 models
> fitmap #34.3 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif C (#34.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.01001, steps = 48
shifted from previous position = 0.00549
rotated from previous position = 0.0119 degrees
atoms outside contour = 624, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif C (#34.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.54954249 0.35524480 -0.75617735 335.65186462
0.52738295 0.84948061 0.01580877 166.84331501
0.64797398 -0.39010744 -0.65417574 271.20127937
Axis -0.27580563 -0.95407086 0.11696174
Axis point 75.43022439 0.00000000 209.05503117
Rotation angle (degrees) 132.61890471
Shift along axis -220.03484367
> fitmap #38 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif D (#38) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008699, steps = 68
shifted from previous position = 1.24
rotated from previous position = 1.92 degrees
atoms outside contour = 2233, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif D (#38) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57954569 0.37609347 0.72296646 229.39627935
-0.04018189 -0.87287444 0.48628760 258.29327164
0.81394853 -0.31087604 -0.49075847 263.86207894
Axis -0.88191705 -0.10065517 -0.46053323
Axis point -0.00000000 129.97172556 41.82519965
Rotation angle (degrees) 153.13118000
Shift along axis -349.82429832
> rename #38 20240711_copi_golph3_alpha_M1-T591.cif
> hide #38 models
> show #38 models
> show #39 models
> hide #!1 models
> hide #38 models
Drag select of 244 residues
> select up
2232 atoms, 2269 bonds, 277 residues, 1 model selected
> select clear
Drag select of 312 residues
Drag select of 574 residues
> select up
4763 atoms, 4880 bonds, 591 residues, 1 model selected
> delete sel
> show #!31 models
> hide #!31 models
> show #!1 models
> fitmap #38 inMap #1
Fit molecule 20240711_copi_golph3_alpha_M1-T591.cif (#38) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008699, steps = 28
shifted from previous position = 0.0348
rotated from previous position = 0.0398 degrees
atoms outside contour = 2232, contour level = 0.0073613
Position of 20240711_copi_golph3_alpha_M1-T591.cif (#38) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57899303 0.37617952 0.72336439 229.39426216
-0.04035202 -0.87289350 0.48623930 258.30795598
0.81433334 -0.31071838 -0.49021965 263.89271024
Axis -0.88175253 -0.10064788 -0.46084974
Axis point 0.00000000 129.96471515 41.78394361
Rotation angle (degrees) 153.13326520
Shift along axis -349.88200523
> fitmap #39 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif D (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2403 atoms
average map value = 0.007323, steps = 68
shifted from previous position = 2.94
rotated from previous position = 3.87 degrees
atoms outside contour = 1477, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif D (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58533449 0.32440303 0.74306541 225.71515771
-0.13492540 -0.86471675 0.48379755 254.86013275
0.79948650 -0.38344179 -0.46237833 264.73941481
Axis -0.88224604 -0.05739740 -0.46727664
Axis point 0.00000000 136.02553898 37.53416349
Rotation angle (degrees) 150.56109739
Shift along axis -337.47115908
> fitmap #39 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif D (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2403 atoms
average map value = 0.007323, steps = 44
shifted from previous position = 0.017
rotated from previous position = 0.048 degrees
atoms outside contour = 1476, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif D (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58552841 0.32361096 0.74325799 225.72064463
-0.13536426 -0.86496102 0.48323798 254.83332258
0.79927029 -0.38356014 -0.46265389 264.72247172
Axis -0.88231571 -0.05701505 -0.46719189
Axis point 0.00000000 136.05872535 37.55009384
Rotation angle (degrees) 150.58009941
Shift along axis -337.36239934
> hide #!1 models
> rename #39 20240711_copi_golph3_alpha_I592-G900.cif
> hide #39 models
> show #34.6 models
> show #!1 models
> fitmap #34.6 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif F (#34.6) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7214 atoms
average map value = 0.008416, steps = 108
shifted from previous position = 0.0102
rotated from previous position = 0.00668 degrees
atoms outside contour = 3515, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif F (#34.6) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58320062 0.35669686 0.72982490 229.42488060
-0.01510074 -0.89352030 0.44876880 249.27477617
0.81218779 -0.27274314 -0.51571521 258.76540818
Axis -0.88437810 -0.10095458 -0.45572310
Axis point 0.00000000 123.72961750 44.43035142
Rotation angle (degrees) 155.92572855
Shift along axis -345.98914492
> hide #34.6 models
> show #34.6 models
> hide #!34 models
> combine #34.6
[Repeated 1 time(s)]
> hide #34.6 models
> hide #42 models
> hide #!1 models
Drag select of 111 residues
> select clear
Drag select of 253 residues
> select up
1997 atoms, 2033 bonds, 254 residues, 1 model selected
> delete sel
Drag select of 64 residues
> delete sel
> select #41/F:587
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> show #!1 models
> fitmap #41 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif F (#41) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4686 atoms
average map value = 0.01004, steps = 64
shifted from previous position = 0.573
rotated from previous position = 1.59 degrees
atoms outside contour = 1755, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif F (#41) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59294693 0.33291104 0.73320132 230.49160519
-0.03655337 -0.89846921 0.43751220 249.48414209
0.80441146 -0.28622249 -0.52057554 258.88679735
Axis -0.88725580 -0.08729940 -0.45294144
Axis point 0.00000000 125.81112779 44.24040475
Rotation angle (degrees) 155.93014878
Shift along axis -343.54539036
> fitmap #41 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif F (#41) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4686 atoms
average map value = 0.01004, steps = 28
shifted from previous position = 0.0225
rotated from previous position = 0.0138 degrees
atoms outside contour = 1751, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif F (#41) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59310238 0.33298355 0.73304264 230.46604751
-0.03651740 -0.89840571 0.43764559 249.47016786
0.80429848 -0.28633746 -0.52068687 258.88830934
Axis -0.88729822 -0.08732963 -0.45285251
Axis point 0.00000000 125.81086103 44.25740174
Rotation angle (degrees) 155.92258977
Shift along axis -343.51647395
> hide #!1 models
> rename #41 20240711_copi_golph3_betaprime_M1-S586.cif
> fitmap #41 inMap #1
Fit molecule 20240711_copi_golph3_betaprime_M1-S586.cif (#41) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4686 atoms
average map value = 0.01004, steps = 44
shifted from previous position = 0.008
rotated from previous position = 0.00435 degrees
atoms outside contour = 1755, contour level = 0.0073613
Position of 20240711_copi_golph3_betaprime_M1-S586.cif (#41) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59312402 0.33303985 0.73299956 230.45895672
-0.03648900 -0.89837760 0.43770565 249.47227469
0.80428381 -0.28636016 -0.52069705 258.89564102
Axis -0.88730336 -0.08735498 -0.45283756
Axis point 0.00000000 125.81189319 44.26297894
Rotation angle (degrees) 155.91981153
Shift along axis -343.51732333
> hide #41 models
> show #42 models
Drag select of 251 residues
> select up
2195 atoms, 2246 bonds, 274 residues, 1 model selected
> delete sel
Drag select of 125 residues, 4 pseudobonds
Drag select of 222 residues, 4 pseudobonds
> select up
2116 atoms, 2152 bonds, 4 pseudobonds, 264 residues, 2 models selected
> delete sel
Drag select of 26 residues, 3 pseudobonds
> delete sel
Drag select of 14 residues, 2 pseudobonds
> delete sel
Drag select of 2 residues, 1 pseudobonds
> delete sel
Drag select of 5 residues, 2 pseudobonds
> select up
48 atoms, 47 bonds, 2 pseudobonds, 6 residues, 2 models selected
> delete sel
Undo failed, probably because structures have been modified.
> close #42
> combine #34.6
Drag select of 302 residues
> delete sel
Drag select of 270 residues
> select up
2254 atoms, 2303 bonds, 282 residues, 1 model selected
Drag select of 285 residues
> select clear
Drag select of 285 residues
> select clear
Drag select of 283 residues
> select up
2262 atoms, 2312 bonds, 284 residues, 1 model selected
> delete sel
> fitmap #42 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif F (#42) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2528 atoms
average map value = 0.007568, steps = 84
shifted from previous position = 5.8
rotated from previous position = 6.74 degrees
atoms outside contour = 1450, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif F (#42) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59124018 0.34103418 0.73084249 226.71930924
-0.11694607 -0.86036468 0.49608088 254.82904919
0.79797160 -0.37877210 -0.46879956 265.13169213
Axis -0.88390636 -0.06782379 -0.46271965
Axis point 0.00000000 134.83865586 38.51143168
Rotation angle (degrees) 150.33824374
Shift along axis -340.36375630
> show #!1 models
> show #39 models
> hide #42 models
> hide #39 models
> rename #42 "20240711_copi_golph3_betaprime_L587-D905.cif F"
> rename #42 20240711_copi_golph3_betaprime_L587-D905.cif
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only.cxs"
> show #34.5 models
> combine #34.5
[Repeated 1 time(s)]
> hide #34.5 models
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7501 atoms
average map value = 0.008391, steps = 60
shifted from previous position = 0.0202
rotated from previous position = 0.0157 degrees
atoms outside contour = 4035, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58728190 0.35087602 0.72937370 227.26547074
-0.08402593 -0.86984861 0.48611011 251.91658958
0.80500908 -0.34676997 -0.48136366 262.66211508
Axis -0.88357135 -0.08023875 -0.46137123
Axis point 0.00000000 130.48829569 40.18584814
Rotation angle (degrees) 151.88033864
Shift along axis -342.20347384
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7501 atoms
average map value = 0.008391, steps = 60
shifted from previous position = 0.0202
rotated from previous position = 0.0157 degrees
atoms outside contour = 4035, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58728190 0.35087602 0.72937370 227.26547074
-0.08402593 -0.86984861 0.48611011 251.91658958
0.80500908 -0.34676997 -0.48136366 262.66211508
Axis -0.88357135 -0.08023875 -0.46137123
Axis point 0.00000000 130.48829569 40.18584814
Rotation angle (degrees) 151.88033864
Shift along axis -342.20347384
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 7501 atoms
average map value = 0.008391, steps = 80
shifted from previous position = 0.0251
rotated from previous position = 0.0158 degrees
atoms outside contour = 4039, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58724649 0.35080437 0.72943667 227.28192342
-0.08428861 -0.86979335 0.48616351 251.91497901
0.80500745 -0.34698102 -0.48121428 262.64428639
Axis -0.88355512 -0.08014329 -0.46141889
Axis point 0.00000000 130.50051036 40.14821271
Rotation angle (degrees) 151.87005385
Shift along axis -342.19444001
> hide #!1 models
> hide #44 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 121 residues
> select up
1052 atoms, 1068 bonds, 132 residues, 1 model selected
> delete sel
Drag select of 88 residues, 1 pseudobonds
> delete sel
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5728 atoms
average map value = 0.008372, steps = 76
shifted from previous position = 1.66
rotated from previous position = 2.84 degrees
atoms outside contour = 2966, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57378754 0.34816301 0.74131665 228.20919476
-0.12686471 -0.85643528 0.50042378 253.80233981
0.80911878 -0.38118385 -0.44724229 263.79645345
Axis -0.87832859 -0.06754995 -0.47326091
Axis point 0.00000000 133.71094787 35.07949807
Rotation angle (degrees) 149.87642729
Shift along axis -342.43154616
> show #!1 models
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5728 atoms
average map value = 0.008372, steps = 76
shifted from previous position = 1.66
rotated from previous position = 2.84 degrees
atoms outside contour = 2966, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57378754 0.34816301 0.74131665 228.20919476
-0.12686471 -0.85643528 0.50042378 253.80233981
0.80911878 -0.38118385 -0.44724229 263.79645345
Axis -0.87832859 -0.06754995 -0.47326091
Axis point 0.00000000 133.71094787 35.07949807
Rotation angle (degrees) 149.87642729
Shift along axis -342.43154616
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5728 atoms
average map value = 0.008372, steps = 76
shifted from previous position = 1.66
rotated from previous position = 2.84 degrees
atoms outside contour = 2966, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57378754 0.34816301 0.74131665 228.20919476
-0.12686471 -0.85643528 0.50042378 253.80233981
0.80911878 -0.38118385 -0.44724229 263.79645345
Axis -0.87832859 -0.06754995 -0.47326091
Axis point 0.00000000 133.71094787 35.07949807
Rotation angle (degrees) 149.87642729
Shift along axis -342.43154616
> hide #!1 models
Drag select of 28 residues
> select up
283 atoms, 287 bonds, 34 residues, 1 model selected
> delete sel
Drag select of 63 residues
> select up
676 atoms, 679 bonds, 88 residues, 1 model selected
> delete sel
Drag select of 9 residues, 1 pseudobonds
> select up
278 atoms, 279 bonds, 1 pseudobond, 34 residues, 2 models selected
Drag select of 59 residues, 2 pseudobonds
> select up
678 atoms, 684 bonds, 2 pseudobonds, 85 residues, 2 models selected
> delete sel
Drag select of 3 residues
> delete sel
> show #!1 models
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4069 atoms
average map value = 0.008155, steps = 68
shifted from previous position = 1.4
rotated from previous position = 0.816 degrees
atoms outside contour = 2109, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57410381 0.34312327 0.74341861 228.36549375
-0.14054360 -0.85318371 0.50231968 255.37589611
0.80663022 -0.39286637 -0.44159224 264.01600817
Axis -0.87810302 -0.06200532 -0.47443695
Axis point 0.00000000 135.52919165 33.77725227
Rotation angle (degrees) 149.35433730
Shift along axis -341.62204503
> show #34.5 models
> hide #34.5 models
> show #34.5 models
> hide #34.5 models
> show #34.5 models
> hide #34.5 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #44 models
> hide #!43 models
> hide #44 models
> show #!43 models
> hide #!1 models
Drag select of 211 residues
> select up
1801 atoms, 1824 bonds, 229 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2268 atoms
average map value = 0.008066, steps = 88
shifted from previous position = 0.913
rotated from previous position = 3.83 degrees
atoms outside contour = 1095, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.54911717 0.39741492 0.73520862 228.50766833
-0.09014896 -0.84640556 0.52485312 256.86574974
0.83086912 -0.35448415 -0.42894929 265.00653117
Axis -0.87062947 -0.09471321 -0.48273568
Axis point 0.00000000 130.86457817 34.34641142
Rotation angle (degrees) 149.66859034
Shift along axis -351.20219705
> hide #!1 models
Drag select of 51 residues
> delete sel
> show #!1 models
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1872 atoms
average map value = 0.008979, steps = 52
shifted from previous position = 0.229
rotated from previous position = 2.06 degrees
atoms outside contour = 765, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55235724 0.42748288 0.71565345 229.23148406
-0.07113425 -0.83119930 0.55140515 257.71360793
0.83056691 -0.35548010 -0.42871028 265.08311295
Axis -0.87093274 -0.11035784 -0.47884999
Axis point 0.00000000 129.66425331 34.28845360
Rotation angle (degrees) 148.62479341
Shift along axis -355.02096685
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1872 atoms
average map value = 0.008979, steps = 48
shifted from previous position = 0.00726
rotated from previous position = 0.0577 degrees
atoms outside contour = 758, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55317939 0.42734298 0.71510178 229.23855785
-0.07089502 -0.83113817 0.55152810 257.71998380
0.83004004 -0.35579113 -0.42947201 265.06819269
Axis -0.87118278 -0.11036053 -0.47839432
Axis point 0.00000000 129.69838305 34.35730714
Rotation angle (degrees) 148.61810567
Shift along axis -354.95791509
> hide #!1 models
> show #!1 models
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1872 atoms
average map value = 0.008979, steps = 60
shifted from previous position = 0.0302
rotated from previous position = 0.0163 degrees
atoms outside contour = 756, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55302467 0.42752497 0.71511266 229.26901259
-0.07069298 -0.83113550 0.55155805 257.73333941
0.83016035 -0.35557865 -0.42941543 265.07013834
Axis -0.87113844 -0.11048221 -0.47844697
Axis point 0.00000000 129.67681632 34.35014664
Rotation angle (degrees) 148.62335798
Shift along axis -355.02200355
> fitmap #43 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1872 atoms
average map value = 0.008979, steps = 44
shifted from previous position = 0.00905
rotated from previous position = 0.0364 degrees
atoms outside contour = 761, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55251064 0.42761388 0.71545675 229.26676177
-0.07087587 -0.83115833 0.55150017 257.73181508
0.83048697 -0.35541834 -0.42891632 265.07188309
Axis -0.87098068 -0.11047200 -0.47873645
Axis point 0.00000000 129.65750307 34.29851952
Rotation angle (degrees) 148.62543510
Shift along axis -355.05864186
> hide #!43 models
> show #44 models
> hide #!1 models
Drag select of 123 residues
> select up
1033 atoms, 1050 bonds, 133 residues, 1 model selected
> delete sel
Drag select of 107 residues, 1 pseudobonds
> select up
934 atoms, 947 bonds, 1 pseudobond, 123 residues, 2 models selected
> select clear
Drag select of 107 residues, 1 pseudobonds
> select up
934 atoms, 947 bonds, 1 pseudobond, 123 residues, 2 models selected
> select clear
Drag select of 108 residues, 1 pseudobonds
> select up
934 atoms, 947 bonds, 1 pseudobond, 123 residues, 2 models selected
> select down
823 atoms, 1 pseudobond, 108 residues, 2 models selected
> select clear
Drag select of 111 residues, 1 pseudobonds
> select clear
Drag select of 106 residues, 1 pseudobonds
> select up
6468 atoms, 6566 bonds, 1 pseudobond, 820 residues, 2 models selected
> select down
804 atoms, 1 pseudobond, 106 residues, 2 models selected
> select clear
Drag select of 108 residues, 1 pseudobonds
> select clear
Drag select of 2 residues
> select clear
> select #44/E:710
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #44/E:710
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #44/E:711
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #44/E:735
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #44/E:736
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
Drag select of 109 residues, 1 pseudobonds
> delete sel
> select clear
> select #44/E:711
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #44/E:711
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!43 models
> select #43/E:711
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #44/E:455
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select #44/E:710
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #44/E:455
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #44/E:711
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> hide #!43 models
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5629 atoms
average map value = 0.009299, steps = 68
shifted from previous position = 0.65
rotated from previous position = 1.89 degrees
atoms outside contour = 2810, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59210262 0.37757492 0.71193516 226.72867709
-0.07064798 -0.85572262 0.51258917 251.65532078
0.80275983 -0.35380217 -0.48000071 262.28033527
Axis -0.88435515 -0.09270784 -0.45751637
Axis point 0.00000000 129.47464566 39.97365136
Rotation angle (degrees) 150.66970068
Shift along axis -343.83664119
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 168 residues
> select up
1391 atoms, 1419 bonds, 172 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4238 atoms
average map value = 0.00908, steps = 52
shifted from previous position = 0.889
rotated from previous position = 0.581 degrees
atoms outside contour = 2177, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59156554 0.37098251 0.71583670 226.98938097
-0.08051789 -0.85623010 0.51028118 251.70697815
0.80222633 -0.35950243 -0.47664549 263.22862441
Axis -0.88411669 -0.08781323 -0.45894064
Axis point 0.00000000 130.27549443 39.75547073
Rotation angle (degrees) 150.53484706
Shift along axis -343.59461614
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4238 atoms
average map value = 0.00908, steps = 64
shifted from previous position = 0.0343
rotated from previous position = 0.0182 degrees
atoms outside contour = 2174, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59182015 0.37092770 0.71565463 226.99041357
-0.08049239 -0.85619924 0.51033699 251.73479534
0.80204107 -0.35963246 -0.47685911 263.24852963
Axis -0.88419130 -0.08779865 -0.45879969
Axis point 0.00000000 130.30411815 39.78107646
Rotation angle (degrees) 150.53066235
Shift along axis -343.58326437
> hide #!1 models
Drag select of 47 residues
> select up
382 atoms, 388 bonds, 48 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3856 atoms
average map value = 0.009018, steps = 48
shifted from previous position = 0.371
rotated from previous position = 0.406 degrees
atoms outside contour = 1995, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58961576 0.36849782 0.71872291 227.35977820
-0.08716202 -0.85562984 0.51019639 252.02457887
0.80296702 -0.36346517 -0.47237383 263.49807121
Axis -0.88342999 -0.08518605 -0.46075458
Axis point 0.00000000 130.78947771 39.10958282
Rotation angle (degrees) 150.36510653
Shift along axis -343.73336977
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3856 atoms
average map value = 0.009019, steps = 48
shifted from previous position = 0.0432
rotated from previous position = 0.0409 degrees
atoms outside contour = 1998, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58981753 0.36878021 0.71841245 227.31394980
-0.08648174 -0.85567229 0.51024096 251.99800272
0.80289239 -0.36307862 -0.47279776 263.47390004
Axis -0.88349987 -0.08546473 -0.46056894
Axis point 0.00000000 130.74073406 39.17680080
Rotation angle (degrees) 150.38044106
Shift along axis -343.71668325
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3856 atoms
average map value = 0.009018, steps = 28
shifted from previous position = 0.0289
rotated from previous position = 0.0173 degrees
atoms outside contour = 1995, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58978570 0.36861431 0.71852371 227.34342395
-0.08678141 -0.85566478 0.51020268 252.00086481
0.80288344 -0.36326474 -0.47266998 263.48577416
Axis -0.88348680 -0.08532741 -0.46061948
Axis point 0.00000000 130.76047116 39.15273292
Rotation angle (degrees) 150.37444458
Shift along axis -343.72417541
> hide #!1 models
Drag select of 8 residues
> select up
137 atoms, 138 bonds, 17 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3719 atoms
average map value = 0.008983, steps = 40
shifted from previous position = 0.186
rotated from previous position = 0.311 degrees
atoms outside contour = 1911, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58940097 0.36876303 0.71876305 227.50271713
-0.09114214 -0.85369825 0.51273034 252.22456685
0.80268276 -0.36771336 -0.46956073 263.59943137
Axis -0.88321410 -0.08418377 -0.46135231
Axis point 0.00000000 131.13925552 38.63367265
Rotation angle (degrees) 150.10370783
Shift along axis -343.77902715
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3719 atoms
average map value = 0.008983, steps = 44
shifted from previous position = 0.0333
rotated from previous position = 0.0452 degrees
atoms outside contour = 1912, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58963985 0.36910282 0.71839262 227.46618481
-0.09039832 -0.85371832 0.51282860 252.19550746
0.80259142 -0.36732566 -0.47002007 263.57825436
Axis -0.88329455 -0.08449921 -0.46114057
Axis point 0.00000000 131.08567575 38.70544988
Rotation angle (degrees) 150.11753520
Shift along axis -343.77658925
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3719 atoms
average map value = 0.008982, steps = 40
shifted from previous position = 0.0258
rotated from previous position = 0.0554 degrees
atoms outside contour = 1912, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58941028 0.36871102 0.71878209 227.49719093
-0.09133467 -0.85364409 0.51278626 252.22381797
0.80265403 -0.36789122 -0.46947050 263.59906269
Axis -0.88321180 -0.08411329 -0.46136956
Axis point 0.00000000 131.15350539 38.61823818
Rotation angle (degrees) 150.09487469
Shift along axis -343.76016394
> hide #!1 models
Drag select of 7 residues
> select up
76 atoms, 77 bonds, 9 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3643 atoms
average map value = 0.009033, steps = 60
shifted from previous position = 0.0939
rotated from previous position = 0.254 degrees
atoms outside contour = 1868, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58721603 0.36738063 0.72125502 227.63928427
-0.09498580 -0.85363227 0.51214221 252.38642438
0.80383769 -0.36924710 -0.46637062 263.59994149
Axis -0.88251536 -0.08268817 -0.46295713
Axis point 0.00000000 131.35972548 38.14252414
Rotation angle (degrees) 150.04219923
Shift along axis -343.80001020
> hide #!1 models
Drag select of 7 residues
> select up
70 atoms, 70 bonds, 8 residues, 1 model selected
> delete sel
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3573 atoms
average map value = 0.009065, steps = 60
shifted from previous position = 0.0944
rotated from previous position = 0.254 degrees
atoms outside contour = 1823, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58804387 0.36337399 0.72260899 227.63918544
-0.09818317 -0.85472554 0.50971003 252.52385510
0.80284772 -0.37067990 -0.46693891 263.68704248
Axis -0.88279454 -0.08045790 -0.46281782
Axis point 0.00000000 131.74225731 38.14775838
Rotation angle (degrees) 150.09006364
Shift along axis -343.31522855
> show #!1 models
> hide #!1 models
Drag select of 15 residues
> select up
118 atoms, 119 bonds, 17 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3455 atoms
average map value = 0.008967, steps = 40
shifted from previous position = 0.17
rotated from previous position = 0.499 degrees
atoms outside contour = 1784, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58481873 0.36251496 0.72565140 227.88550631
-0.10569784 -0.85289709 0.51126757 252.84421015
0.80424811 -0.37569864 -0.46047314 263.73281084
Axis -0.88164404 -0.07812509 -0.46540333
Axis point 0.00000000 132.22551733 37.13312945
Rotation angle (degrees) 149.80010785
Shift along axis -343.40950360
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3455 atoms
average map value = 0.008967, steps = 28
shifted from previous position = 0.00479
rotated from previous position = 0.0195 degrees
atoms outside contour = 1783, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58487473 0.36266704 0.72553026 227.88007614
-0.10536217 -0.85292825 0.51128486 252.83430841
0.80425143 -0.37548104 -0.46064480 263.72708147
Axis -0.88166605 -0.07826844 -0.46533754
Axis point 0.00000000 132.19898703 37.16183201
Rotation angle (degrees) 149.80847079
Shift along axis -343.42518480
> hide #!1 models
Drag select of 24 residues
> select clear
Drag select of 14 residues
> select up
127 atoms, 128 bonds, 17 residues, 1 model selected
> select up
3455 atoms, 3497 bonds, 439 residues, 1 model selected
> select down
127 atoms, 128 bonds, 17 residues, 1 model selected
> select clear
Drag select of 12 residues
> select up
144 atoms, 145 bonds, 20 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3311 atoms
average map value = 0.008976, steps = 44
shifted from previous position = 0.294
rotated from previous position = 0.626 degrees
atoms outside contour = 1710, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58670575 0.35271088 0.72895226 227.91230109
-0.11307811 -0.85566093 0.50503239 253.22324625
0.80186639 -0.37873396 -0.46213731 263.98791614
Axis -0.88230346 -0.07279344 -0.46501798
Axis point 0.00000000 133.15706792 37.19930453
Rotation angle (degrees) 149.94513746
Shift along axis -342.27992947
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3311 atoms
average map value = 0.008976, steps = 28
shifted from previous position = 0.034
rotated from previous position = 0.014 degrees
atoms outside contour = 1710, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58675841 0.35280118 0.72886617 227.88952369
-0.11284029 -0.85569344 0.50503050 253.19118511
0.80186136 -0.37857636 -0.46227513 263.97734405
Axis -0.88232341 -0.07288916 -0.46496512
Axis point 0.00000000 133.12775430 37.22686107
Rotation angle (degrees) 149.95186985
Shift along axis -342.26741368
> hide #!1 models
Drag select of 16 residues
> select up
155 atoms, 154 bonds, 19 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3156 atoms
average map value = 0.008983, steps = 48
shifted from previous position = 0.199
rotated from previous position = 0.616 degrees
atoms outside contour = 1643, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58674709 0.34943351 0.73049577 228.00257976
-0.12309162 -0.85313185 0.50696598 253.65282207
0.80036011 -0.38737872 -0.45756030 264.14363985
Axis -0.88207505 -0.06890586 -0.46604248
Axis point 0.00000000 134.11030158 36.32607643
Rotation angle (degrees) 149.53878453
Shift along axis -341.69570906
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3156 atoms
average map value = 0.008984, steps = 28
shifted from previous position = 0.0368
rotated from previous position = 0.0358 degrees
atoms outside contour = 1640, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58674017 0.34919477 0.73061548 228.01580783
-0.12369875 -0.85300580 0.50703030 253.70390106
0.80027157 -0.38787127 -0.45729781 264.15982126
Axis -0.88206005 -0.06865655 -0.46610766
Axis point 0.00000000 134.18067121 36.27293002
Rotation angle (degrees) 149.51722667
Shift along axis -341.66898578
> hide #!1 models
Drag select of 13 residues
> fitmap sel inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 98 atoms
average map value = 0.01059, steps = 64
shifted from previous position = 5.08
rotated from previous position = 17.1 degrees
atoms outside contour = 33, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.52262471 0.58169356 0.62329449 222.36519551
-0.10358496 -0.68234325 0.72365589 255.15673104
0.84624676 -0.44276438 -0.29635473 268.14156148
Axis -0.85073322 -0.16261111 -0.49981058
Axis point 0.00000000 126.34776879 23.08470181
Rotation angle (degrees) 136.72204990
Shift along axis -364.68476855
> show #!1 models
> fitmap sel inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 98 atoms
average map value = 0.01059, steps = 64
shifted from previous position = 5.08
rotated from previous position = 17.1 degrees
atoms outside contour = 33, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.52262471 0.58169356 0.62329449 222.36519551
-0.10358496 -0.68234325 0.72365589 255.15673104
0.84624676 -0.44276438 -0.29635473 268.14156148
Axis -0.85073322 -0.16261111 -0.49981058
Axis point 0.00000000 126.34776879 23.08470181
Rotation angle (degrees) 136.72204990
Shift along axis -364.68476855
> hide #!1 models
Drag select of 51 residues
> delete sel
> show #!1 models
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2760 atoms
average map value = 0.009631, steps = 40
shifted from previous position = 0.152
rotated from previous position = 0.785 degrees
atoms outside contour = 1317, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59165911 0.34960901 0.72643860 227.97227162
-0.13150098 -0.84715870 0.51481029 254.04935900
0.79539109 -0.40011959 -0.45525523 264.34118038
Axis -0.88312792 -0.06655578 -0.46438713
Axis point 0.00000000 135.18775272 35.66164218
Rotation angle (degrees) 148.80145452
Shift along axis -340.99377341
> fitmap #44 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2760 atoms
average map value = 0.009632, steps = 44
shifted from previous position = 0.0176
rotated from previous position = 0.0174 degrees
atoms outside contour = 1318, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59142336 0.34972639 0.72657406 227.98648145
-0.13155370 -0.84713303 0.51483906 254.06420020
0.79555769 -0.40007135 -0.45500646 264.34597440
Axis -0.88305467 -0.06658173 -0.46452268
Axis point 0.00000000 135.18357708 35.63165379
Rotation angle (degrees) 148.79931483
Shift along axis -341.03526101
> hide #!1 models
> combine #34.5
> hide #!44 models
> rename #43 20240711_copi_golph3_beta_S711-L953.cif
> rename #44 "20240711_copi_golph3_beta_H311-E659.cif E"
> hide #45 models
> show #45 models
Drag select of 119 residues
> select up
983 atoms, 1001 bonds, 126 residues, 1 model selected
> delete sel
Drag select of 125 residues, 1 pseudobonds
> select up
984 atoms, 997 bonds, 1 pseudobond, 130 residues, 2 models selected
> select clear
Drag select of 98 residues, 1 pseudobonds
> select up
854 atoms, 864 bonds, 1 pseudobond, 113 residues, 2 models selected
> delete sel
Drag select of 3 residues
> delete sel
> select #45/E:711
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select clear
[Repeated 1 time(s)]
> show #!1 models
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5629 atoms
average map value = 0.009299, steps = 84
shifted from previous position = 0.657
rotated from previous position = 1.9 degrees
atoms outside contour = 2808, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59225848 0.37767571 0.71175203 226.72630080
-0.07049743 -0.85566692 0.51270288 251.66003249
0.80265809 -0.35382932 -0.48015082 262.27101331
Axis -0.88440020 -0.09278056 -0.45741453
Axis point 0.00000000 129.47368947 39.98608571
Rotation angle (degrees) 150.66610695
Shift along axis -343.83251595
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 5629 atoms
average map value = 0.009298, steps = 80
shifted from previous position = 0.0192
rotated from previous position = 0.00781 degrees
atoms outside contour = 2811, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59223513 0.37773154 0.71174183 226.71200459
-0.07036932 -0.85569058 0.51268098 251.64790293
0.80268656 -0.35371247 -0.48018932 262.26276156
Axis -0.88439596 -0.09283444 -0.45741179
Axis point 0.00000000 129.45801962 39.99582134
Rotation angle (degrees) 150.67110775
Shift along axis -343.82685295
> hide #!1 models
Drag select of 311 residues
> select up
2750 atoms, 2784 bonds, 348 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 52
shifted from previous position = 1.26
rotated from previous position = 0.253 degrees
atoms outside contour = 1288, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59321265 0.38003875 0.70969663 225.96482374
-0.07094065 -0.85345417 0.51631716 250.99038089
0.80191407 -0.35663221 -0.47931961 261.53126127
Axis -0.88455702 -0.09344367 -0.45697610
Axis point 0.00000000 129.20184570 39.73542944
Rotation angle (degrees) 150.43314979
Shift along axis -342.84576864
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 40
shifted from previous position = 0.0535
rotated from previous position = 0.101 degrees
atoms outside contour = 1290, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59430648 0.37945725 0.70909238 225.97131630
-0.07012750 -0.85388494 0.51571567 251.02518193
0.80117535 -0.35622004 -0.48085896 261.42747744
Axis -0.88491636 -0.09345382 -0.45627779
Axis point 0.00000000 129.21745407 39.86020483
Rotation angle (degrees) 150.48406493
Shift along axis -342.70852907
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 44
shifted from previous position = 0.0151
rotated from previous position = 0.0169 degrees
atoms outside contour = 1288, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59421798 0.37952808 0.70912864 225.97949150
-0.07032210 -0.85377549 0.51587034 251.02058532
0.80122393 -0.35640685 -0.48063954 261.44695153
Axis -0.88488174 -0.09342609 -0.45635060
Axis point 0.00000000 129.22398147 39.83839206
Rotation angle (degrees) 150.47009089
Shift along axis -342.72846959
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 40
shifted from previous position = 0.00768
rotated from previous position = 0.029 degrees
atoms outside contour = 1287, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59398329 0.37942187 0.70938205 225.98517523
-0.07074672 -0.85373977 0.51587140 251.00885385
0.80136056 -0.35660544 -0.48026431 261.46806297
Axis -0.88480505 -0.09327818 -0.45652953
Axis point 0.00000000 129.23630835 39.79919946
Rotation angle (degrees) 150.45984747
Shift along axis -342.73436402
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 48
shifted from previous position = 0.0372
rotated from previous position = 0.0583 degrees
atoms outside contour = 1291, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59328440 0.37979142 0.70976904 225.97057232
-0.07111790 -0.85353201 0.51616407 250.97978551
0.80184528 -0.35670937 -0.47937727 261.52731805
Axis -0.88458081 -0.09331121 -0.45695712
Axis point 0.00000000 129.21347923 39.73550342
Rotation angle (degrees) 150.43685085
Shift along axis -342.81522902
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 40
shifted from previous position = 0.0196
rotated from previous position = 0.0316 degrees
atoms outside contour = 1289, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59366012 0.37940807 0.70965990 225.98643656
-0.07121481 -0.85364606 0.51596207 250.98998086
0.80155855 -0.35684440 -0.47975615 261.50442466
Axis -0.88469823 -0.09315074 -0.45676250
Axis point 0.00000000 129.24460273 39.75420461
Rotation angle (degrees) 150.44365724
Shift along axis -342.75511812
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 28
shifted from previous position = 0.00929
rotated from previous position = 0.0509 degrees
atoms outside contour = 1287, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59406746 0.37908202 0.70949325 225.99557899
-0.07075223 -0.85395714 0.51551075 250.99082556
0.80129768 -0.35644639 -0.48048724 261.46701123
Axis -0.88484216 -0.09316104 -0.45648151
Axis point 0.00000000 129.23418246 39.82618575
Rotation angle (degrees) 150.48054736
Shift along axis -342.70783910
> fitmap #45 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif E (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 28
shifted from previous position = 0.0463
rotated from previous position = 0.0829 degrees
atoms outside contour = 1289, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif E (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59463580 0.37964339 0.70871656 225.96009472
-0.06946606 -0.85393703 0.51571893 251.03681805
0.80098860 -0.35589669 -0.48140920 261.39286546
Axis -0.88502478 -0.09369157 -0.45601866
Axis point 0.00000000 129.19288135 39.91860954
Rotation angle (degrees) 150.49994385
Shift along axis -342.70034326
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!44 models
> show #!43 models
> show #34.5 models
> hide #34.5 models
> show #34.5 models
> hide #34.5 models
> show #!1 models
> hide #!1 models
> hide #!44 models
> hide #!43 models
> rename #45 20240711_copi_golph3_beta_.cif
> rename #44 20240711_copi_golph3_beta_H311-E659.cif
> rename #45 20240711_copi_golph3_beta_M1-H311_.cif
> rename #45 20240711_copi_golph3_beta_M1-H311_K660-.cif
> rename #45 20240711_copi_golph3_beta_M1-H311_K660-A710.cif
> hide #!45 models
> show #!43 models
> hide #!43 models
> show #!44 models
> hide #!44 models
> show #34.7 models
> show #!1 models
> fitmap #45 inMap #1
Fit molecule 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 40
shifted from previous position = 0.0532
rotated from previous position = 0.117 degrees
atoms outside contour = 1289, contour level = 0.0073613
Position of 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59367617 0.37945842 0.70961956 225.98435835
-0.07111226 -0.85364991 0.51596985 250.98930930
0.80155577 -0.35678165 -0.47980746 261.50161854
Axis -0.88470437 -0.09319534 -0.45674152
Axis point 0.00000000 129.23778490 39.76170662
Rotation angle (degrees) 150.44592891
Shift along axis -342.75902783
> fitmap #45 inMap #1
Fit molecule 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 40
shifted from previous position = 0.00742
rotated from previous position = 0.0217 degrees
atoms outside contour = 1288, contour level = 0.0073613
Position of 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59385384 0.37940106 0.70950155 225.98248456
-0.07085124 -0.85375028 0.51583967 250.98962919
0.80144726 -0.35660244 -0.48012184 261.48337883
Axis -0.88476585 -0.09324450 -0.45661237
Axis point 0.00000000 129.22894867 39.79401808
Rotation angle (degrees) 150.45970162
Shift along axis -342.74153332
> fitmap #45 inMap #1
Fit molecule 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 44
shifted from previous position = 0.0064
rotated from previous position = 0.0264 degrees
atoms outside contour = 1288, contour level = 0.0073613
Position of 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59360615 0.37954711 0.70963069 225.97882798
-0.07109608 -0.85361527 0.51602937 250.98864595
0.80160906 -0.35677017 -0.47972697 261.50497336
Axis -0.88468172 -0.09323055 -0.45677819
Axis point 0.00000000 129.23274682 39.75680712
Rotation angle (degrees) 150.44330889
Shift along axis -342.76891558
> show #!40 models
> hide #!1 models
> hide #34.7 models
> show #!43 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> fitmap #40 inMap #1
Fit molecule fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 39508 atoms
average map value = 0.005223, steps = 144
shifted from previous position = 8
rotated from previous position = 9.35 degrees
atoms outside contour = 28718, contour level = 0.0073613
Position of fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif (#40)
relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.52035327 0.84085371 0.14898840 220.06435873
0.84298688 0.53366200 -0.06766092 260.64248984
-0.13640238 0.09038768 -0.98652140 268.85959648
Axis 0.48445666 0.87479082 0.00653869
Axis point 50.37526868 0.00000000 130.77574819
Rotation angle (degrees) 170.61199384
Shift along axis 336.37729411
> show #!1 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #34.1 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!43 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> hide #34.1 models
> hide #!1 models
> show #34.7 models
> combine #34.7
> hide #46 models
> show #46 models
> hide #46 models
> show #46 models
> fitmap #46 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif G (#46) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2130 atoms
average map value = 0.007774, steps = 64
shifted from previous position = 0.0353
rotated from previous position = 0.0322 degrees
atoms outside contour = 1201, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif G (#46) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60593369 0.38236496 0.69759688 225.81172809
-0.05311428 -0.85550993 0.51505498 251.49986226
0.79374003 -0.34914152 -0.49807324 260.96387774
Axis -0.88865037 -0.09886368 -0.44780184
Axis point 0.00000000 128.90476162 41.80977945
Rotation angle (degrees) 150.90618802
Shift along axis -342.39198394
> show #!1 models
> hide #!1 models
> rename #46 20240711_copi_golph3_delta.cif
> rename #46 20240711_copi_golph3_delta_M1-S273.cif
> show #!45 models
> hide #!45 models
> show #!45 models
> show #!1 models
> hide #34.7 models
> hide #46 models
> hide #!45 models
> hide #!1 models
> combine #34.8
[Repeated 2 time(s)]
> hide #48 models
> hide #49 models
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4752 atoms
average map value = 0.007743, steps = 124
shifted from previous position = 0.0191
rotated from previous position = 0.0392 degrees
atoms outside contour = 2924, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60757687 0.39435331 0.68944602 230.62659179
-0.16054833 -0.78913935 0.59286029 257.82317050
0.77786540 -0.47089761 -0.41615005 262.55404626
Axis -0.88422199 -0.07349639 -0.46124803
Axis point 0.00000000 138.97213742 27.15377344
Rotation angle (degrees) 143.02102194
Shift along axis -343.97671300
Drag select of 5 residues
> select up
227 atoms, 230 bonds, 31 residues, 1 model selected
> delete sel
Drag select of 54 residues
> select up
479 atoms, 486 bonds, 60 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4046 atoms
average map value = 0.007971, steps = 104
shifted from previous position = 0.284
rotated from previous position = 0.641 degrees
atoms outside contour = 2487, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60948011 0.40184910 0.68341151 230.98340907
-0.15038863 -0.78776834 0.59733098 257.45116911
0.77840687 -0.46683868 -0.41969560 262.45085439
Axis -0.88482933 -0.07898616 -0.45917127
Axis point 0.00000000 138.04760312 27.81377692
Rotation angle (degrees) 143.03394478
Shift along axis -345.22586461
> hide #!1 models
Drag select of 103 residues
> select down
819 atoms, 103 residues, 1 model selected
> select up
859 atoms, 872 bonds, 108 residues, 1 model selected
> delete sel
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3187 atoms
average map value = 0.007182, steps = 116
shifted from previous position = 2.92
rotated from previous position = 6.31 degrees
atoms outside contour = 2018, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.66603189 0.42601441 0.61230160 234.45007200
-0.06317257 -0.78569984 0.61537386 254.56011043
0.74324340 -0.44853928 -0.49638872 264.42690822
Axis -0.90293190 -0.11112893 -0.41516785
Axis point 0.00000000 134.36385127 39.39423841
Rotation angle (degrees) 143.90373958
Shift along axis -349.76299266
> show #!1 models
> hide #!1 models
Drag select of 69 residues
> select up
709 atoms, 716 bonds, 91 residues, 1 model selected
Drag select of 93 residues
> select up
826 atoms, 833 bonds, 108 residues, 1 model selected
> delete sel
> select clear
Drag select of 2 residues
> delete sel
Drag select of 22 residues
> select up
180 atoms, 182 bonds, 23 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2162 atoms
average map value = 0.0089, steps = 104
shifted from previous position = 7.41
rotated from previous position = 15.8 degrees
atoms outside contour = 1181, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.81943643 0.23081206 0.52464247 241.33474078
-0.08568686 -0.85571732 0.51029955 263.44202167
0.56672894 -0.46311301 -0.68142839 275.80845765
Axis -0.95019103 -0.04108247 -0.30894859
Axis point 0.00000000 151.92138588 62.40884770
Rotation angle (degrees) 149.18822401
Shift along axis -325.34758904
> hide #!1 models
> show #!21 models
> hide #!21 models
> show #!18 models
> hide #!18 models
> show #!29 models
> hide #!29 models
> show #!26.2 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!47 to #26.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif B, chain B (#26.2) with
copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#47), sequence
alignment score = 1218.4
RMSD between 231 pruned atom pairs is 0.343 angstroms; (across all 249 pairs:
2.083)
> hide #!47 models
> show #!47 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #48 models
> hide #!47 models
> hide #48 models
> show #34.8 models
> hide #34.8 models
> show #!29 models
> hide #!29 models
> hide #!26.2 models
> show #!26.2 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #!26.2 models
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2162 atoms
average map value = 0.01194, steps = 48
shifted from previous position = 0.11
rotated from previous position = 0.562 degrees
atoms outside contour = 875, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.70971931 0.58971035 0.38540915 247.36545771
0.22219868 -0.70653520 0.67188969 250.98140616
0.66852543 -0.39121568 -0.63247453 271.39793443
Axis -0.91653394 -0.24408275 -0.31684246
Axis point 0.00000000 119.21261675 65.09791303
Rotation angle (degrees) 144.55229672
Shift along axis -373.96945993
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2162 atoms
average map value = 0.01194, steps = 40
shifted from previous position = 0.00676
rotated from previous position = 0.0205 degrees
atoms outside contour = 878, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.70954007 0.58999755 0.38529961 247.37542938
0.22244451 -0.70636110 0.67199140 250.96234102
0.66863393 -0.39109704 -0.63243321 271.38651874
Axis -0.91647918 -0.24426002 -0.31686424
Axis point 0.00000000 119.17339623 65.09831713
Rotation angle (degrees) 144.55050910
Shift along axis -374.00718183
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> show #!1 models
> hide #!1 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #48 to #47
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#47) with
copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#48), sequence
alignment score = 2607.1
RMSD between 277 pruned atom pairs is 0.000 angstroms; (across all 277 pairs:
0.000)
> show #48 models
> show #!1 models
> hide #!1 models
> hide #!47 models
> show #!47 models
> hide #48 models
> show #48 models
> show #!1 models
> hide #!1 models
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
Drag select of 86 residues
> delete sel
> hide #!47 models
> show #!47 models
Drag select of 151 residues, 2 pseudobonds
> delete sel
Drag select of 1 pseudobonds
> delete sel
[Repeated 1 time(s)]
> select add #48
2885 atoms, 2926 bonds, 2 pseudobonds, 372 residues, 2 models selected
> select subtract #48
Nothing selected
Drag select of 20 residues, 2 pseudobonds
> \
Unknown command: \
> delete sel
> select clear
[Repeated 1 time(s)]Drag select of 1 pseudobonds
> delete sel
> close #48
> combine #34.8
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #48 to #47
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#47) with
copy of fold_20240711_copi_golph3_model_0.cif H, chain H (#48), sequence
alignment score = 2607.1
RMSD between 277 pruned atom pairs is 0.000 angstroms; (across all 277 pairs:
0.000)
Drag select of 6 residues
> select up
227 atoms, 230 bonds, 31 residues, 1 model selected
> delete sel
Drag select of 28 residues
> delete sel
Drag select of 119 residues
> select up
4305 atoms, 4371 bonds, 550 residues, 1 model selected
> select down
947 atoms, 119 residues, 1 model selected
> delete sel
> hide #!47 models
> show #!47 models
Drag select of 38 residues
> select up
334 atoms, 339 bonds, 41 residues, 1 model selected
> delete sel
Drag select of 57 residues
> select up
542 atoms, 545 bonds, 72 residues, 1 model selected
> delete sel
> hide #!47 models
> show #!47 models
> hide #!47 models
> show #!47 models
> hide #48 models
> show #48 models
> hide #48 models
> show #48 models
Drag select of 6 residues
> select up
140 atoms, 141 bonds, 18 residues, 1 model selected
> delete sel
> hide #!47 models
> show #!47 models
> hide #48 models
> show #48 models
> hide #48 models
> show #46 models
> hide #!47 models
> hide #46 models
> show #46 models
> hide #46 models
> show #!47 models
> show #48 models
> hide #48 models
> hide #!47 models
> show #!47 models
> show #48 models
> hide #48 models
> show #48 models
> close #47
> combine #34.8
> hide #47 models
> show #!1 models
> fitmap #48 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#48) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2342 atoms
average map value = 0.01138, steps = 60
shifted from previous position = 0.0651
rotated from previous position = 0.195 degrees
atoms outside contour = 1014, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#48) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.71115890 0.58912332 0.38364923 247.39861189
0.22410392 -0.70720387 0.67055210 250.94518669
0.66635610 -0.39089180 -0.63495917 271.61936050
Axis -0.91700758 -0.24423744 -0.31534927
Axis point 0.00000000 119.24873787 65.52138932
Rotation angle (degrees) 144.63703576
Shift along axis -373.81158195
> fitmap #48 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#48) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2342 atoms
average map value = 0.01138, steps = 40
shifted from previous position = 0.0265
rotated from previous position = 0.0312 degrees
atoms outside contour = 1014, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#48) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.71140727 0.58868677 0.38385881 247.37086149
0.22374794 -0.70750308 0.67035532 250.99066812
0.66621060 -0.39100802 -0.63504028 271.62910057
Axis -0.91708532 -0.24396987 -0.31533033
Axis point 0.00000000 119.31297346 65.51699851
Rotation angle (degrees) 144.64356816
Shift along axis -373.74723998
> fitmap #48 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#48) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2342 atoms
average map value = 0.01138, steps = 28
shifted from previous position = 0.0378
rotated from previous position = 0.0647 degrees
atoms outside contour = 1014, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#48) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.71085766 0.58959184 0.38348773 247.41765408
0.22438320 -0.70685733 0.67082405 250.91144646
0.66658350 -0.39081221 -0.63476945 271.59805846
Axis -0.91691149 -0.24450348 -0.31542253
Axis point 0.00000000 119.19010859 65.50641851
Rotation angle (degrees) 144.62540379
Shift along axis -373.87695812
> fitmap #48 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#48) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2342 atoms
average map value = 0.01138, steps = 36
shifted from previous position = 0.0123
rotated from previous position = 0.0407 degrees
atoms outside contour = 1014, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#48) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.71124414 0.58902886 0.38363626 247.39861223
0.22405044 -0.70725020 0.67052111 250.94807788
0.66628311 -0.39095033 -0.63499973 271.62700923
Axis -0.91703322 -0.24418608 -0.31531450
Axis point 0.00000000 119.26151546 65.52755174
Rotation angle (degrees) 144.63711740
Shift along axis -373.79870608
> hide #!1 models
Drag select of 1 residues
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete sel
> show #!1 models
> hide #!1 models
> rename #48 20240711_copi_golph3_gamma1_M1-.cif
> rename #48 20240711_copi_golph3_gamma1_M1-P299.cif
> hide #48 models
> show #48 models
> show #47 models
> hide #47 models
> show #49 models
> hide #49 models
> show #47 models
> hide #48 models
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4752 atoms
average map value = 0.007743, steps = 124
shifted from previous position = 0.0191
rotated from previous position = 0.0392 degrees
atoms outside contour = 2924, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60757687 0.39435331 0.68944602 230.62659179
-0.16054833 -0.78913935 0.59286029 257.82317050
0.77786540 -0.47089761 -0.41615005 262.55404626
Axis -0.88422199 -0.07349639 -0.46124803
Axis point 0.00000000 138.97213742 27.15377344
Rotation angle (degrees) 143.02102194
Shift along axis -343.97671300
> show #49 models
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4752 atoms
average map value = 0.007743, steps = 104
shifted from previous position = 0.00703
rotated from previous position = 0.0108 degrees
atoms outside contour = 2927, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60743054 0.39443811 0.68952644 230.63380408
-0.16056711 -0.78913122 0.59286602 257.82805616
0.77797580 -0.47084019 -0.41600861 262.54601287
Axis -0.88417588 -0.07352104 -0.46133249
Axis point 0.00000000 138.96283890 27.13220472
Rotation angle (degrees) 143.02086830
Shift along axis -343.99763979
> hide #49 models
Drag select of 50 residues
> select up
618 atoms, 629 bonds, 78 residues, 1 model selected
> delete sel
Drag select of 83 residues
> select up
690 atoms, 696 bonds, 90 residues, 1 model selected
> delete sel
> show #!1 models
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3444 atoms
average map value = 0.008708, steps = 68
shifted from previous position = 0.469
rotated from previous position = 2.57 degrees
atoms outside contour = 1900, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62018224 0.35375614 0.70016468 228.85507380
-0.18985557 -0.79832412 0.57151856 259.33965078
0.76113655 -0.48737583 -0.42794386 263.29720774
Axis -0.88845160 -0.05115766 -0.45611035
Axis point 0.00000000 143.49126811 27.87004377
Rotation angle (degrees) 143.42166543
Shift along axis -336.68644741
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 3444 atoms
average map value = 0.008708, steps = 96
shifted from previous position = 0.029
rotated from previous position = 0.0136 degrees
atoms outside contour = 1901, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62021708 0.35362394 0.70020060 228.82245994
-0.18978418 -0.79845951 0.57135311 259.34581465
0.76112597 -0.48724996 -0.42810599 263.30010916
Axis -0.88847111 -0.05113383 -0.45607502
Axis point 0.00000000 143.49650857 27.90034895
Rotation angle (degrees) 143.43429526
Shift along axis -336.64809142
> hide #!1 models
Drag select of 65 residues
> select up
597 atoms, 608 bonds, 74 residues, 1 model selected
> delete sel
Drag select of 21 residues
> delete sel
Drag select of 17 residues
> delete sel
Drag select of 18 residues
> delete sel
> select #47/H:299
7 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2419 atoms
average map value = 0.01024, steps = 44
shifted from previous position = 0.284
rotated from previous position = 1.02 degrees
atoms outside contour = 1151, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62119616 0.36398811 0.69399423 228.98038917
-0.19221934 -0.78776013 0.58522278 259.54027074
0.75971512 -0.49693726 -0.41938801 263.08595483
Axis -0.88810416 -0.05393564 -0.45646682
Axis point 0.00000000 143.67946123 26.52760116
Rotation angle (degrees) 142.46449868
Shift along axis -337.44691426
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2419 atoms
average map value = 0.01024, steps = 60
shifted from previous position = 0.0143
rotated from previous position = 0.00854 degrees
atoms outside contour = 1148, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62131237 0.36393339 0.69391889 228.97598227
-0.19220002 -0.78775480 0.58523631 259.54869305
0.75962496 -0.49698578 -0.41949380 263.07832863
Axis -0.88814013 -0.05392258 -0.45639837
Axis point 0.00000000 143.69008420 26.53435500
Rotation angle (degrees) 142.46375765
Shift along axis -337.42681283
> show #!1 models
> hide #!1 models
> hide #47 models
> show #47 models
Drag select of 52 residues
> select up
459 atoms, 467 bonds, 61 residues, 1 model selected
> delete sel
Drag select of 100 residues
> delete sel
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1163 atoms
average map value = 0.01156, steps = 68
shifted from previous position = 0.58
rotated from previous position = 3.44 degrees
atoms outside contour = 468, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.63759665 0.40239523 0.65692358 230.93358222
-0.14062120 -0.77761789 0.61281000 258.39112625
0.75742735 -0.48310299 -0.43922126 263.51570190
Axis -0.89302698 -0.08189754 -0.44248798
Axis point 0.00000000 139.97272064 30.35060145
Rotation angle (degrees) 142.15013070
Shift along axis -343.99404715
> show #!1 models
> fitmap #47 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1163 atoms
average map value = 0.01156, steps = 44
shifted from previous position = 0.0398
rotated from previous position = 0.0682 degrees
atoms outside contour = 469, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.63844248 0.40177726 0.65648019 230.94848014
-0.14041420 -0.77782291 0.61259723 258.41035864
0.75675297 -0.48328724 -0.44017996 263.52900178
Axis -0.89330160 -0.08173657 -0.44196310
Axis point 0.00000000 140.03543333 30.45542839
Rotation angle (degrees) 142.16497515
Shift along axis -343.89831746
> hide #!1 models
> rename #47 20240711_copi_golph3_gamma1_K300-F448.cif
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!26.2 models
> hide #!26.2 models
> hide #47 models
> show #47 models
> show #48 models
> hide #48 models
> show #48 models
> hide #48 models
> hide #47 models
> show #49 models
Drag select of 144 residues
> select up
1164 atoms, 1180 bonds, 148 residues, 1 model selected
> delete sel
Drag select of 113 residues
> select up
1009 atoms, 1027 bonds, 128 residues, 1 model selected
> delete sel
Drag select of 109 residues
> select up
851 atoms, 860 bonds, 114 residues, 1 model selected
> delete sel
> fitmap #49 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif H (#49) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1728 atoms
average map value = 0.01048, steps = 52
shifted from previous position = 1.15
rotated from previous position = 3.81 degrees
atoms outside contour = 801, contour level = 0.0073613
Position of copy of fold_20240711_copi_golph3_model_0.cif H (#49) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.61805201 0.33351201 0.71188584 227.92732460
-0.18854207 -0.81623462 0.54608876 258.90803305
0.76319303 -0.47173168 -0.44159440 264.15773596
Axis -0.88889010 -0.04480796 -0.45592394
Axis point 0.00000000 143.45556759 30.46288448
Rotation angle (degrees) 145.07363431
Shift along axis -334.63931738
> show #!1 models
> hide #!1 models
Drag select of 21 residues
> select up
300 atoms, 303 bonds, 36 residues, 1 model selected
> delete sel
Drag select of 4 residues
> delete sel
> select clear
Drag select of 4 residues, 1 pseudobonds
> delete sel
Drag select of 11 residues
> delete sel
> select #49/H:447
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #49/H:448
11 atoms, 11 bonds, 1 residue, 1 model selected
> delete sel
> rename #49 20240711_copi_golph3_gammm1_T449-.cif
> rename #49 20240711_copi_golph3_gammm1_T449-R609.cif
> show #!1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v2.cxs"
> hide #!1 models
> hide #!49 models
> show #48 models
> hide #48 models
> show #47 models
> hide #47 models
> show #!49 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v2.cxs"
> fitmap #49 inMap #1
Fit molecule 20240711_copi_golph3_gammm1_T449-R609.cif (#49) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1264 atoms
average map value = 0.009619, steps = 80
shifted from previous position = 0.462
rotated from previous position = 0.922 degrees
atoms outside contour = 624, contour level = 0.0073613
Position of 20240711_copi_golph3_gammm1_T449-R609.cif (#49) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.61374753 0.32116926 0.72122415 227.71817899
-0.19898081 -0.82110208 0.53497477 259.15238914
0.76401611 -0.47184921 -0.44004285 264.55513680
Axis -0.88780842 -0.03773356 -0.45866370
Axis point 0.00000000 144.29403366 30.27810400
Rotation angle (degrees) 145.45678076
Shift along axis -333.29069740
> hide #!49 models
> show #34.1 models
> fitmap #34.1 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif A (#34.1) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2371 atoms
average map value = 0.00748, steps = 40
shifted from previous position = 0.0303
rotated from previous position = 0.0201 degrees
atoms outside contour = 1257, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif A (#34.1) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.52743413 0.46261732 0.71259978 230.64249169
0.01546111 -0.84383896 0.53637372 257.96942955
0.84945523 -0.27188422 -0.45222204 263.21843979
Axis -0.86556951 -0.14655953 -0.47886295
Axis point 0.00000000 122.21935439 38.51117125
Rotation angle (degrees) 152.16715037
Shift along axis -363.49054517
> hide #34.1 models
> show #34.2 models
> fitmap #34.2 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif B (#34.2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 48
shifted from previous position = 0.00177
rotated from previous position = 0.00707 degrees
atoms outside contour = 833, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif B (#34.2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64422761 0.35685772 0.67647864 226.67911377
-0.02945305 -0.87224662 0.48817861 253.34478005
0.76426651 -0.33442250 -0.55141481 256.81467971
Axis -0.90096195 -0.09615053 -0.42311066
Axis point 0.00000000 129.87656483 45.56303427
Rotation angle (degrees) 152.83769521
Shift along axis -337.24952092
> show #34.3 models
> fitmap #34.3 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif C (#34.3) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.01001, steps = 48
shifted from previous position = 0.0263
rotated from previous position = 0.0703 degrees
atoms outside contour = 625, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif C (#34.3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.54970504 0.35440909 -0.75645130 335.69327096
0.52748818 0.84943598 0.01465384 166.87860828
0.64775041 -0.39096383 -0.65388584 271.22208974
Axis -0.27558852 -0.95405575 0.11759501
Axis point 75.42683569 0.00000000 209.16244404
Rotation angle (degrees) 132.61568455
Shift along axis -219.83034570
> hide #34.3 models
> show #34.9 models
> fitmap #34.9 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif I (#34.9) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.009574, steps = 48
shifted from previous position = 0.145
rotated from previous position = 1.13 degrees
atoms outside contour = 675, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif I (#34.9) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73435854 0.57870236 0.35471269 247.45554258
0.24940833 -0.71608940 0.65192901 251.86879523
0.63127886 -0.39028134 -0.67019956 274.80631520
Axis -0.92440250 -0.24530409 -0.29207178
Axis point 0.00000000 120.90579003 71.44053765
Rotation angle (degrees) 145.68647177
Shift along axis -370.79613621
> fitmap #34.9 inMap #1
Fit molecule fold_20240711_copi_golph3_model_0.cif I (#34.9) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.009573, steps = 28
shifted from previous position = 0.0418
rotated from previous position = 0.0849 degrees
atoms outside contour = 674, contour level = 0.0073613
Position of fold_20240711_copi_golph3_model_0.cif I (#34.9) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73385633 0.57878680 0.35561316 247.42525713
0.24844240 -0.71590736 0.65249752 251.87628137
0.63224303 -0.39049005 -0.66916833 274.71078782
Axis -0.92423836 -0.24513422 -0.29273309
Axis point 0.00000000 120.90736206 71.25729870
Rotation angle (degrees) 145.65035277
Shift along axis -370.84034745
> hide #34.2 models
> show #34.1 models
> show #34.2 models
> show #34.3 models
> show #34.4 models
> show #34.5 models
> show #34.6 models
> show #34.7 models
> show #34.8 models
> show #38 models
> show #39 models
> show #!40 models
> hide #!40 models
> show #41 models
> show #42 models
> show #!43 models
> show #!44 models
> show #!45 models
> show #46 models
> show #47 models
> show #48 models
> show #!49 models
> show #!1 models
> hide #34.4 models
> hide #34.5 models
> hide #34.6 models
> hide #34.7 models
> hide #34.8 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v3.cxs"
> volume #1 level 0.00566
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/becca/Desktop/movie1.mp4
Movie saved to /Users/becca/Desktop/movie1.mp4
> volume #1 level 0.004904
> volume #1 level 0.00755
> volume #1 level 0.005849
> hide #42 models
> show #42 models
> hide #41 models
> show #41 models
> hide #47 models
> show #47 models
> hide #!1 models
> show #34.8 models
> hide #34.8 models
> show #34.8 models
> hide #34.8 models
> show #34.8 models
> hide #34.8 models
> show #34.8 models
> hide #34.8 models
> show #34.8 models
> hide #34.8 models
> show #!1 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #23 models
> hide #23 models
> show #22 models
> hide #22 models
> show #22 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v4.cxs"
——— End of log from Wed Jul 24 16:40:43 2024 ———
opened ChimeraX session
> hide #!49 models
> hide #48 models
> hide #47 models
> hide #46 models
> show #46 models
> show #47 models
> show #48 models
> hide #48 models
> show #!49 models
> show #48 models
> hide #34.9 models
> show #34.9 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #38 inMap #1
Fit molecule 20240711_copi_golph3_alpha_M1-T591.cif (#38) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008699, steps = 44
shifted from previous position = 0.0233
rotated from previous position = 0.0214 degrees
atoms outside contour = 1803, contour level = 0.0058489
Position of 20240711_copi_golph3_alpha_M1-T591.cif (#38) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57928342 0.37611015 0.72316794 229.39206867
-0.04023814 -0.87290909 0.48622075 258.29781268
0.81413243 -0.31075855 -0.49052779 263.87511201
Axis -0.88184067 -0.10065027 -0.46068054
Axis point 0.00000000 129.96605027 41.81021370
Rotation angle (degrees) 153.13537908
Shift along axis -349.84712980
> hide #39 models
> show #39 models
> combine #34.9
> hide #34.9 models
> hide #!49 models
> hide #48 models
> hide #47 models
> hide #46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #42 models
> hide #41 models
> hide #39 models
> hide #38 models
> hide #34.3 models
> hide #34.2 models
> hide #34.1 models
> fitmap #50 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif I (#50) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.009574, steps = 28
shifted from previous position = 0.0408
rotated from previous position = 0.068 degrees
atoms outside contour = 589, contour level = 0.0058489
Position of copy of fold_20240711_copi_golph3_model_0.cif I (#50) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73431871 0.57860445 0.35495479 247.44441726
0.24911606 -0.71613386 0.65199192 251.87236537
0.63144057 -0.39034494 -0.67001016 274.79529283
Axis -0.92438844 -0.24519930 -0.29220425
Axis point 0.00000000 120.91785184 71.40627014
Rotation angle (degrees) 145.68113010
Shift along axis -370.79003714
> fitmap #50 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif I (#50) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.009573, steps = 28
shifted from previous position = 0.0372
rotated from previous position = 0.0715 degrees
atoms outside contour = 588, contour level = 0.0058489
Position of copy of fold_20240711_copi_golph3_model_0.cif I (#50) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73383141 0.57880777 0.35563043 247.42412190
0.24841612 -0.71588088 0.65253657 251.87349377
0.63228227 -0.39050751 -0.66912106 274.71167249
Axis -0.92422993 -0.24513816 -0.29275642
Axis point 0.00000000 120.90618853 71.25299813
Rotation angle (degrees) 145.64787358
Shift along axis -370.84418966
> fitmap #50 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif I (#50) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.009574, steps = 28
shifted from previous position = 0.0348
rotated from previous position = 0.0675 degrees
atoms outside contour = 590, contour level = 0.0058489
Position of copy of fold_20240711_copi_golph3_model_0.cif I (#50) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73429425 0.57859687 0.35501774 247.44244987
0.24906331 -0.71614294 0.65200210 251.87347979
0.63148983 -0.39033950 -0.66996690 274.79017546
Axis -0.92438098 -0.24518406 -0.29224062
Axis point 0.00000000 120.91792431 71.39713333
Rotation angle (degrees) 145.68063673
Shift along axis -370.79130830
> fitmap #50 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif I (#50) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.009573, steps = 28
shifted from previous position = 0.0362
rotated from previous position = 0.0737 degrees
atoms outside contour = 588, contour level = 0.0058489
Position of copy of fold_20240711_copi_golph3_model_0.cif I (#50) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73379774 0.57879982 0.35571284 247.42116016
0.24833408 -0.71588294 0.65256554 251.87411343
0.63235358 -0.39051550 -0.66904901 274.70620339
Axis -0.92421916 -0.24511679 -0.29280829
Axis point 0.00000000 120.90704736 71.24013812
Rotation angle (degrees) 145.64603009
Shift along axis -370.84620633
> fitmap #50 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif I (#50) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.009574, steps = 28
shifted from previous position = 0.0359
rotated from previous position = 0.0685 degrees
atoms outside contour = 590, contour level = 0.0058489
Position of copy of fold_20240711_copi_golph3_model_0.cif I (#50) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73426229 0.57859784 0.35508226 247.44015914
0.24900080 -0.71613881 0.65203051 251.87330676
0.63155164 -0.39034565 -0.66990505 274.78627468
Axis -0.92437078 -0.24517082 -0.29228400
Axis point 0.00000000 120.91787349 71.38689486
Rotation angle (degrees) 145.67890818
Shift along axis -370.79406718
> fitmap #50 inMap #1
Fit molecule copy of fold_20240711_copi_golph3_model_0.cif I (#50) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1420 atoms
average map value = 0.009573, steps = 28
shifted from previous position = 0.0374
rotated from previous position = 0.0746 degrees
atoms outside contour = 588, contour level = 0.0058489
Position of copy of fold_20240711_copi_golph3_model_0.cif I (#50) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73376385 0.57879138 0.35579647 247.41816530
0.24825171 -0.71588596 0.65259357 251.87483810
0.63242524 -0.39052249 -0.66897719 274.70055088
Axis -0.92420837 -0.24509508 -0.29286054
Axis point 0.00000000 120.90789483 71.22715847
Rotation angle (degrees) 145.64425753
Shift along axis -370.84817350
> rename #50 20240711_copi_golph3_zeta1.cif
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!49 models
> show #48 models
> hide #!1 models
> ui mousemode right select
Drag select of 16 residues
> select up
149 atoms, 150 bonds, 18 residues, 1 model selected
> delete sel
Drag select of 7 residues
> delete sel
Drag select of 1 residues
> delete sel
Drag select of 1 residues
> delete sel
> show #!1 models
> hide #!1 models
> show #12 models
> hide #12 models
> show #10 models
> hide #10 models
> show #26.3 models
> hide #26.3 models
> show #26.3 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_update_v1.cxs"
> hide #50 models
> show #50 models
> hide #26.3 models
> hide #50 models
> hide #!49 models
> hide #48 models
> show #34.2 models
> hide #34.2 models
> show #!1 models
> combine #34.2
> combine #34.3
> show #34.2 models
> hide #34.2 models
> show #34.2 models
> show #34.3 models
> hide #34.3 models
> hide #34.2 models
> show #34.2 models
> show #34.3 models
> hide #51 models
> hide #52 models
> hide #34.3 models
> hide #34.2 models
> hide #22 models
> show #51 models
> show #52 models
> rename #51 20240711_copi_golph3_Arf1_.cif
> rename #52 20240711_copi_golph3_Arf1_.cif
> hide #52 models
> show #52 models
> show #!49 models
> show #48 models
> hide #48 models
> hide #!49 models
> show #!45 models
> show #!44 models
> hide #!45 models
> hide #!44 models
> hide #51 models
> show #51 models
> hide #51 models
> show #51 models
> hide #51 models
> rename #51 20240711_copi_golph3_beta_Arf1_.cif
> rename #52 20240711_copi_golph3_gamma_Arf1_.cif
> hide #52 models
> show #52 models
> hide #52 models
> show #51 models
> combine #34.2
> hide #51 models
> show #!37 models
> hide #!37 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!36 models
> hide #!36 models
> matchmaker #53 to #36
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of 3tjz_yeast_cow_Arf1_gamma_zeta_COPI.cif A, chain A (#36)
with copy of fold_20240711_copi_golph3_model_0.cif B, chain B (#53), sequence
alignment score = 717.9
RMSD between 159 pruned atom pairs is 0.586 angstroms; (across all 159 pairs:
0.586)
> show #!37 models
> hide #!37 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> hide #53 models
> rename #53 20240711_copi_golph3_third_Arf1.cif
> show #51 models
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007696, steps = 48
shifted from previous position = 0.00615
rotated from previous position = 0.0275 degrees
atoms outside contour = 688, contour level = 0.0058489
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64457520 0.35659608 0.67628548 226.70008894
-0.02948840 -0.87231016 0.48806293 253.33598453
0.76397202 -0.33453583 -0.55175404 256.79298601
Axis -0.90106555 -0.09605086 -0.42291265
Axis point 0.00000000 129.88971353 45.58172879
Rotation angle (degrees) 152.84115898
Shift along axis -337.20578188
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.007695, steps = 64
shifted from previous position = 0.00981
rotated from previous position = 0.0296 degrees
atoms outside contour = 688, contour level = 0.0058489
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.64420575 0.35687129 0.67649230 226.67308114
-0.02949189 -0.87222673 0.48821180 253.34669641
0.76428344 -0.33445989 -0.55136867 256.81918555
Axis -0.90095431 -0.09614504 -0.42312818
Axis point 0.00000000 129.88010697 45.56012856
Rotation angle (degrees) 152.83492327
Shift along axis -337.24755383
> show #52 models
> fitmap #52 inMap #1
Fit molecule 20240711_copi_golph3_gamma_Arf1_.cif (#52) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.01001, steps = 84
shifted from previous position = 0.027
rotated from previous position = 0.0679 degrees
atoms outside contour = 497, contour level = 0.0058489
Position of 20240711_copi_golph3_gamma_Arf1_.cif (#52) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.54981633 0.35457906 -0.75629075 335.68690009
0.52678693 0.84985645 0.01547717 166.87961505
0.64822645 -0.38989448 -0.65405257 271.15412697
Axis -0.27539685 -0.95418515 0.11699266
Axis point 75.48645841 0.00000000 209.07432900
Rotation angle (degrees) 132.61013952
Shift along axis -219.95812251
> show #53 models
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.00665, steps = 44
shifted from previous position = 0.31
rotated from previous position = 2.81 degrees
atoms outside contour = 711, contour level = 0.0058489
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73474151 0.66767249 0.11986808 227.72567702
0.67552614 -0.70407307 -0.21896472 323.51774462
-0.06180084 0.24185649 -0.96834193 187.17487412
Axis 0.93019969 0.36671135 0.01585314
Axis point 0.00000000 104.57055845 105.25607505
Rotation angle (degrees) 165.65853934
Shift along axis 333.43529205
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.00665, steps = 40
shifted from previous position = 0.0136
rotated from previous position = 0.0308 degrees
atoms outside contour = 713, contour level = 0.0058489
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73476750 0.66754990 0.12039046 227.72558336
0.67553483 -0.70406983 -0.21894833 323.51171062
-0.06139564 0.24220407 -0.96828083 187.19776419
Axis 0.93020512 0.36668652 0.01610666
Axis point 0.00000000 104.56609656 105.24562509
Rotation angle (degrees) 165.64809683
Shift along axis 333.47401758
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.006651, steps = 28
shifted from previous position = 0.0356
rotated from previous position = 0.0154 degrees
atoms outside contour = 710, contour level = 0.0058489
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73472974 0.66763686 0.12013838 227.74881556
0.67555870 -0.70405152 -0.21893356 323.53092283
-0.06158450 0.24201753 -0.96831548 187.18349736
Axis 0.93019581 0.36671541 0.01598621
Axis point 0.00000000 104.57069352 105.24747902
Rotation angle (degrees) 165.65434959
Shift along axis 333.48712519
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.00665, steps = 40
shifted from previous position = 0.0139
rotated from previous position = 0.0172 degrees
atoms outside contour = 711, contour level = 0.0058489
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73469719 0.66763496 0.12034777 227.73810152
0.67562058 -0.70405850 -0.21872005 323.53156953
-0.06129328 0.24200244 -0.96833773 187.20374727
Axis 0.93018806 0.36672909 0.01612277
Axis point 0.00000000 104.57889965 105.23349404
Rotation angle (degrees) 165.66149440
Shift along axis 333.50594426
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1457 atoms
average map value = 0.00665, steps = 40
shifted from previous position = 0.00406
rotated from previous position = 0.0122 degrees
atoms outside contour = 710, contour level = 0.0058489
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73468704 0.66761159 0.12053931 227.74415717
0.67563895 -0.70401573 -0.21880095 323.53301656
-0.06121248 0.24219128 -0.96829562 187.20665379
Axis 0.93018391 0.36673632 0.01619750
Axis point 0.00000000 104.57131692 105.23348164
Rotation angle (degrees) 165.65285419
Shift along axis 333.52753885
> hide #53 models
> hide #52 models
> hide #51 models
> show #51 models
> hide #!1 models
Drag select of 14 residues
> delete sel
> show #!1 models
> show #53 models
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.007965, steps = 44
shifted from previous position = 0.1
rotated from previous position = 1.93 degrees
atoms outside contour = 589, contour level = 0.0058489
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62705671 0.37531487 0.68259697 225.36835982
-0.03832747 -0.86035100 0.50825895 253.00409308
0.77803013 -0.34486940 -0.52510400 258.42181793
Axis -0.89528843 -0.10014929 -0.43408380
Axis point 0.00000000 129.63459702 43.56218732
Rotation angle (degrees) 151.54590708
Shift along axis -339.28459171
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.007965, steps = 48
shifted from previous position = 0.00646
rotated from previous position = 0.023 degrees
atoms outside contour = 589, contour level = 0.0058489
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62729835 0.37514040 0.68247084 225.37847302
-0.03855985 -0.86029805 0.50833100 252.99193667
0.77782383 -0.34519117 -0.52519820 258.41030972
Axis -0.89535433 -0.10002635 -0.43397620
Axis point 0.00000000 129.65621524 43.55537227
Rotation angle (degrees) 151.53386009
Shift along axis -339.24337871
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.007965, steps = 48
shifted from previous position = 0.0346
rotated from previous position = 0.0831 degrees
atoms outside contour = 588, contour level = 0.0058489
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62745791 0.37612970 0.68177930 225.39126078
-0.03718967 -0.86011531 0.50874215 253.06743887
0.77776185 -0.34456943 -0.52569802 258.38364351
Axis -0.89540639 -0.10071747 -0.43370887
Axis point 0.00000000 129.60201318 43.61261413
Rotation angle (degrees) 151.54332975
Shift along axis -339.36836705
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.007965, steps = 44
shifted from previous position = 0.00857
rotated from previous position = 0.0157 degrees
atoms outside contour = 587, contour level = 0.0058489
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62730945 0.37603713 0.68196696 225.39058721
-0.03722893 -0.86021603 0.50856896 253.06736810
0.77787972 -0.34441902 -0.52562219 258.39662102
Axis -0.89536738 -0.10067804 -0.43379855
Axis point 0.00000000 129.59805167 43.61433360
Rotation angle (degrees) 151.55375336
Shift along axis -339.37778698
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.007965, steps = 28
shifted from previous position = 0.0306
rotated from previous position = 0.0409 degrees
atoms outside contour = 589, contour level = 0.0058489
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62735278 0.37558998 0.68217348 225.37506975
-0.03793517 -0.86022217 0.50850638 253.03260293
0.77781065 -0.34489126 -0.52541470 258.40373752
Axis -0.89537305 -0.10034121 -0.43386489
Axis point 0.00000000 129.63520070 43.58472205
Rotation angle (degrees) 151.53904146
Shift along axis -339.29667052
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.007965, steps = 40
shifted from previous position = 0.0063
rotated from previous position = 0.0343 degrees
atoms outside contour = 589, contour level = 0.0058489
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62699890 0.37538872 0.68260947 225.35986129
-0.03823037 -0.86035812 0.50825421 253.01464233
0.77808150 -0.34477124 -0.52509235 258.42330346
Axis -0.89527282 -0.10020043 -0.43410420
Axis point 0.00000000 129.63081003 43.56565676
Rotation angle (degrees) 151.54911088
Shift along axis -339.29337407
> volume #1 level 0.006237
> hide #!1 models
Drag select of 14 residues
> delete sel
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.006839, steps = 60
shifted from previous position = 0.0556
rotated from previous position = 0.867 degrees
atoms outside contour = 667, contour level = 0.0062369
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73564428 0.66850898 0.10919360 227.56125236
0.67445861 -0.70797958 -0.20945285 323.63792784
-0.06271427 0.22772935 -0.97170276 187.16264710
Axis 0.93056255 0.36591386 0.01266407
Axis point 0.00000000 105.36896352 104.95840087
Rotation angle (degrees) 166.41414785
Shift along axis 332.55382421
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.006838, steps = 44
shifted from previous position = 0.0062
rotated from previous position = 0.0283 degrees
atoms outside contour = 666, contour level = 0.0062369
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73571781 0.66850697 0.10870938 227.55121537
0.67435081 -0.70809718 -0.20940241 323.63220049
-0.06301016 0.22736934 -0.97176793 187.14580120
Axis 0.93058458 0.36586515 0.01245087
Axis point 0.00000000 105.38345388 104.96517112
Rotation angle (degrees) 166.42747489
Shift along axis 332.49152464
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.006838, steps = 40
shifted from previous position = 0.0168
rotated from previous position = 0.0486 degrees
atoms outside contour = 665, contour level = 0.0062369
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73590946 0.66841543 0.10797257 227.53734802
0.67407145 -0.70824781 -0.20979208 323.59975740
-0.06375693 0.22716920 -0.97176602 187.10118130
Axis 0.93063601 0.36574786 0.01204613
Axis point 0.00000000 105.37700519 105.00023128
Rotation angle (degrees) 166.42223682
Shift along axis 332.36421596
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.006839, steps = 44
shifted from previous position = 0.0167
rotated from previous position = 0.0249 degrees
atoms outside contour = 666, contour level = 0.0062369
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73578108 0.66850477 0.10829395 227.54808611
0.67424697 -0.70815872 -0.20952865 323.62383235
-0.06338160 0.22718408 -0.97178710 187.12517723
Axis 0.93060214 0.36582774 0.01223620
Axis point 0.00000000 105.38408978 104.98039973
Rotation angle (degrees) 166.42960463
Shift along axis 332.43701163
> show #!1 models
> show #52 models
> hide #!1 models
Drag select of 12 residues
> select up
103 atoms, 105 bonds, 13 residues, 1 model selected
> delete sel
Drag select of 1 residues
> delete sel
> fitmap #52 inMap #1
Fit molecule 20240711_copi_golph3_gamma_Arf1_.cif (#52) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.01044, steps = 96
shifted from previous position = 0.0478
rotated from previous position = 1.37 degrees
atoms outside contour = 447, contour level = 0.0062369
Position of 20240711_copi_golph3_gamma_Arf1_.cif (#52) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.55739175 0.36533697 -0.74554901 335.06611515
0.54035502 0.84139599 0.00832090 166.90426300
0.63034189 -0.39822315 -0.66639885 272.90142887
Axis -0.28128070 -0.95195479 0.12109191
Axis point 75.64388097 0.00000000 208.37368288
Rotation angle (degrees) 133.72496068
Shift along axis -220.08678665
> fitmap #52 inMap #1
Fit molecule 20240711_copi_golph3_gamma_Arf1_.cif (#52) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.01044, steps = 64
shifted from previous position = 0.0226
rotated from previous position = 0.0378 degrees
atoms outside contour = 443, contour level = 0.0062369
Position of 20240711_copi_golph3_gamma_Arf1_.cif (#52) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.55693555 0.36555126 -0.74578487 335.05111132
0.54036894 0.84138141 0.00887302 166.86167507
0.63073307 -0.39805728 -0.66612776 272.87607279
Axis -0.28141528 -0.95193988 0.12089630
Axis point 75.59745709 0.00000000 208.37065311
Rotation angle (degrees) 133.69671413
Shift along axis -220.14107742
> show #!1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_update_v1.cxs"
> hide #51 models
> hide #52 models
> hide #53 models
> show #50 models
> hide #50 models
> show #50 models
> hide #50 models
> combine #34.1
[Repeated 1 time(s)]
> rename #54 "20240711_copi_golph3_model_0.cif A"
> rename #54 "20240711_copi_golph3_golph3_M1-.cif A"
> rename #55 20240711_copi_golph3_golph3_.cif
> rename #54 20240711_copi_golph3_golph3_M1-.cif
> hide #55 models
> show #55 models
> hide #55 models
> show #!45 models
> show #!44 models
> show #!43 models
> show #!40 models
> hide #!1 models
> show #55 models
> hide #55 models
> show #55 models
> hide #55 models
Drag select of 197 residues
> select up
1963 atoms, 1993 bonds, 243 residues, 1 model selected
> delete sel
Drag select of 2 residues, 1 pseudobonds
> delete sel
> select add #54
392 atoms, 391 bonds, 53 residues, 1 model selected
> select subtract #54
Nothing selected
> select add #54
392 atoms, 391 bonds, 53 residues, 1 model selected
> select subtract #54
Nothing selected
> hide #!54 models
> hide #!45 models
> show #!45 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_update_v1.cxs"
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!40 to #43
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20240711_copi_golph3_beta_S711-L953.cif, chain E (#43) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 3704.9
RMSD between 224 pruned atom pairs is 1.090 angstroms; (across all 243 pairs:
1.912)
> show #!54 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> select add #40
39508 atoms, 40254 bonds, 5000 residues, 1 model selected
Drag select of 3 residues
> select add #40
39524 atoms, 40254 bonds, 5002 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.63005,0.76404,0.13884,282.83,0.76732,0.64002,-0.040012,341.37,-0.11943,0.081328,-0.98951,347.6,#54,0.53204,0.47156,0.70325,293.71,0.013564,-0.8352,0.54978,332.87,0.84661,-0.28297,-0.45076,340.97
> view matrix models
> #40,-0.63005,0.76404,0.13884,284.05,0.76732,0.64002,-0.040012,341.21,-0.11943,0.081328,-0.98951,346.63,#54,0.53204,0.47156,0.70325,294.93,0.013564,-0.8352,0.54978,332.72,0.84661,-0.28297,-0.45076,339.99
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.43737,0.7871,0.43495,284.57,0.88971,0.44911,0.081929,343.29,-0.13085,0.42281,-0.89672,343.66,#54,0.2348,0.40499,0.88366,295.58,-0.22418,-0.862,0.45463,333.83,0.94584,-0.30485,-0.11161,338.75
> hide #!43 models
> select subtract #40
16 atoms, 2 residues, 3 models selected
> select add #40
39524 atoms, 40254 bonds, 5002 residues, 2 models selected
> show #!43 models
> hide #!43 models
> show #!43 models
> ui tool show Matchmaker
> matchmaker #!40 to #43
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20240711_copi_golph3_beta_S711-L953.cif, chain E (#43) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 3704.9
RMSD between 224 pruned atom pairs is 1.090 angstroms; (across all 243 pairs:
1.912)
> select subtract #40
16 atoms, 2 residues, 3 models selected
> select add #54
392 atoms, 391 bonds, 53 residues, 1 model selected
> select subtract #54
Nothing selected
> select add #54
392 atoms, 391 bonds, 53 residues, 1 model selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!54 to #40
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain H (#40)
with 20240711_copi_golph3_golph3_M1-.cif, chain A (#54), sequence alignment
score = 198
RMSD between 18 pruned atom pairs is 0.685 angstroms; (across all 47 pairs:
13.519)
> view matrix models
> #54,-0.7223,0.66641,-0.1849,309.42,-0.25424,-0.5045,-0.82513,354.87,-0.64316,-0.54898,0.53382,337.9
> view matrix models
> #54,0.28193,0.78651,0.54948,302.7,-0.88272,-0.011762,0.46975,337.54,0.37592,-0.61747,0.69095,338.3
> ui mousemode right "translate selected models"
> view matrix models
> #54,0.28193,0.78651,0.54948,304.53,-0.88272,-0.011762,0.46975,356.14,0.37592,-0.61747,0.69095,316.77
> ui mousemode right select
> select subtract #54
Nothing selected
Drag select of 22 residues
> delete sel
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!54 to #40
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain H (#40)
with 20240711_copi_golph3_golph3_M1-.cif, chain A (#54), sequence alignment
score = 188.4
RMSD between 13 pruned atom pairs is 1.080 angstroms; (across all 31 pairs:
10.676)
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!54 models
> show #!1 models
> hide #!40 models
> volume #1 level 0.005461
> hide #!1 models
> fitmap #54 inMap #1
Fit molecule 20240711_copi_golph3_golph3_M1-.cif (#54) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 229 atoms
average map value = 0.01065, steps = 468
shifted from previous position = 13.9
rotated from previous position = 160 degrees
atoms outside contour = 75, contour level = 0.0054608
Position of 20240711_copi_golph3_golph3_M1-.cif (#54) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.50958231 0.51380053 0.69017018 237.15892878
-0.26830832 0.85702309 -0.43991143 297.92467750
-0.81751851 0.03899268 0.57458077 262.58133868
Axis 0.27137979 0.85435943 -0.44319632
Axis point 414.93124846 0.00000000 30.84815820
Rotation angle (degrees) 61.92719804
Shift along axis 202.51981387
> show #!40 models
> hide #!54 models
> hide #!43 models
> hide #!40 models
> show #!43 models
> show #!40 models
> hide #!43 models
> hide #!40 models
> show #!44 models
> show #!43 models
> hide #!44 models
> show #!54 models
> ui mousemode right "translate selected models"
> show #!1 models
> select add #54
229 atoms, 228 bonds, 31 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #54,0.53997,0.59854,0.59176,294.71,-0.11296,-0.64517,0.75564,334.85,0.83407,-0.47487,-0.28076,338.78
> view matrix models
> #54,0.65695,0.31239,0.68617,291.47,-0.33645,-0.693,0.63761,335.1,0.6747,-0.64974,-0.35016,337.55
> hide #!1 models
> view matrix models
> #54,0.22732,0.11704,0.96676,286.7,-0.70153,-0.66886,0.24592,338.13,0.67541,-0.73412,-0.069938,334.41
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!54 to #40
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain H (#40)
with 20240711_copi_golph3_golph3_M1-.cif, chain A (#54), sequence alignment
score = 188.4
RMSD between 13 pruned atom pairs is 1.080 angstroms; (across all 31 pairs:
10.676)
> select subtract #54
Nothing selected
> show #!1 models
> show #!40 models
> hide #!1 models
> hide #!40 models
> show #!40 models
> hide #!43 models
> ui mousemode right select
Drag select of 3 residues
> select up
99 atoms, 98 bonds, 14 residues, 2 models selected
> select clear
Drag select of 19 residues
> select up
163 atoms, 162 bonds, 22 residues, 2 models selected
> delete sel
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!40 to #43
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20240711_copi_golph3_beta_S711-L953.cif, chain E (#43) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 3682.1
RMSD between 205 pruned atom pairs is 1.038 angstroms; (across all 221 pairs:
1.606)
> hide #!43 models
Drag select of 7 residues
> select up
7344 atoms, 7463 bonds, 931 residues, 2 models selected
> select down
60 atoms, 7 residues, 2 models selected
> delete sel
> show #!43 models
> hide #!40 models
> show #!40 models
> hide #!43 models
> show #!43 models
> hide #!43 models
Drag select of 9 residues
> select up
170 atoms, 172 bonds, 21 residues, 2 models selected
> delete sel
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!40 to #43
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20240711_copi_golph3_beta_S711-L953.cif, chain E (#43) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 3640.1
RMSD between 175 pruned atom pairs is 0.948 angstroms; (across all 193 pairs:
1.612)
> show #!43 models
> hide #!43 models
Drag select of 5 residues
> select up
63 atoms, 64 bonds, 9 residues, 2 models selected
> delete sel
> select #40/B:914
7 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #40/B:912
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/B:913
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
Drag select of 13 residues
> select up
207 atoms, 209 bonds, 26 residues, 2 models selected
> delete sel
Drag select of 6 residues
> select up
63 atoms, 63 bonds, 9 residues, 2 models selected
> delete sel
> ui tool show Matchmaker
> show #!43 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!43 models
> show #!43 models
> matchmaker #!40 to #43
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 20240711_copi_golph3_beta_S711-L953.cif, chain E (#43) with
fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain B (#40), sequence
alignment score = 3556.1
RMSD between 139 pruned atom pairs is 0.782 angstroms; (across all 147 pairs:
1.500)
> select add #40
38766 atoms, 39496 bonds, 3 pseudobonds, 4904 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.66043,0.73847,0.13602,283.55,0.7459,0.66603,0.0056796,340.95,-0.0864,0.10521,-0.99069,347.42
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.75937,0.64372,0.09483,283.83,0.63647,0.76515,-0.097246,338.49,-0.13516,-0.013489,-0.99073,348.53
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.75937,0.64372,0.09483,283.83,0.63647,0.76515,-0.097246,338.96,-0.13516,-0.013489,-0.99073,347.45
> view matrix models
> #40,-0.75937,0.64372,0.09483,286.4,0.63647,0.76515,-0.097246,338.89,-0.13516,-0.013489,-0.99073,347.57
> ui mousemode right "rotate selected models"
> view matrix models
> #40,-0.53707,0.84336,-0.017352,284.75,0.82966,0.52441,-0.19145,342.43,-0.15236,-0.11722,-0.98135,348.76
> view matrix models
> #40,-0.7265,0.67539,-0.1267,284.95,0.66634,0.64734,-0.37007,338.91,-0.16792,-0.35327,-0.92033,351.84
> view matrix models
> #40,-0.52618,0.83563,-0.15768,284.1,0.8447,0.49222,-0.21024,342.8,-0.09807,-0.24381,-0.96485,350.71
> view matrix models
> #40,-0.55523,0.74609,-0.36752,283.79,0.81558,0.40187,-0.41632,342.51,-0.16292,-0.5309,-0.83163,354.51
> view matrix models
> #40,-0.59018,0.77596,0.22264,286.61,0.78627,0.61504,-0.059293,341.84,-0.18294,0.14006,-0.9731,345.54
> view matrix models
> #40,-0.56806,0.78726,0.23987,286.71,0.8054,0.59172,-0.034679,342.38,-0.16924,0.17349,-0.97019,345.24
> ui mousemode right "translate selected models"
> view matrix models
> #40,-0.56806,0.78726,0.23987,284.52,0.8054,0.59172,-0.034679,341.56,-0.16924,0.17349,-0.97019,347.55
> view matrix models
> #40,-0.56806,0.78726,0.23987,283.34,0.8054,0.59172,-0.034679,342.14,-0.16924,0.17349,-0.97019,346.83
> select subtract #40
2 models selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!54 to #40
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif, chain H (#40)
with 20240711_copi_golph3_golph3_M1-.cif, chain A (#54), sequence alignment
score = 188.4
RMSD between 13 pruned atom pairs is 1.080 angstroms; (across all 31 pairs:
10.676)
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!1 models
> hide #!1 models
> show #55 models
> hide #!54 models
> show #!54 models
> hide #!54 models
> show #!1 models
> hide #!1 models
> hide #!43 models
> ui mousemode right select
Drag select of 18 residues
> select up
225 atoms, 224 bonds, 30 residues, 1 model selected
> delete sel
Drag select of 21 residues
> select up
167 atoms, 166 bonds, 23 residues, 1 model selected
> delete sel
> select #55/A:54
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> show #!1 models
> fitmap #55 inMap #1
Fit molecule 20240711_copi_golph3_golph3_.cif (#55) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1971 atoms
average map value = 0.008364, steps = 44
shifted from previous position = 0.155
rotated from previous position = 0.745 degrees
atoms outside contour = 620, contour level = 0.0054608
Position of 20240711_copi_golph3_golph3_.cif (#55) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.52149365 0.47001719 0.71212935 230.49002012
0.01135098 -0.83835072 0.54501305 257.47176105
0.85317966 -0.27613748 -0.44252974 262.84155594
Axis -0.86338510 -0.14830501 -0.48225698
Axis point -0.00000000 121.73438799 37.23458310
Rotation angle (degrees) 151.60540101
Shift along axis -363.94317469
> fitmap #55 inMap #1
Fit molecule 20240711_copi_golph3_golph3_.cif (#55) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1971 atoms
average map value = 0.008363, steps = 40
shifted from previous position = 0.0326
rotated from previous position = 0.0372 degrees
atoms outside contour = 617, contour level = 0.0054608
Position of 20240711_copi_golph3_golph3_.cif (#55) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.52173357 0.47042314 0.71168543 230.53965220
0.01161038 -0.83806431 0.54544790 257.46018997
0.85302947 -0.27631555 -0.44270808 262.85484380
Axis -0.86344537 -0.14851337 -0.48208491
Axis point 0.00000000 121.71304452 37.24831631
Rotation angle (degrees) 151.58444406
Shift along axis -364.01303162
> hide #!1 models
> show #!54 models
> show #!43 models
> show #34.1 models
> hide #!43 models
> show #41 models
> show #!43 models
> show #!44 models
> show #42 models
> show #39 models
> show #38 models
> show #!45 models
> show #46 models
> show #47 models
> show #48 models
> show #!49 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #!1 models
> hide #34.1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_update_v2.cxs"
> hide #41 models
> hide #42 models
> hide #!43 models
> hide #!44 models
> hide #!45 models
> hide #46 models
> hide #47 models
> hide #48 models
> hide #!49 models
> hide #50 models
> hide #51 models
> hide #53 models
> hide #52 models
> hide #!54 models
> hide #55 models
> hide #!1 models
Drag select of 10 residues
> select up
74 atoms, 75 bonds, 11 residues, 1 model selected
> delete sel
> hide #39 models
> show #39 models
> hide #38 models
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2329 atoms
average map value = 0.00752, steps = 44
shifted from previous position = 0.0203
rotated from previous position = 0.018 degrees
atoms outside contour = 1192, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58557972 0.32386603 0.74310644 225.70705057
-0.13511522 -0.86489862 0.48341933 254.83102732
0.79927484 -0.38348555 -0.46270787 264.72353564
Axis -0.88232925 -0.05716777 -0.46714766
Axis point 0.00000000 136.04140665 37.56516457
Rotation angle (degrees) 150.57661567
Shift along axis -337.38103518
Drag select of 9 residues
> delete sel
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2256 atoms
average map value = 0.007692, steps = 44
shifted from previous position = 0.0477
rotated from previous position = 0.0822 degrees
atoms outside contour = 1123, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58606274 0.32257416 0.74328755 225.67480968
-0.13550295 -0.86540137 0.48241001 254.81278925
0.79885507 -0.38344018 -0.46346975 264.68459062
Axis -0.88250171 -0.05663616 -0.46688658
Axis point 0.00000000 136.09588960 37.63718480
Rotation angle (degrees) 150.62222794
Shift along axis -337.16770619
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2256 atoms
average map value = 0.007693, steps = 44
shifted from previous position = 0.036
rotated from previous position = 0.0445 degrees
atoms outside contour = 1120, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58571763 0.32326751 0.74325835 225.67941678
-0.13520957 -0.86519945 0.48285431 254.80826181
0.79915782 -0.38331193 -0.46305371 264.72109065
Axis -0.88238808 -0.05694638 -0.46706358
Axis point 0.00000000 136.05210514 37.61678218
Rotation angle (degrees) 150.60629759
Shift along axis -337.28881532
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2256 atoms
average map value = 0.007693, steps = 48
shifted from previous position = 0.0158
rotated from previous position = 0.0402 degrees
atoms outside contour = 1121, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58587561 0.32288083 0.74330191 225.68344466
-0.13585522 -0.86509142 0.48286664 254.79486458
0.79893249 -0.38388123 -0.46297092 264.71592302
Axis -0.88242423 -0.05663674 -0.46703294
Axis point 0.00000000 136.10226685 37.58138913
Rotation angle (degrees) 150.58594517
Shift along axis -337.21034398
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2256 atoms
average map value = 0.007693, steps = 48
shifted from previous position = 0.00851
rotated from previous position = 0.0433 degrees
atoms outside contour = 1121, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58579119 0.32343012 0.74312963 225.68292591
-0.13514934 -0.86509974 0.48304978 254.81625439
0.79911410 -0.38339978 -0.46305644 264.72194129
Axis -0.88240463 -0.05701539 -0.46702388
Axis point 0.00000000 136.05373122 37.61313871
Rotation angle (degrees) 150.59634525
Shift along axis -337.30357599
Drag select of 5 residues
> select up
229 atoms, 232 bonds, 31 residues, 1 model selected
> delete sel
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2027 atoms
average map value = 0.008501, steps = 44
shifted from previous position = 0.0433
rotated from previous position = 0.229 degrees
atoms outside contour = 896, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58769912 0.32000785 0.74310479 225.59331066
-0.13607732 -0.86627875 0.48067046 254.70507979
0.79755421 -0.38360932 -0.46556544 264.58615592
Axis -0.88304153 -0.05563140 -0.46598585
Axis point 0.00000000 136.18804161 37.84144087
Rotation angle (degrees) 150.70038215
Shift along axis -336.67126673
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2027 atoms
average map value = 0.0085, steps = 44
shifted from previous position = 0.0109
rotated from previous position = 0.0851 degrees
atoms outside contour = 898, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.58870044 0.31899070 0.74274943 225.56253675
-0.13658149 -0.86638189 0.48034146 254.67400066
0.79672912 -0.38422305 -0.46647118 264.52906130
Axis -0.88334458 -0.05515223 -0.46546813
Axis point 0.00000000 136.26566156 37.89878558
Rotation angle (degrees) 150.70082407
Shift along axis -336.42513097
Drag select of 7 residues
> delete sel
Drag select of 4 residues
> delete sel
Drag select of 4 residues
> delete sel
Drag select of 4 residues
> select up
61 atoms, 60 bonds, 10 residues, 1 model selected
> select clear
Drag select of 6 residues
> delete sel
Drag select of 3 residues
> delete sel
> select #39/D:825
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1856 atoms
average map value = 0.009053, steps = 48
shifted from previous position = 0.123
rotated from previous position = 1.09 degrees
atoms outside contour = 737, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60090436 0.30593525 0.73845621 225.14344658
-0.13729666 -0.87061879 0.47241141 254.16814824
0.78744116 -0.38526165 -0.48115474 263.62381403
Axis -0.88724197 -0.05067374 -0.45851266
Axis point 0.00000000 136.73303752 39.17666397
Rotation angle (degrees) 151.09645074
Shift along axis -333.51122226
> show #!1 models
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1856 atoms
average map value = 0.009053, steps = 44
shifted from previous position = 0.0157
rotated from previous position = 0.0987 degrees
atoms outside contour = 737, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60197049 0.30463672 0.73812465 225.11508006
-0.13793837 -0.87080078 0.47188876 254.14705450
0.78651417 -0.38587882 -0.48217528 263.55192322
Axis -0.88756662 -0.05007058 -0.45795025
Axis point 0.00000000 136.82747679 39.23508340
Rotation angle (degrees) 151.10453619
Shift along axis -333.22359063
> show #38 models
> show #41 models
> show #42 models
Drag select of 1 relion_locres_filtered_20240326_GT.mrc , 12 residues
> select clear
Drag select of 12 residues
> select up
104 atoms, 103 bonds, 13 residues, 1 model selected
> delete sel
Drag select of 5 residues
> select up
58 atoms, 57 bonds, 7 residues, 1 model selected
> delete sel
Drag select of 11 residues
> select down
87 atoms, 11 residues, 1 model selected
> select up
357 atoms, 363 bonds, 47 residues, 1 model selected
> delete sel
> hide #!1 models
> show #34.6 models
> hide #34.6 models
> hide #42 models
> hide #41 models
> show #34.6 models
> hide #34.6 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_final.cxs"
> show #41 models
> show #42 models
> show #!1 models
> show #!43 models
> show #!44 models
> show #!45 models
> hide #!44 models
> hide #!43 models
> show #!44 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 8 residues
> select up
334 atoms, 338 bonds, 44 residues, 1 model selected
> select down
60 atoms, 8 residues, 1 model selected
> hide #41 models
> hide #42 models
> select add #44
2760 atoms, 2795 bonds, 349 residues, 1 model selected
> select subtract #44
Nothing selected
Drag select of 27 residues
> delete sel
> select #44/E:535
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/E:507
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #44/E:535
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #44/E:507
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete sel
> select #44/E:506
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #44/E:505
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #44/E:504
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #44/E:503
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #44/E:502
7 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #44/E:501
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #44/E:500
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> show #!1 models
> hide #!1 models
> show #!1 models
> show #41 models
> show #42 models
> show #!43 models
> fitmap #38 inMap #1
Fit molecule 20240711_copi_golph3_alpha_M1-T591.cif (#38) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008699, steps = 28
shifted from previous position = 0.0236
rotated from previous position = 0.0106 degrees
atoms outside contour = 1690, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_M1-T591.cif (#38) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57925682 0.37627919 0.72310131 229.40958245
-0.04014637 -0.87283727 0.48635724 258.31641239
0.81415588 -0.31075565 -0.49049070 263.88915314
Axis -0.88182995 -0.10073184 -0.46068322
Axis point -0.00000000 129.96563876 41.80706218
Rotation angle (degrees) 153.13016134
Shift along axis -349.89023416
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1856 atoms
average map value = 0.009052, steps = 44
shifted from previous position = 0.0187
rotated from previous position = 0.0387 degrees
atoms outside contour = 737, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60146802 0.30500027 0.73838408 225.11946579
-0.13791350 -0.87073810 0.47201169 254.14091566
0.78690284 -0.38573307 -0.48165747 263.58198922
Axis -0.88741319 -0.05019697 -0.45823366
Axis point 0.00000000 136.79731935 39.19893697
Rotation angle (degrees) 151.09991048
Shift along axis -333.31322885
> fitmap #41 inMap #1
Fit molecule 20240711_copi_golph3_betaprime_M1-S586.cif (#41) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4686 atoms
average map value = 0.01004, steps = 28
shifted from previous position = 0.0318
rotated from previous position = 0.0303 degrees
atoms outside contour = 1305, contour level = 0.0054608
Position of 20240711_copi_golph3_betaprime_M1-S586.cif (#41) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59284247 0.33283311 0.73332116 230.50393053
-0.03649999 -0.89855685 0.43733664 249.48895575
0.80449087 -0.28603795 -0.52055426 258.87555685
Axis -0.88723039 -0.08729077 -0.45299289
Axis point 0.00000000 125.80360538 44.23524482
Rotation angle (degrees) 155.94214965
Shift along axis -343.55696233
> fitmap #42 inMap #1
Fit molecule 20240711_copi_golph3_betaprime_L587-D905.cif (#42) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2009 atoms
average map value = 0.009611, steps = 44
shifted from previous position = 0.0988
rotated from previous position = 0.255 degrees
atoms outside contour = 808, contour level = 0.0054608
Position of 20240711_copi_golph3_betaprime_L587-D905.cif (#42) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59344452 0.33741789 0.73073440 226.60067008
-0.11753036 -0.86182622 0.49339860 254.74842883
0.79624759 -0.37868817 -0.47178920 265.07497120
Axis -0.88464715 -0.06645675 -0.46150072
Axis point 0.00000000 134.99509957 38.84469376
Rotation angle (degrees) 150.46857105
Shift along axis -339.72367958
> fitmap #43 inMap #1
Fit molecule 20240711_copi_golph3_beta_S711-L953.cif (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1872 atoms
average map value = 0.008979, steps = 48
shifted from previous position = 0.0388
rotated from previous position = 0.0207 degrees
atoms outside contour = 594, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_S711-L953.cif (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55236813 0.42744455 0.71566794 229.22862876
-0.07118249 -0.83120460 0.55139094 257.71229740
0.83055554 -0.35551381 -0.42870436 265.08166205
Axis -0.87093568 -0.11033100 -0.47885082
Axis point 0.00000000 129.66807422 34.28649497
Rotation angle (degrees) 148.62415981
Shift along axis -355.01161890
> fitmap #44 inMap #1
Fit molecule 20240711_copi_golph3_beta_H311-E659.cif (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2488 atoms
average map value = 0.01049, steps = 48
shifted from previous position = 0.0818
rotated from previous position = 0.312 degrees
atoms outside contour = 856, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_H311-E659.cif (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59143363 0.34566993 0.72850433 227.95503666
-0.13172257 -0.84990236 0.51021089 253.99753634
0.79552211 -0.39771634 -0.45712830 264.39375573
Axis -0.88322158 -0.06519415 -0.46440215
Axis point 0.00000000 135.21602975 35.96393996
Rotation angle (degrees) 149.07029165
Shift along axis -340.67899136
> fitmap #44 inMap #1
Fit molecule 20240711_copi_golph3_beta_H311-E659.cif (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2488 atoms
average map value = 0.01049, steps = 28
shifted from previous position = 0.039
rotated from previous position = 0.00945 degrees
atoms outside contour = 854, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_H311-E659.cif (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59149766 0.34577423 0.72840284 227.92948108
-0.13166947 -0.84983342 0.51033941 254.02784025
0.79548329 -0.39777299 -0.45714657 264.39514247
Axis -0.88323725 -0.06524297 -0.46436549
Axis point 0.00000000 135.23245815 35.96762681
Rotation angle (degrees) 149.06389878
Shift along axis -340.66532049
> fitmap #44 inMap #1
Fit molecule 20240711_copi_golph3_beta_H311-E659.cif (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2488 atoms
average map value = 0.01049, steps = 40
shifted from previous position = 0.0274
rotated from previous position = 0.041 degrees
atoms outside contour = 857, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_H311-E659.cif (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59164557 0.34604757 0.72815287 227.92017434
-0.13097253 -0.84993837 0.51034396 253.97764784
0.79548835 -0.39731077 -0.45753955 264.38682197
Axis -0.88329404 -0.06552825 -0.46421728
Axis point 0.00000000 135.16371112 36.03866076
Rotation angle (degrees) 149.08340997
Shift along axis -340.69617475
> fitmap #45 inMap #1
Fit molecule 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 28
shifted from previous position = 0.0124
rotated from previous position = 0.0648 degrees
atoms outside contour = 1088, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59421777 0.37915482 0.70932846 225.99164989
-0.07052607 -0.85395625 0.51554321 250.98951359
0.80120616 -0.35637109 -0.48069568 261.45591263
Axis -0.88488945 -0.09324495 -0.45637269
Axis point 0.00000000 129.22523857 39.84864996
Rotation angle (degrees) 150.48387508
Shift along axis -342.70247180
> show #46 models
> hide #!1 models
> hide #38 models
> hide #39 models
> hide #41 models
> hide #42 models
> hide #!43 models
> hide #!44 models
> hide #!45 models
Drag select of 4 residues
> delete sel
Drag select of 23 residues
> delete sel
> show #!1 models
Drag select of 9 residues
> delete sel
> hide #!1 models
Drag select of 7 residues
> delete sel
> show #!1 models
> hide #!1 models
Drag select of 18 residues
> delete sel
> show #!1 models
> show #!45 models
> select clear
> select #46/G:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #46/G:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> fitmap #46 inMap #1
Fit molecule 20240711_copi_golph3_delta_M1-S273.cif (#46) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1687 atoms
average map value = 0.00921, steps = 40
shifted from previous position = 0.0802
rotated from previous position = 0.432 degrees
atoms outside contour = 625, contour level = 0.0054608
Position of 20240711_copi_golph3_delta_M1-S273.cif (#46) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60555376 0.37694317 0.70086981 225.92253777
-0.05371617 -0.85933682 0.50858116 251.52404936
0.79398943 -0.34562128 -0.50012670 260.89204460
Axis -0.88873380 -0.09688401 -0.44806887
Axis point 0.00000000 128.95140527 42.03723196
Rotation angle (degrees) 151.27718631
Shift along axis -342.05125874
> fitmap #46 inMap #1
Fit molecule 20240711_copi_golph3_delta_M1-S273.cif (#46) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1687 atoms
average map value = 0.00921, steps = 36
shifted from previous position = 0.0026
rotated from previous position = 0.0212 degrees
atoms outside contour = 625, contour level = 0.0054608
Position of 20240711_copi_golph3_delta_M1-S273.cif (#46) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60557554 0.37667940 0.70099279 225.92943929
-0.05370995 -0.85952398 0.50826545 251.52366578
0.79397324 -0.34544341 -0.50027527 260.88843027
Axis -0.88875022 -0.09679693 -0.44805513
Axis point 0.00000000 128.95257916 42.05397738
Rotation angle (degrees) 151.29590684
Shift along axis -342.03395646
> fitmap #46 inMap #1
Fit molecule 20240711_copi_golph3_delta_M1-S273.cif (#46) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1687 atoms
average map value = 0.00921, steps = 40
shifted from previous position = 0.034
rotated from previous position = 0.0445 degrees
atoms outside contour = 621, contour level = 0.0054608
Position of 20240711_copi_golph3_delta_M1-S273.cif (#46) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60573039 0.37695519 0.70071070 225.92868374
-0.05399153 -0.85915229 0.50886369 251.48998984
0.79383601 -0.34606664 -0.50006226 260.88507598
Axis -0.88877335 -0.09681175 -0.44800605
Axis point 0.00000000 128.96117324 42.01611838
Rotation angle (degrees) 151.25182612
Shift along axis -342.02467069
> select #46/G:223
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> fitmap #46 inMap #1
Fit molecule 20240711_copi_golph3_delta_M1-S273.cif (#46) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1681 atoms
average map value = 0.009232, steps = 44
shifted from previous position = 0.0363
rotated from previous position = 0.0461 degrees
atoms outside contour = 619, contour level = 0.0054608
Position of 20240711_copi_golph3_delta_M1-S273.cif (#46) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60565962 0.37737338 0.70054676 225.91375703
-0.05319936 -0.85921597 0.50883961 251.54232654
0.79394349 -0.34545224 -0.50031639 260.88614007
Axis -0.88876437 -0.09716549 -0.44794728
Axis point 0.00000000 128.92911445 42.06422472
Rotation angle (degrees) 151.27497962
Shift along axis -342.08856667
> fitmap #46 inMap #1
Fit molecule 20240711_copi_golph3_delta_M1-S273.cif (#46) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1681 atoms
average map value = 0.009232, steps = 36
shifted from previous position = 0.0019
rotated from previous position = 0.0132 degrees
atoms outside contour = 619, contour level = 0.0054608
Position of 20240711_copi_golph3_delta_M1-S273.cif (#46) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60565255 0.37723336 0.70062827 225.91751968
-0.05316674 -0.85933407 0.50864355 251.54284148
0.79395106 -0.34531138 -0.50040160 260.88418454
Axis -0.88876887 -0.09712736 -0.44794661
Axis point 0.00000000 128.92708608 42.07511626
Rotation angle (degrees) 151.28752213
Shift along axis -342.08233740
> hide #!1 models
> show #34.7 models
> hide #34.7 models
> show #47 models
> hide #47 models
> show #48 models
> hide #48 models
> show #!49 models
> hide #!49 models
> show #!1 models
> hide #!1 models
> show #!44 models
> show #!43 models
> show #38 models
> show #39 models
> show #41 models
> show #42 models
> show #47 models
> show #48 models
> show #!49 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #!54 models
> show #55 models
> show #!1 models
> hide #!1 models
> hide #55 models
> hide #!54 models
> hide #53 models
> hide #52 models
> hide #51 models
> hide #50 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #42 models
> hide #41 models
Drag select of 12 residues
> delete sel
Drag select of 6 residues
> delete sel
Drag select of 8 residues
> delete sel
> select #49/H:583
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete sel
> show #41 models
> show #42 models
> show #!43 models
> show #!44 models
> show #!45 models
> show #!46 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #!54 models
> show #55 models
> show #!1 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_final.cxs"
> fitmap #38 inMap #1
Fit molecule 20240711_copi_golph3_alpha_M1-T591.cif (#38) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4763 atoms
average map value = 0.008699, steps = 44
shifted from previous position = 0.0236
rotated from previous position = 0.0107 degrees
atoms outside contour = 1689, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_M1-T591.cif (#38) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.57928803 0.37610754 0.72316561 229.39213966
-0.04023911 -0.87290929 0.48622030 258.29778260
0.81412910 -0.31076114 -0.49053167 263.87493687
Axis -0.88184203 -0.10064906 -0.46067820
Axis point 0.00000000 129.96633324 41.81045087
Rotation angle (degrees) 153.13534603
Shift along axis -349.84648868
> fitmap #39 inMap #1
Fit molecule 20240711_copi_golph3_alpha_I592-G900.cif (#39) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1856 atoms
average map value = 0.009052, steps = 28
shifted from previous position = 0.0199
rotated from previous position = 0.0556 degrees
atoms outside contour = 735, contour level = 0.0054608
Position of 20240711_copi_golph3_alpha_I592-G900.cif (#39) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60219289 0.30452316 0.73799009 225.08404402
-0.13785076 -0.87084661 0.47182979 254.13974261
0.78635926 -0.38586504 -0.48243889 263.52424373
Axis -0.88763619 -0.05005770 -0.45781680
Axis point 0.00000000 136.82920972 39.25982451
Rotation angle (degrees) 151.10969654
Shift along axis -333.16021952
> fitmap #41 inMap #1
Fit molecule 20240711_copi_golph3_betaprime_M1-S586.cif (#41) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 4686 atoms
average map value = 0.01004, steps = 40
shifted from previous position = 0.0209
rotated from previous position = 0.0155 degrees
atoms outside contour = 1306, contour level = 0.0054608
Position of 20240711_copi_golph3_betaprime_M1-S586.cif (#41) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59295682 0.33298464 0.73315990 230.47565312
-0.03646127 -0.89845596 0.43754710 249.47671776
0.80440835 -0.28617848 -0.52060454 258.88405677
Axis -0.88725890 -0.08734777 -0.45292605
Axis point 0.00000000 125.80239586 44.24867975
Rotation angle (degrees) 155.93056047
Shift along axis -343.53814387
> fitmap #42 inMap #1
Fit molecule 20240711_copi_golph3_betaprime_L587-D905.cif (#42) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2009 atoms
average map value = 0.009612, steps = 40
shifted from previous position = 0.0365
rotated from previous position = 0.0376 degrees
atoms outside contour = 806, contour level = 0.0054608
Position of 20240711_copi_golph3_betaprime_L587-D905.cif (#42) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59391500 0.33716394 0.73046934 226.60180837
-0.11776757 -0.86173358 0.49350384 254.76376583
0.79586165 -0.37912493 -0.47208952 265.08713080
Axis -0.88478071 -0.06630295 -0.46126674
Axis point 0.00000000 135.04800086 38.86518440
Rotation angle (degrees) 150.45330024
Shift along axis -339.66037675
> fitmap #43 inMap #1
Fit molecule 20240711_copi_golph3_beta_S711-L953.cif (#43) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1872 atoms
average map value = 0.008979, steps = 48
shifted from previous position = 0.00928
rotated from previous position = 0.058 degrees
atoms outside contour = 595, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_S711-L953.cif (#43) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.55318541 0.42731135 0.71511601 229.23248395
-0.07089264 -0.83116159 0.55149311 257.71582932
0.83003622 -0.35577440 -0.42949324 265.07353083
Axis -0.87118608 -0.11034991 -0.47839074
Axis point 0.00000000 129.69852811 34.36494916
Rotation angle (degrees) 148.62023071
Shift along axis -354.95179266
> fitmap #44 inMap #1
Fit molecule 20240711_copi_golph3_beta_H311-E659.cif (#44) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2488 atoms
average map value = 0.01049, steps = 44
shifted from previous position = 0.00269
rotated from previous position = 0.0158 degrees
atoms outside contour = 858, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_H311-E659.cif (#44) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59165406 0.34602484 0.72815677 227.91923540
-0.13120248 -0.84983644 0.51045464 253.98345606
0.79544414 -0.39754854 -0.45740986 264.38893676
Axis -0.88328859 -0.06545590 -0.46423786
Axis point 0.00000000 135.18382181 36.01531658
Rotation angle (degrees) 149.07002452
Shift along axis -340.68253036
> fitmap #45 inMap #1
Fit molecule 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2879 atoms
average map value = 0.01059, steps = 28
shifted from previous position = 0.013
rotated from previous position = 0.0445 degrees
atoms outside contour = 1087, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_M1-H311_K660-A710.cif (#45) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.59382688 0.37913834 0.70966454 225.99540182
-0.07111890 -0.85383085 0.51566945 250.98421627
0.80144354 -0.35668894 -0.48006380 261.49180825
Axis -0.88475932 -0.09308367 -0.45665783
Axis point 0.00000000 129.24450465 39.78412987
Rotation angle (degrees) 150.46257765
Shift along axis -342.72635212
> fitmap #46 inMap #1
Fit molecule 20240711_copi_golph3_delta_M1-S273.cif (#46) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1681 atoms
average map value = 0.009232, steps = 36
shifted from previous position = 0.00229
rotated from previous position = 0.00138 degrees
atoms outside contour = 619, contour level = 0.0054608
Position of 20240711_copi_golph3_delta_M1-S273.cif (#46) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.60565582 0.37721154 0.70063719 225.91936681
-0.05317775 -0.85934408 0.50862547 251.54408309
0.79394783 -0.34531029 -0.50040748 260.88506982
Axis -0.88877025 -0.09711704 -0.44794611
Axis point 0.00000000 128.92865681 42.07546274
Rotation angle (degrees) 151.28827510
Shift along axis -342.08208254
> fitmap #47 inMap #1
Fit molecule 20240711_copi_golph3_gamma1_K300-F448.cif (#47) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1163 atoms
average map value = 0.01156, steps = 28
shifted from previous position = 0.0359
rotated from previous position = 0.0812 degrees
atoms outside contour = 406, contour level = 0.0054608
Position of 20240711_copi_golph3_gamma1_K300-F448.cif (#47) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.63735883 0.40216824 0.65729326 230.92053426
-0.14074376 -0.77789273 0.61243292 258.40212385
0.75760472 -0.48284946 -0.43919413 263.51538032
Axis -0.89296796 -0.08178249 -0.44262834
Axis point 0.00000000 139.97276575 30.34735340
Rotation angle (degrees) 142.17280564
Shift along axis -343.97678385
> fitmap #48 inMap #1
Fit molecule 20240711_copi_golph3_gamma1_M1-P299.cif (#48) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 2333 atoms
average map value = 0.0114, steps = 40
shifted from previous position = 0.0337
rotated from previous position = 0.107 degrees
atoms outside contour = 861, contour level = 0.0054608
Position of 20240711_copi_golph3_gamma1_M1-P299.cif (#48) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.71018130 0.58934449 0.38511764 247.34816708
0.22353933 -0.70748588 0.67044306 250.99527366
0.66758722 -0.39004718 -0.63418491 271.51829102
Axis -0.91672557 -0.24417677 -0.31621502
Axis point 0.00000000 119.18898752 65.35215486
Rotation angle (degrees) 144.66106725
Shift along axis -373.89576549
> fitmap #49 inMap #1
Fit molecule 20240711_copi_golph3_gammm1_T449-R609.cif (#49) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1064 atoms
average map value = 0.01126, steps = 48
shifted from previous position = 0.0682
rotated from previous position = 0.523 degrees
atoms outside contour = 327, contour level = 0.0054608
Position of 20240711_copi_golph3_gammm1_T449-R609.cif (#49) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.61465895 0.32811241 0.71731208 227.85211531
-0.19740465 -0.81645485 0.54261669 259.14664332
0.76369220 -0.47512495 -0.43707037 264.40938172
Axis -0.88781089 -0.04045897 -0.45842654
Axis point 0.00000000 144.12846306 29.79812316
Rotation angle (degrees) 145.02808860
Shift along axis -333.98667268
> fitmap #49 inMap #1
Fit molecule 20240711_copi_golph3_gammm1_T449-R609.cif (#49) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1064 atoms
average map value = 0.01126, steps = 44
shifted from previous position = 0.0321
rotated from previous position = 0.0462 degrees
atoms outside contour = 324, contour level = 0.0054608
Position of 20240711_copi_golph3_gammm1_T449-R609.cif (#49) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.61502244 0.32743635 0.71730944 227.85342077
-0.19788856 -0.81649374 0.54238187 259.17556224
0.76327421 -0.47552436 -0.43736606 264.41457129
Axis -0.88792245 -0.04009519 -0.45824240
Axis point 0.00000000 144.20961212 29.80746923
Rotation angle (degrees) 145.02664345
Shift along axis -333.87382959
> fitmap #50 inMap #1
Fit molecule 20240711_copi_golph3_zeta1.cif (#50) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1200 atoms
average map value = 0.01052, steps = 56
shifted from previous position = 0.0555
rotated from previous position = 0.263 degrees
atoms outside contour = 378, contour level = 0.0054608
Position of 20240711_copi_golph3_zeta1.cif (#50) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73251414 0.58212836 0.35291585 247.54139535
0.25167844 -0.71327099 0.65414252 251.74744250
0.63251956 -0.39034733 -0.66899025 274.75204630
Axis -0.92380856 -0.24729804 -0.29226944
Axis point 0.00000000 120.61570766 71.40135804
Rotation angle (degrees) 145.57567415
Shift along axis -371.23913687
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.007965, steps = 44
shifted from previous position = 0.0233
rotated from previous position = 0.0494 degrees
atoms outside contour = 559, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62732550 0.37583357 0.68206440 225.38688247
-0.03751618 -0.86023530 0.50851526 253.05396861
0.77785298 -0.34459304 -0.52554770 258.39723144
Axis -0.89537005 -0.10053381 -0.43382649
Axis point 0.00000000 129.61295180 43.60190483
Rotation angle (degrees) 151.54946723
Shift along axis -339.34470784
> fitmap #50 inMap #1
Fit molecule 20240711_copi_golph3_zeta1.cif (#50) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1200 atoms
average map value = 0.01052, steps = 40
shifted from previous position = 0.00431
rotated from previous position = 0.0156 degrees
atoms outside contour = 378, contour level = 0.0054608
Position of 20240711_copi_golph3_zeta1.cif (#50) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73264141 0.58211201 0.35267856 247.55303951
0.25173348 -0.71318961 0.65421007 251.74165773
0.63235023 -0.39052039 -0.66904932 274.76063038
Axis -0.92384305 -0.24731042 -0.29214991
Axis point 0.00000000 120.62565732 71.41736433
Rotation angle (degrees) 145.56809476
Shift along axis -371.22978396
> fitmap #51 inMap #1
Fit molecule 20240711_copi_golph3_beta_Arf1_.cif (#51) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.007965, steps = 40
shifted from previous position = 0.0158
rotated from previous position = 0.0445 degrees
atoms outside contour = 559, contour level = 0.0054608
Position of 20240711_copi_golph3_beta_Arf1_.cif (#51) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.62717948 0.37536024 0.68245922 225.37524868
-0.03825161 -0.86031031 0.50833354 253.00868258
0.77793490 -0.34492153 -0.52521084 258.41418396
Axis -0.89532324 -0.10018293 -0.43400422
Axis point 0.00000000 129.63691056 43.56713286
Rotation angle (degrees) 151.54250251
Shift along axis -339.28369878
> fitmap #52 inMap #1
Fit molecule 20240711_copi_golph3_gamma_Arf1_.cif (#52) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.01044, steps = 84
shifted from previous position = 0.032
rotated from previous position = 0.0719 degrees
atoms outside contour = 392, contour level = 0.0054608
Position of 20240711_copi_golph3_gamma_Arf1_.cif (#52) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.55783285 0.36551831 -0.74513010 335.04867435
0.54045417 0.84133441 0.00810603 166.90739297
0.62986650 -0.39818686 -0.66686987 272.93165463
Axis -0.28128830 -0.95194984 0.12111314
Axis point 75.68867820 0.00000000 208.33038989
Rotation angle (degrees) 133.76357273
Shift along axis -220.07712654
> fitmap #53 inMap #1
Fit molecule 20240711_copi_golph3_third_Arf1.cif (#53) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1350 atoms
average map value = 0.006839, steps = 48
shifted from previous position = 0.00299
rotated from previous position = 0.0179 degrees
atoms outside contour = 557, contour level = 0.0054608
Position of 20240711_copi_golph3_third_Arf1.cif (#53) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.73571856 0.66852635 0.10858508 227.55132607
0.67433984 -0.70810015 -0.20942768 323.63250252
-0.06311881 0.22730308 -0.97177638 187.14042400
Axis 0.93058498 0.36586629 0.01238737
Axis point 0.00000000 105.38358680 104.96924755
Rotation angle (degrees) 166.42877878
Shift along axis 332.48024794
> fitmap #55 inMap #1
Fit molecule 20240711_copi_golph3_golph3_.cif (#55) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 1971 atoms
average map value = 0.008363, steps = 44
shifted from previous position = 0.0108
rotated from previous position = 0.00908 degrees
atoms outside contour = 616, contour level = 0.0054608
Position of 20240711_copi_golph3_golph3_.cif (#55) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.52175848 0.47050138 0.71161545 230.53217799
0.01176338 -0.83804772 0.54547012 257.45975389
0.85301214 -0.27623265 -0.44279319 262.85417733
Axis -0.86345476 -0.14858128 -0.48204718
Axis point 0.00000000 121.70495834 37.26275203
Rotation angle (degrees) 151.58706973
Shift along axis -364.01592063
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_final.cxs"
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> show #!26.2 models
> hide #!26.2 models
> show #!29 models
> hide #!29 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!19 models
> show #!18 models
> hide #!19 models
> hide #!18 models
> show #!13 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #41 models
> hide #42 models
> hide #47 models
> show #47 models
> hide #!54 models
> hide #55 models
> hide #38 models
> hide #39 models
> hide #53 models
> show #53 models
> hide #52 models
> show #52 models
> hide #52 models
> show #52 models
> hide #51 models
> hide #!13 models
> hide #!43 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #38 models
> show #39 models
> show #41 models
> show #42 models
> show #!43 models
> show #51 models
> show #!54 models
> show #55 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_final.cxs"
[Repeated 1 time(s)]
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Reference structures/emd_3720_2017_leaf.map"
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.226, step 1, values float32
> color #56 #ebebebff models
> select add #56
2 models selected
> volume #56 level 0.1086
> ui mousemode right "translate selected models"
> view matrix models #56,1,0,0,51.457,0,1,0,21.433,0,0,1,260.83
> view matrix models #56,1,0,0,189.96,0,1,0,166,0,0,1,244.2
> view matrix models #56,1,0,0,216.08,0,1,0,189.21,0,0,1,215.66
> ui mousemode right "rotate selected models"
> view matrix models
> #56,-0.87728,0.47929,0.025732,368.35,-0.21391,-0.43841,0.87295,282.24,0.42968,0.76032,0.48713,136.71
> fitmap #56 inMap #1
Fit map emd_3720_2017_leaf.map in map relion_locres_filtered_20240326_GT.mrc
using 99958 points
correlation = 0.5332, correlation about mean = 0.05426, overlap = 74.42
steps = 144, shift = 15.2, angle = 12.9 degrees
Position of emd_3720_2017_leaf.map (#56) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.90915636 0.40926168 0.07706874 310.78139643
-0.21592730 -0.62148653 0.75308027 244.94933932
0.35610408 0.66802647 0.65339920 44.26322602
Axis -0.12328500 -0.40446016 -0.90620792
Axis point 169.37967541 84.23413949 0.00000000
Rotation angle (degrees) 159.82138625
Shift along axis -177.49862073
> ui mousemode right "rotate selected models"
> view matrix models
> #56,0.028586,0.99946,0.016018,204.25,-0.69926,0.0085431,0.71482,305.01,0.7143,-0.031634,0.69912,158.33
> fitmap #56 inMap #1
Fit map emd_3720_2017_leaf.map in map relion_locres_filtered_20240326_GT.mrc
using 99958 points
correlation = 0.5732, correlation about mean = 0.05181, overlap = 74.18
steps = 216, shift = 16.7, angle = 26.2 degrees
Position of emd_3720_2017_leaf.map (#56) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.14815005 0.98893922 -0.00712591 129.99058546
-0.92169370 0.14068110 0.36151011 287.97813152
0.35851401 -0.04698983 0.93234096 80.90258523
Axis -0.20551046 -0.18394820 -0.96121200
Axis point 206.90335990 79.49737141 0.00000000
Rotation angle (degrees) 83.65090012
Shift along axis -157.45201883
> view matrix models
> #56,0.81181,0.50827,0.28746,140.28,-0.55069,0.50271,0.66635,242.95,0.19417,-0.69925,0.688,282.81
> fitmap #56 inMap #1
Fit map emd_3720_2017_leaf.map in map relion_locres_filtered_20240326_GT.mrc
using 99958 points
correlation = 0.5782, correlation about mean = 0.05654, overlap = 72.54
steps = 184, shift = 11.1, angle = 13.7 degrees
Position of emd_3720_2017_leaf.map (#56) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.79081078 0.58143750 0.19117727 89.38509923
-0.58500230 0.62618736 0.51542379 168.56102034
0.17997393 -0.51944183 0.83533799 176.11718788
Axis -0.66364076 0.00718450 -0.74801693
Axis point 203.46435974 136.15873957 0.00000000
Rotation angle (degrees) 51.23202796
Shift along axis -189.84720692
> view matrix models
> #56,-0.83504,0.54577,0.069577,354.99,-0.34302,-0.61532,0.70973,342.82,0.43016,0.56879,0.70103,110.03
> fitmap #56 inMap #1
Fit map emd_3720_2017_leaf.map in map relion_locres_filtered_20240326_GT.mrc
using 99958 points
correlation = 0.5284, correlation about mean = 0.07061, overlap = 73.11
steps = 124, shift = 3.19, angle = 3.81 degrees
Position of emd_3720_2017_leaf.map (#56) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.87267930 0.47932627 0.09315128 299.02701674
-0.27622892 -0.64192017 0.71528740 259.36655497
0.40265173 0.59848543 0.69259423 35.62977534
Axis -0.14161228 -0.37524252 -0.91604531
Axis point 169.69435247 90.03733869 0.00000000
Rotation angle (degrees) 155.64427649
Shift along axis -172.30974707
> view matrix models
> #56,-0.31115,0.95004,0.024789,250.19,-0.80196,-0.27647,0.52955,373.37,0.50994,0.14489,0.84792,135.75
> ui mousemode right "translate selected models"
> view matrix models
> #56,-0.31115,0.95004,0.024789,225.77,-0.80196,-0.27647,0.52955,368.63,0.50994,0.14489,0.84792,152.32
> fitmap #56 inMap #1
Fit map emd_3720_2017_leaf.map in map relion_locres_filtered_20240326_GT.mrc
using 99958 points
correlation = 0.6869, correlation about mean = 0.2749, overlap = 157.2
steps = 236, shift = 22.7, angle = 34.9 degrees
Position of emd_3720_2017_leaf.map (#56) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.53804556 0.84152368 -0.04842391 217.98901816
-0.84278716 -0.53807848 0.01346669 404.62940756
-0.01472333 0.04805674 0.99873609 145.40110324
Axis 0.02052818 -0.02000031 -0.99958921
Axis point 220.49314606 140.31883812 0.00000000
Rotation angle (degrees) 122.59477625
Shift along axis -148.95916903
> select subtract #56
Nothing selected
> volume #56 level 0.1553
> fitmap #56 inMap #1
Fit map emd_3720_2017_leaf.map in map relion_locres_filtered_20240326_GT.mrc
using 58464 points
correlation = 0.7124, correlation about mean = 0.2183, overlap = 126.6
steps = 48, shift = 0.054, angle = 0.0916 degrees
Position of emd_3720_2017_leaf.map (#56) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.53769722 0.84167956 -0.04957021 218.02664044
-0.84301410 -0.53769614 0.01449435 404.48271442
-0.01445412 0.04958195 0.99866546 145.17220156
Axis 0.02081826 -0.02083516 -0.99956615
Axis point 220.50989620 140.13520956 0.00000000
Rotation angle (degrees) 122.57233532
Shift along axis -148.99774609
> open "/Users/becca/Desktop/Postdoc/Structure files/COPI
> structures/5nzr_COPI_coat_leaf_2017.cif"
5nzr_COPI_coat_leaf_2017.cif title:
The structure of the COPI coat leaf [more info...]
Chain information for 5nzr_COPI_coat_leaf_2017.cif #57
---
Chain | Description | UniProt
A | Coatomer subunit alpha | COPA_MOUSE 1-1224
B | Coatomer subunit beta | COPB_MOUSE 16-968
C | Coatomer subunit beta' | COPB2_MOUSE 1-905
D | Coatomer subunit delta | COPD_MOUSE 1-511
F M R | ADP-ribosylation factor 1 | ARF1_YEAST 1-181
G K | Coatomer subunit gamma-1 | COPG1_MOUSE 1-874
L Z | Coatomer subunit zeta-1 | COPZ1_MOUSE 1-177
> select add #57
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> view matrix models #57,1,0,0,121.05,0,1,0,117.63,0,0,1,248.75
> view matrix models #57,1,0,0,188.14,0,1,0,202.34,0,0,1,265.38
> ui mousemode right "rotate selected models"
> view matrix models
> #57,-0.53664,0.8067,-0.24751,289.81,-0.76516,-0.58887,-0.2603,504.63,-0.35574,0.049695,0.93326,306.25
> ui mousemode right "translate selected models"
> view matrix models
> #57,-0.53664,0.8067,-0.24751,305.82,-0.76516,-0.58887,-0.2603,520.33,-0.35574,0.049695,0.93326,310.17
> view matrix models
> #57,-0.53664,0.8067,-0.24751,316.06,-0.76516,-0.58887,-0.2603,517.32,-0.35574,0.049695,0.93326,286.43
> fitmap #57 inMap #1
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#57) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 18970 atoms
average map value = 0.01164, steps = 192
shifted from previous position = 19.8
rotated from previous position = 19.8 degrees
atoms outside contour = 5803, contour level = 0.0054608
Position of 5nzr_COPI_coat_leaf_2017.cif (#57) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
-0.53780069 0.84149893 -0.05147785 218.34726608
-0.84289565 -0.53793379 0.01241606 404.81621695
-0.01724357 0.05006782 0.99859695 145.66655773
Axis 0.02234309 -0.02031511 -0.99954394
Axis point 220.87010415 140.20104413 0.00000000
Rotation angle (degrees) 122.58626121
Shift along axis -148.94545734
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #57 inMap #56
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#57) to map emd_3720_2017_leaf.map
(#56) using 18970 atoms
average map value = 0.2037, steps = 48
shifted from previous position = 0.242
rotated from previous position = 0.13 degrees
atoms outside contour = 4747, contour level = 0.15531
Position of 5nzr_COPI_coat_leaf_2017.cif (#57) relative to
emd_3720_2017_leaf.map (#56) coordinates:
Matrix rotation and translation
0.99999980 0.00000142 0.00063110 -0.06591244
-0.00000152 0.99999999 0.00016366 -0.04258127
-0.00063110 -0.00016366 0.99999979 0.08970355
Axis -0.25102649 0.96797759 -0.00225653
Axis point 142.01093826 0.00000000 114.37935577
Rotation angle (degrees) 0.03735560
Shift along axis -0.02487437
> fitmap #57 inMap #56
Fit molecule 5nzr_COPI_coat_leaf_2017.cif (#57) to map emd_3720_2017_leaf.map
(#56) using 18970 atoms
average map value = 0.2037, steps = 40
shifted from previous position = 0.0347
rotated from previous position = 0.00433 degrees
atoms outside contour = 4741, contour level = 0.15531
Position of 5nzr_COPI_coat_leaf_2017.cif (#57) relative to
emd_3720_2017_leaf.map (#56) coordinates:
Matrix rotation and translation
0.99999980 0.00003994 0.00063608 -0.06331889
-0.00004000 1.00000000 0.00009884 0.00276701
-0.00063608 -0.00009886 0.99999980 0.09022728
Axis -0.15326201 0.98624069 -0.06196826
Axis point 142.48451750 0.00000000 97.94240538
Rotation angle (degrees) 0.03695303
Shift along axis 0.00684209
> select subtract #57
Nothing selected
> hide #!1 models
> hide #!57 models
> show #!57 models
> hide #!57 models
> show #!57 models
> hide #55 models
> hide #!54 models
> hide #53 models
> hide #52 models
> hide #51 models
> hide #50 models
> hide #!49 models
> hide #48 models
> hide #47 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #42 models
> hide #41 models
> hide #39 models
> hide #38 models
> hide #!56 models
> show #38 models
> show #39 models
> show #!56 models
> hide #!56 models
> show #!56 models
> show #!1 models
> hide #!1 models
> hide #!56 models
> hide #38 models
> hide #39 models
> show #41 models
> show #42 models
> show #!1 models
> hide #!1 models
> hide #41 models
> hide #42 models
> show #!43 models
> show #!44 models
> show #!45 models
> show #!56 models
> color #56 #ebebeb68 models
> color #56 #ebebeb69 models
> show #!1 models
> color #1 #76d6ffff models
> color #1 #76d6ffa1 models
> hide #!1 models
> hide #!56 models
> show #!1 models
> show #41 models
> show #42 models
> show #39 models
> show #38 models
> show #!46 models
> show #47 models
> show #48 models
> show #!49 models
> show #!56 models
> hide #!1 models
> hide #!56 models
> hide #!49 models
> hide #48 models
> hide #47 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #42 models
> hide #41 models
> hide #39 models
> hide #38 models
> show #!43 models
> show #!44 models
> show #!45 models
> hide #!45 models
> show #!45 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> show #!46 models
> show #!1 models
> volume #1 level 0.003895
> hide #!1 models
> show #!56 models
> hide #!56 models
> show #!1 models
> show #!56 models
> hide #!56 models
> hide #!1 models
> hide #!46 models
> show #47 models
> show #48 models
> show #!49 models
> hide #!49 models
> hide #48 models
> hide #47 models
> show #50 models
> hide #50 models
> show #!54 models
> hide #!54 models
> show #!54 models
> show #55 models
> show #38 models
> show #39 models
> show #50 models
> show #41 models
> hide #41 models
> show #42 models
> hide #42 models
> show #!44 models
> hide #!44 models
> show #!45 models
> hide #!45 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #41 models
> hide #41 models
> show #47 models
> show #48 models
> show #!43 models
> show #!44 models
> hide #48 models
> hide #47 models
> hide #!44 models
> hide #!43 models
> hide #38 models
> hide #39 models
> hide #50 models
> hide #!54 models
> hide #55 models
> hide #!57 models
> show #!56 models
> show #!1 models
> volume #1 level 0.005983
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #1 darkgrey models
> hide #!56 models
> show #55 models
> show #!54 models
> show #53 models
> show #52 models
> show #51 models
> show #50 models
> show #!49 models
> show #48 models
> show #47 models
> show #!46 models
> show #!45 models
> show #!44 models
> show #!43 models
> show #42 models
> show #41 models
> show #39 models
> show #38 models
> save "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240805_leaf_fitting_AF3_final_with_2017comp.cxs"
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240805_COPI_leaf_fitting_AF3_final.cxs"
> volume #1 level 0.006
> save /Users/becca/Desktop/image1.png supersample 3
> volume #1 level 0.004985
> volume #1 level 0.005
> save /Users/becca/Desktop/image2.png supersample 3
> volume #1 level 0.0006
> volume #1 level 0.006
> volume #1 level 0.007
> volume #1 level 0.005
> save /Users/becca/Desktop/image3.png supersample 3
> save /Users/becca/Desktop/image4.png supersample 3
> volume #1 level 0.007
> volume #1 level 0.008
> save /Users/becca/Desktop/image5.png supersample 3
> save /Users/becca/Desktop/image6.png supersample 3
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> lighting soft
> lighting full
> graphics silhouettes false
> lighting shadows false
> lighting simple
> set bgColor white
> surface dust #1 size 17.1
> volume #!1 style surface
> volume #!1 style mesh
[Repeated 1 time(s)]
> volume #!1 style surface
> volume #!1 showOutlineBox true
> volume #!1 showOutlineBox false
> volume #!1 showOutlineBox true
> volume #!1 showOutlineBox false
> set bgColor white
> lighting simple
> save /Users/becca/Desktop/image1.png supersample 3
> graphics silhouettes true
> save /Users/becca/Desktop/image1.png supersample 3
[Repeated 1 time(s)]
> volume #1 level 0.005
> save /Users/becca/Desktop/image1.png supersample 3
[Repeated 1 time(s)]
> volume #1 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT.mrc as #58, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 2, values float32
> select add #58
2 models selected
> view matrix models #58,1,0,0,64.329,0,1,0,76.949,0,0,1,20.463
> view matrix models #58,1,0,0,68.607,0,1,0,91.17,0,0,1,74.656
> fitmap #58 inMap #1
Fit map relion_locres_filtered_20240326_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30918 points
correlation = 0.6038, correlation about mean = 0.1653, overlap = 1.453
steps = 84, shift = 5.22, angle = 2.66 degrees
Position of relion_locres_filtered_20240326_GT.mrc (#58) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99895433 -0.00859686 -0.04490377 18.37182947
0.00961465 0.99970062 0.02249936 1.28166739
0.04469690 -0.02290757 0.99873792 -9.26075418
Axis -0.44478721 -0.87769046 0.17839225
Axis point 171.87024853 0.00000000 296.68672427
Rotation angle (degrees) 2.92584492
Shift along axis -10.94850867
> view matrix models
> #58,0.999,-0.021218,-0.039478,80.16,0.021704,0.99969,0.011922,65.861,0.039213,-0.012766,0.99915,66.634
> fitmap #58 inMap #1
Fit map relion_locres_filtered_20240326_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30918 points
correlation = 1, correlation about mean = 1, overlap = 3.367
steps = 124, shift = 2.8, angle = 2.92 degrees
Position of relion_locres_filtered_20240326_GT.mrc (#58) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 -0.00010768 -0.00013271 0.06368984
0.00010767 0.99999999 -0.00005201 -0.02406001
0.00013271 0.00005200 0.99999999 -0.05210822
Axis 0.29111674 -0.74291984 0.60276128
Axis point 415.41817640 0.00000000 468.90051984
Rotation angle (degrees) 0.01023486
Shift along axis 0.00500702
> volume #58 level 0.008
> color #58 silver models
> color #58 white models
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> color zone #58 near #38 distance 10.26
> hide #!1 models
> select subtract #58
Nothing selected
> color zone #58 near #38 distance 10.93
> color zone #58 near #38 distance 4.35
> color zone #58 near #38 distance 5.21
> color zone #58 near #38 distance 5.14
> color zone #58 near #39 distance 5.14
> volume splitbyzone #58
Opened relion_locres_filtered_20240326_GT.mrc 0 as #59.1, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc 1 as #59.2, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
> hide #!59.2 models
> show #!59.2 models
> hide #!59.1 models
> show #!59.1 models
> hide #!59.2 models
> show #!59.2 models
> color zone #58 near #38 distance 5.14
[Repeated 1 time(s)]
> color zone #59.1 near #38 distance 10.26
[Repeated 1 time(s)]
> color zone #59.1 near #41 distance 9.26
> color zone #59.1 near #41 distance 9.16
> color zone #59.1 near #41 distance 9.06
> color zone #59.1 near #41 distance 8.96
> color zone #59.1 near #41 distance 8.86
> color zone #59.1 near #41 distance 8.76
> color zone #59.1 near #41 distance 8.66
> color zone #59.1 near #41 distance 8.56
> color zone #59.1 near #41 distance 8.46
> color zone #59.1 near #41 distance 8.36
> color zone #59.1 near #41 distance 8.26
> color zone #59.1 near #41 distance 8.16
> color zone #59.1 near #41 distance 8.06
> color zone #59.1 near #41 distance 7.96
> color zone #59.1 near #38 distance 7.96
> help help:user/tools/colorzone.html
> close #59.1
> close #59
> show #!58 models
> color zone #58 near #38 distance 5.14
> color zone #58 near #39 distance 5.14
> combine #38 #39 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'G'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'H'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'I'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'J'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'K'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'L'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'M'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'N'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'O'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'P'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Q'
> hide #!59 models
> show #!59 models
> hide #55 models
> hide #!54 models
> hide #53 models
> hide #52 models
> hide #51 models
> hide #50 models
> hide #!49 models
> hide #48 models
> hide #47 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #42 models
> hide #41 models
> hide #39 models
> hide #38 models
> hide #!58 models
> color zone #58 near #59 distance 5.14
> show #!58 models
> hide #!59 models
> color zone #58 near #59 distance 4.97
> color zone #58 near #59 distance 4.45
> surface dust #58 size 17.1
> color zone #58 near #59 distance 4.31
> color zone #58 near #59 distance 4.7
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #58 step 1
> volume #58 level 0.005
> color zone #58 near #59 distance 5.19
> set bgColor white
> save /Users/becca/Desktop/image1.png supersample 3
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> volume #58 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
> volume #58 level 0.005
> color zone #58 near #59 distance 5.43
> color zone #58 near #59 distance 6.99
> save /Users/becca/Desktop/image1.png supersample 3
> volume #58 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
> hide #!58 models
> show #!59 models
> rename #59 combined_model_COPI_GOLPH3
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v1.cxs"
> show #!1 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v1.cxs"
> hide #!59 models
> show #!58 models
> hide #!1 models
> volume #58 level 0.005
> ui mousemode right "map eraser"
> volume erase #58 center 281.84,261.87,305.71 radius 22.725
Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> surface dust #61 size 17.1
> color zone #61 near #59 distance 10.26
> color zone #61 near #59 distance 10.16
> color zone #61 near #59 distance 6.84
> save /Users/becca/Desktop/image1.png supersample 3
> volume #61 level 0.008
> save /Users/becca/Desktop/image2.png supersample 3
> volume #61 level 0.005
> save /Users/becca/Desktop/image3.png supersample 3
> volume #61 level 0.008
> save /Users/becca/Desktop/image4.png supersample 3
> color zone #61 near #59 distance 4.76
> color zone #61 near #59 distance 4.4
> color zone #61 near #59 distance 5.99
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!61 models
> show #!1 models
> color #1 #a9a9a9a0 models
> hide #!1 models
> color #1 #a9a9a9a1 models
> show #!1 models
> show #!57 models
> hide #!57 models
> show #!59 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right select
> select #59/O:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 6 atom styles
> show #!1 models
> hide #!1 models
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #59/O:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #59/O:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #59/O:106
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #59/Q:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> select #59/Q:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #59/Q:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #59/Q:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #59/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select clear
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #59/Q:226@CB
1 atom, 1 residue, 1 model selected
> select #59/Q:226@CA
1 atom, 1 residue, 1 model selected
> select #59/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #59/O:107@NZ
1 atom, 1 residue, 1 model selected
> select #59/Q:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/O:106@CG
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #59/O:106
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #59/O:108@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> undo
> select #59/O:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #59/Q:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> select #59/M:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #59/M:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/M:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/M:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:5
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #59/M:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #59/M:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:8
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1
2 models selected
> select #59/M:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1
2 models selected
> select #1
2 models selected
> select clear
> select #1
2 models selected
> select clear
> select #59/M:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:13
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:14
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:15
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/K:255
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:254
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:250
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:249
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"
> show #!61 models
> hide #!1 models
> color zone #61 near #59 distance 5.86
> color zone #61 near #59 distance 5.55
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"
——— End of log from Tue Aug 6 15:17:45 2024 ———
opened ChimeraX session
> hide #!61 models
> show #!61 models
> hide #!59 models
> show #!59 models
> hide #!61 models
> show #!58 models
> hide #!58 models
> show #!58 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!61 models
> show #!56 models
> hide #!56 models
> show #!57 models
> close #61
> combine #1
No structures specified
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT.mrc as #60, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 2, values float32
> select add #60
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #60,1,0,0,94.293,0,1,0,59.794,0,0,1,17.203
> view matrix models #60,1,0,0,87.011,0,1,0,46.591,0,0,1,75.712
> view matrix models #60,1,0,0,62.484,0,1,0,72.607,0,0,1,72.836
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #60 inMap #1
Fit map relion_locres_filtered_20240326_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30918 points
correlation = 1, correlation about mean = 1, overlap = 3.365
steps = 92, shift = 5.1, angle = 0.971 degrees
Position of relion_locres_filtered_20240326_GT.mrc (#60) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00004012 -0.00014956 0.04461249
-0.00004012 1.00000000 0.00001176 -0.00027160
0.00014956 -0.00001176 0.99999999 -0.04335390
Axis -0.07572659 -0.96307673 -0.25835770
Axis point 275.92599265 0.00000000 302.35452588
Rotation angle (degrees) 0.00889794
Shift along axis 0.00808403
> select subtract #60
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #60 step 1
> volume #60 level 0.005
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v5.cxs"
> color #24 #98fcffff
> color #24 label_red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #24 alphav1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color name label_red #E32723
Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723
> color name label_purple #6C4896
Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896
> color name arf1v2 #EB70A8
Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8
> color name alphav1 #5786F5
Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5
> color name alphav2 #2A4B9B
Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b
> color name betapv1 #53EAF3
Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3
> color name betapv2 #759ED9
Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9
> color name betav1 #37863D
Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d
> color name betav2 #207B35
Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35
> color name deltav1 #CE8041
Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041
> color name deltav2 #E97408
Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408
> color name epsilonv1 #F06969
Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969
> color name gammav1 #2AFF3C
Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c
> color name gammav2 #61B230
Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230
> color name zetav1 #E0C819
Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819
> color name zetav2 #EFE30C
Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c
> color name arf1v1 #FF76AF
Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af
> color #24 label_red
> color #60 white models
> color #56 white models
> hide #!57 models
> hide #!58 models
> hide #!59 models
> color #38 alphav1
> show #38 models
> hide #!60 models
> show #39 models
> show #41 models
> show #42 models
> show #!43 models
> show #!44 models
> show #!45 models
> show #!46 models
> show #48 models
> show #47 models
> show #!49 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #!54 models
> color #39 alphav1
> color #41 betapv1
> color #42 betapv1
> color #43 betav1
> color #44 betav1
> color #45 betav1
> color #46 deltav1
> color #47 gammav1
> color #47 gammav2
> color #48 gammav2
> color #49 gammav2
> color #43 betav2
> color #44 betav2
> color #45 betav2
> color #50 zetav1
> color #51 arf1v1
> color #52 arf1v1
> color #53 arf1v1
> color #47 #acacacff
> color #47 gammav2
> color #47 #61db30ff
> color #47 #61c730ff
> color #47 #58c730ff
> color #47 #58de30ff
> color name gammav3 #58DE30
Color 'gammav3' is opaque: rgb(34.5%, 87.1%, 18.8%) hex: #58de30
> color #48 gammav3
> color #49 gammav3
> color #51 arf1v2
> color #52 arf1v2
> color #53 arf1v2
> color #38 alphav1
> color #38 alphav2
> color #39 alphav2
> color #54 label_purple
> color #55 label_purple
> show #55 models
> color #11 #801effff
> color #11 #801ed1ff
> color name label_purplev2 #7F1ED1
Color 'label_purplev2' is opaque: rgb(49.8%, 11.8%, 82%) hex: #7f1ed1
> color #54 label_purplev2
> color #55 label_purplev2
> combine #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54
> #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'D' in fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif
#40 to 'I'
Remapping chain ID 'E' in fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif
#40 to 'J'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_M1-S586.cif #41 to
'K'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'L'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'M'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'N'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'O'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'P'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'Q'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'R'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'S'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'T'
Remapping chain ID 'B' in 20240711_copi_golph3_beta_Arf1_.cif #51 to 'U'
Remapping chain ID 'C' in 20240711_copi_golph3_gamma_Arf1_.cif #52 to 'V'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'W'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_M1-.cif #54 to 'X'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Y'
> hide #38 models
> hide #39 models
> hide #41 models
> hide #42 models
> hide #!43 models
> hide #!44 models
> hide #!45 models
> hide #!46 models
> hide #47 models
> hide #48 models
> hide #!49 models
> hide #50 models
> hide #51 models
> hide #52 models
> hide #53 models
> hide #!54 models
> hide #55 models
> rename #59 combined_model_COPI_GOLPH3_colorset1
> rename #58 relion_locres_filtered_20240326_GT_colorset1.mrc
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!60 models
> color zone #60 near #61 distance 10.26
> color zone #60 near #61 distance 10.73
> color zone #60 near #61 distance 4.91
> volume #60 level 0.01316
> close #61
> combine #38 #39 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'G'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'H'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'I'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'J'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'K'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'L'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'M'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'N'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'O'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'P'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Q'
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #60 near #61 distance 4.91
> hide #!60 models
> ui mousemode right select
> select #61/K:255
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:254
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #61/K:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select clear
> select #61/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:250
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:249
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete sel
> show #!60 models
> color single #60
> color zone #60 near #61 distance 4.91
> volume #60 level 0.008979
> color zone #60 near #61 distance 4.85
> color zone #60 near #61 distance 6.64
> color #1 #ebebebff models
> color #1 #d6d6d6ff models
> volume #60 level 0.008
> hide #!61 models
> rename #61 combine_model_COPI_GOLPH3_colorset2
> rename #60 relion_locres_filtered_20240326_GT_colorset2.mrc
> save /Users/becca/Desktop/image1.png supersample 3
> color #1 #d6d6d6cc models
> color #1 #d6d6d69a models
> color #1 #d6d6d699 models
> show #!1 models
> hide #!60 models
> show #!61 models
> save /Users/becca/Desktop/image2.png supersample 3
> save /Users/becca/Desktop/image3.png supersample 3
> hide #!61 models
> show #!60 models
> hide #!1 models
> save /Users/becca/Desktop/image4.png supersample 3
> color #60 #ffffffb9 models
> color #60 #ffffffb7 models
> color zone #60 near #61 distance 6.64
> color #60 #ffffffb8 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v6.cxs"
> hide #!60 models
> show #!61 models
> color #61/chain Q label_purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #61/chainQ label_purple
> color #61/chainP label_purple
> color #61/chainP blue
> color #61/P blue
> undo
> color #61/Q label_purple
> color #61/R label_purple
> color #61/p label_purple
> undo
> color #61/o label_purple
> undo
> color #61/a label_purple
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32
> color #62 white models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #62 step 1
> volume #62 level 0.008
> select add #62
2 models selected
> show #!60 models
> ui mousemode right "translate selected models"
> view matrix models #62,1,0,0,82.731,0,1,0,56.524,0,0,1,33.509
> view matrix models #62,1,0,0,79.094,0,1,0,68.742,0,0,1,76.061
> view matrix models #62,1,0,0,75.329,0,1,0,66.28,0,0,1,82.958
> view matrix models #62,1,0,0,62.569,0,1,0,73.325,0,0,1,77.393
> fitmap #62 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 1, correlation about mean = 1, overlap = 21.45
steps = 52, shift = 2.4, angle = 0.977 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#62) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00001875 -0.00002627 0.01893074
0.00001875 1.00000000 -0.00002003 -0.00224731
0.00002628 0.00002003 1.00000000 0.00132667
Axis 0.52718994 -0.69167549 0.49361502
Axis point 178.51353821 0.00000000 475.91658522
Rotation angle (degrees) 0.00217651
Shift along axis 0.01218937
> select subtract #62
Nothing selected
> color zone #62 near #61 distance 10.26
> hide #!60 models
> hide #!61 models
> surface dust #62 size 17.1
> show #!60 models
> surface dust #60 size 17.1
> surface dust #62 size 17.1
> hide #!62 models
> hide #!60 models
> show #!62 models
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image6.png supersample 3
> hide #!1 models
> show #!1 models
> save /Users/becca/Desktop/image7.png supersample 3
> hide #!1 models
> hide #!61 models
> show #!62 models
> save /Users/becca/Desktop/image8.png supersample 3
> save /Users/becca/Desktop/image9.png supersample 3
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image10.png supersample 3
> hide #!1 models
> color #61/b gammav2
> color #61/c gammav2
> color #61/d gammav2
> color #61/e gammav2
> color #61/f gammav2
> color #61/g gammav2
> color #61/f betapv2
> color #61/g betapv2
> color #61/h gammav2
> color #61/i gammav2
> color #61/j gammav2
> color #61/k gammav2
> color #61/l gammav2
> color #61/m gammav2
> color #61/n gammav2
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32
> color #63 white models
> select add #63
2 models selected
> view matrix models #63,1,0,0,75.253,0,1,0,55.49,0,0,1,11.12
> view matrix models #63,1,0,0,90.631,0,1,0,59.745,0,0,1,63.045
> view matrix models #63,1,0,0,68.515,0,1,0,55.118,0,0,1,78.162
> view matrix models #63,1,0,0,66.634,0,1,0,67.567,0,0,1,67.24
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #63 step 1
> volume #63 level 0.008
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 0.5415, correlation about mean = 0.1363, overlap = 7.061
steps = 116, shift = 7.07, angle = 5.74 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99362306 0.08167924 -0.07772850 -0.92565197
-0.08058175 0.99660031 0.01715800 10.92285128
0.07886570 -0.01078508 0.99682691 -23.17442071
Axis -0.12297538 -0.68915930 -0.71409839
Axis point 213.07603457 14.21459699 0.00000000
Rotation angle (degrees) 6.52360209
Shift along axis 9.13506435
> show #!1 models
> view matrix models
> #63,0.99499,0.069158,-0.072244,60.427,-0.06889,0.99761,0.0061881,84.855,0.072498,-0.0011802,0.99737,52.494
> view matrix models
> #63,0.99499,0.069158,-0.072244,61.276,-0.06889,0.99761,0.0061881,84.838,0.072498,-0.0011802,0.99737,55.066
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> hide #!61 models
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 0.5415, correlation about mean = 0.1362, overlap = 7.06
steps = 64, shift = 3.65, angle = 0.0144 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99360075 0.08181777 -0.07786785 -0.90541724
-0.08073064 0.99659074 0.01701358 11.00212074
0.07899439 -0.01061838 0.99681851 -23.23121300
Axis -0.12141808 -0.68927119 -0.71425687
Axis point 213.54257878 14.23471065 0.00000000
Rotation angle (degrees) 6.53375156
Shift along axis 9.11954274
> view matrix models
> #63,0.99497,0.069297,-0.072381,72.42,-0.069041,0.9976,0.006042,87.797,0.072626,-0.0010144,0.99736,54.674
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 1, correlation about mean = 1, overlap = 21.46
steps = 152, shift = 9.34, angle = 6.54 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00003458 0.00000150 0.00697228
0.00003458 1.00000000 -0.00002441 0.00466924
-0.00000150 0.00002441 1.00000000 -0.01150830
Axis 0.57631042 0.03541164 0.81646330
Axis point -140.35346721 288.49393815 0.00000000
Rotation angle (degrees) 0.00242674
Shift along axis -0.00521256
> select subtract #63
Nothing selected
> hide #!1 models
> show #!62 models
> hide #!62 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> color zone #63 near #61 distance 10.26
> color zone #63 near #61 distance 10.66
> color zone #63 near #61 distance 8.31
> surface dust #63 size 17.1
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> save /Users/becca/Desktop/image1.png supersample 3
> hide #!63 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image2.png supersample 3
> save /Users/becca/Desktop/image3.png supersample 3
> hide #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!61 models
> show #!63 models
> save /Users/becca/Desktop/image4.png supersample 3
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!63 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image6.png supersample 3
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_02_final_volume.mrc"
Opened cryosparc_P126_J2191_class_02_final_volume.mrc as #64, grid size
180,180,180, pixel 2.42, shown at level 0.333, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_01_final_volume.mrc"
Opened cryosparc_P126_J2191_class_01_final_volume.mrc as #65, grid size
180,180,180, pixel 2.42, shown at level 0.333, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_00_final_volume.mrc"
Opened cryosparc_P126_J2191_class_00_final_volume.mrc as #66, grid size
180,180,180, pixel 2.42, shown at level 0.337, step 1, values float32
> close #66
> close #65
> close #64
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"
——— End of log from Fri Aug 9 13:21:55 2024 ———
opened ChimeraX session
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"
> includeMaps true
——— End of log from Wed Sep 25 22:56:27 2024 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!62 models
> hide #!1 models
> hide #!61 models
> hide #!62 models
> show #!63 models
> save /Users/becca/Desktop/image1.png supersample 3
> save /Users/becca/Desktop/image2.png supersample 3
> hide #!63 models
> show #!1 models
> show #!61 models
> save /Users/becca/Desktop/image3.png supersample 3
> hide #!1 models
> ui mousemode right select
> select #61/O:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel red
> select #61/O:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel red
> select #61/O:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel red
> select #61/O:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #61/O:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/C:68
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #61/O:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select #61/Q:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel red
> select #61/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel red
> select #61/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel red
> select #61/Q:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select clear
> select #61/Q:260
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/Q:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> show #!1 models
> select clear
> save /Users/becca/Desktop/image4.png supersample 3
> ui tool show "Side View"
> save /Users/becca/Desktop/image5.png supersample 3
> save /Users/becca/Desktop/image6.png supersample 3
> save /Users/becca/Desktop/image7.png supersample 3
> hide #!1 models
Drag select of 48 atoms, 66 residues, 43 bonds
> hide sel atoms
> select clear
> select #61/O:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/O:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/O:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel zetav2
> select #61/O:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel zetav2
> select #61/O:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel zetav2
> select #61/O:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel zetav2
> select #61/F:177
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel golph
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel golphv2
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel golph3v2
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel golph3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel purple
> select #61/F:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel golph3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel darkred purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel purple
> undo
> select clear
[Repeated 2 time(s)]
> select #61/Q:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel purple
> select #61/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel purple
> select #61/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel purple
> select #61/Q:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel purple
> select #61/Q:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 7 atom styles
> color sel red
> select #61/Q:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/Q:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select #61/Q:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/Q:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:194
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #61/Q:199
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:198
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel red
> select #61/D:136
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 10 atom styles
> color sel red
> select clear
> select #61/D:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 8 atom styles
> color sel red
> select #61/D:137
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> select #61/Q:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #61/Q:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select clear
> select #61/Q:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select #61/Q:175
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select #61/Q:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select #61/D:312
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #61/D:10
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #61/D:312
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #61/D:311
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/D:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel red
> select #61/D:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel red
> show #!1 models
> select clear
> save /Users/becca/Desktop/image8.png supersample 3
> save /Users/becca/Desktop/image9.png supersample 3
> hide #!1 models
> select #61/D:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel red
> show #!1 models
> select clear
> save /Users/becca/Desktop/image10.png supersample 3
> save /Users/becca/Desktop/image11.png supersample 3
> hide #!1 models
> select #61/A:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/A:12
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #61/A:13
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #61/A:14
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel red
> select #61/L:444
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/L:443
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/L:444
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/L:445
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel red
> select #61/L:441
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/L:442
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #61/L:440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #61/C:28
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #61/L:444
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/C:31
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #61/L:447
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select clear
> show #!1 models
> save /Users/becca/Desktop/image12.png supersample 3
> save /Users/becca/Desktop/image13.png supersample 3
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241009_COPI_leaf_AF3_for_figs_v8.cxs"
——— End of log from Wed Oct 9 16:21:15 2024 ———
opened ChimeraX session
> show #!62 models
> hide #!62 models
> show #!63 models
> hide #!63 models
> show #!33 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!40 models
> hide #!40 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241017_COPI_leaf_all_AF3_results_aligned.cxs"
> close #2
> close #5-6#3-4
> close #8#7,9
> close #10-12
> close #13-15
> close #16-18
> close #19-21
> close #22-23
> close #24
> close #26
> close #27
> close #28
> close #29
> close #30
> close #31
> close #32
> close #33
> close #35
> close #36
> close #37
> show #!40 models
> hide #!40 models
> show #!56 models
> hide #!56 models
> show #!57 models
> hide #!57 models
> ui tool show "Side View"
> show #!60 models
> hide #!60 models
> show #!58 models
> close #58
> show #!59 models
> hide #!1 models
> hide #!61 models
> hide #!59 models
> show #!61 models
> hide #!61 models
> show #!59 models
> close #59
> show #!60 models
> hide #!60 models
> show #!61 models
> show #!62 models
> hide #!62 models
> show #!63 models
> hide #!63 models
> hide #!61 models
> show #!62 models
> hide #!62 models
> show #!60 models
> hide #!60 models
> show #!62 models
> hide #!62 models
> show #!60 models
> hide #!60 models
> show #!63 models
> hide #!63 models
> show #!60 models
> close #60
> show #!61 models
> hide #!61 models
> show #!63 models
> hide #!63 models
> show #!61 models
> hide #!61 models
> show #!62 models
> show #!63 models
> hide #!63 models
> close #62
> show #!57 models
> show #!56 models
> hide #!56 models
> select #57/A
3251 atoms, 3250 bonds, 813 residues, 1 model selected
> color sel alphav2
> select #57/B
3198 atoms, 3193 bonds, 4 pseudobonds, 800 residues, 2 models selected
> color sel betav2
> select #57/C
3371 atoms, 3370 bonds, 843 residues, 1 model selected
> color sel betapv2
> select #57/D
706 atoms, 704 bonds, 1 pseudobond, 177 residues, 2 models selected
> color sel deltav2
> select #57/G
3190 atoms, 3188 bonds, 1 pseudobond, 798 residues, 2 models selected
> color sel gammav2
> select #57/K
2239 atoms, 2237 bonds, 1 pseudobond, 560 residues, 2 models selected
> color sel gammav2
> select #57/L
555 atoms, 554 bonds, 139 residues, 1 model selected
> color sel zetav2
> select #57/Z
555 atoms, 554 bonds, 139 residues, 1 model selected
> color sel zetav2
> select #57/F
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel arf1v2
> select #57/M
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel arf1v2
> select #57/R
635 atoms, 634 bonds, 159 residues, 1 model selected
> color sel arf1v2
> select add #57
18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected
> select subtract #57
Nothing selected
> hide #!57 models
> show #!56 models
> show #!57 models
> hide #!57 models
> hide #!56 models
> show #!61 models
> show #!63 models
> hide #!63 models
> show #!1 models
> show #!40 models
> hide #!40 models
> hide #!34 models
> show #!34 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241017_COPI_leaf_all_AF3_results_aligned.cxs"
——— End of log from Thu Oct 17 14:08:25 2024 ———
opened ChimeraX session
> ui tool show "Side View"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!61 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!61 atoms
> show #!57 models
> hide #!57 models
> show #!57 models
> volume #1 level 0.00726
> hide #!57 models
> hide #!34 models
> show #!34 models
> show #34.1 models
> show #34.2 models
> show #34.3 models
> show #34.4 models
> show #34.5 models
> show #34.6 models
> show #34.7 models
> show #34.8 models
> show #34.9 models
> hide #34.9 models
> hide #34.7 models
> hide #34.8 models
> hide #34.6 models
> hide #34.5 models
> hide #34.4 models
> hide #34.3 models
> hide #34.2 models
> hide #34.1 models
> hide #!34 models
> color list
19 custom colors: alphav1
, alphav2
, arf1v1
, arf1v2
, betapv1
, betapv2
, betav1
, betav2
, deltav1
, deltav2
, epsilonv1
, gammav1
, gammav2
, gammav3
, label_purple
, label_purplev2
, label_red
, zetav1
, and zetav2
.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> show #!54 models
> select add #54
229 atoms, 228 bonds, 31 residues, 1 model selected
> select subtract #54
Nothing selected
> show #55 models
> hide #55 models
> hide #!54 models
> select #61/A
229 atoms, 228 bonds, 31 residues, 1 model selected
> color sel label_purple
> select #61/B
1350 atoms, 1373 bonds, 167 residues, 1 model selected
> color sel arf1v2
> select #61/C
1350 atoms, 1373 bonds, 167 residues, 1 model selected
> color sel arf1v2
> select #61/C
1350 atoms, 1373 bonds, 167 residues, 1 model selected
> select #61/D
4763 atoms, 4880 bonds, 591 residues, 1 model selected
> color sel alphav2
> select #61/E
1856 atoms, 1891 bonds, 233 residues, 1 model selected
> color sel alphav2
> select #61/E
1856 atoms, 1891 bonds, 233 residues, 1 model selected
> select #61/G
2009 atoms, 2048 bonds, 252 residues, 1 model selected
> color sel betapv2
> select #61/H
1872 atoms, 1904 bonds, 243 residues, 1 model selected
> color sel betav2
> select #61/G
2009 atoms, 2048 bonds, 252 residues, 1 model selected
> color sel betapv2
> select #61/F
4686 atoms, 4798 bonds, 586 residues, 1 model selected
> color sel betapv2
> select #61/H
1872 atoms, 1904 bonds, 243 residues, 1 model selected
> color sel betav2
> select #61/I
2488 atoms, 2518 bonds, 1 pseudobond, 313 residues, 2 models selected
> color sel betav2
> select #61/J
2879 atoms, 2928 bonds, 1 pseudobond, 362 residues, 2 models selected
> color sel betav2
> select #61/K
1626 atoms, 1645 bonds, 1 pseudobond, 201 residues, 2 models selected
> color sel deltav2
> select #61/L
1163 atoms, 1177 bonds, 149 residues, 1 model selected
> color sel gammav3
> select #61/M
2333 atoms, 2372 bonds, 299 residues, 1 model selected
> color sel gammav3
> select #61/M
2333 atoms, 2372 bonds, 299 residues, 1 model selected
> color sel gammav3
> select #61/N
1064 atoms, 1080 bonds, 1 pseudobond, 135 residues, 2 models selected
> color sel gammav3
> select #61/O
1200 atoms, 1218 bonds, 150 residues, 1 model selected
> color sel zetav2
> select #61/O
1200 atoms, 1218 bonds, 150 residues, 1 model selected
> select #61/P
1350 atoms, 1373 bonds, 167 residues, 1 model selected
> color sel arf1v2
> select #61/Q
1971 atoms, 2002 bonds, 244 residues, 1 model selected
> color sel label_purple
> select add #61
34189 atoms, 34808 bonds, 4 pseudobonds, 4290 residues, 2 models selected
> select subtract #61
Nothing selected
> show #!63 models
> hide #!1 models
> hide #!61 models
> volume #63 level 0.005298
[Repeated 1 time(s)]
> volume #1 level 0.004804
> volume #1 level 0.005
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting soft
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> lighting full
> lighting simple
> show #!61 models
> volume #1 level 0.005
> save /Users/becca/Desktop/image1.png supersample 3
> open
> /Users/becca/Desktop/Postdoc/Icknield_workshop/My_processing/COPI_Golph/Model/Flexfit_tempy_ref_copi_golph_AF3_aligned/flex_fit_out/final.pdb
Chain information for final.pdb #2
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> hide #2#!61 atoms
> show #2#!61 cartoons
> show #!63 models
> hide #!63 models
> select add #2
35468 atoms, 36117 bonds, 4477 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> save /Users/becca/Desktop/image2.png supersample 3
> save /Users/becca/Desktop/image3.png supersample 3
> volume #1 level 0.008439
> volume #1 level 0.008
> save /Users/becca/Desktop/image4.png supersample 3
> save /Users/becca/Desktop/image5.png supersample 3
> save /Users/becca/Desktop/image6.png supersample 3
> volume #1 level 0.008
> rename #2 CopI_Golph_AF3_TEMPyReff_FF.pdb
> select add #2
35468 atoms, 36117 bonds, 4477 residues, 1 model selected
> show #2 models
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-31.19,0,1,0,49.912,0,0,1,-16.182
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.86751,-0.49534,0.045513,112.21,0.48448,0.86212,0.1484,-68.876,-0.11275,-0.10669,0.98788,40.337
> view matrix models
> #2,0.35175,-0.74534,-0.56634,453.85,0.28095,0.66117,-0.69564,245.76,0.89294,0.085576,0.44197,-106.93
> view matrix models
> #2,0.35414,-0.41531,-0.83791,440.5,0.025342,0.89991,-0.43533,180.32,0.93485,0.13294,0.32922,-99.832
> view matrix models
> #2,0.071998,0.33036,-0.94111,348.01,-0.37176,0.88445,0.28203,94.9,0.92553,0.32956,0.18649,-110.12
> view matrix models
> #2,0.35685,-0.71818,-0.59739,453.82,0.25685,0.69027,-0.67643,239.31,0.89816,0.087945,0.43079,-105.89
> view matrix models
> #2,0.0056735,-0.99781,-0.065887,470.96,0.78232,0.045468,-0.62121,261.08,0.62285,-0.04802,0.78087,-96.169
> view matrix models
> #2,0.37415,-0.55777,-0.74088,446.43,0.04545,0.80897,-0.58608,236.83,0.92625,0.18561,0.32803,-110.62
> view matrix models
> #2,0.035147,0.12676,-0.99131,420.41,-0.65475,0.75232,0.072984,248.66,0.75503,0.64649,0.10944,-128.9
> view matrix models
> #2,-0.037528,0.19288,-0.9805,418.43,-0.70286,0.69238,0.1631,251.98,0.71034,0.69528,0.10959,-130.48
> view matrix models
> #2,-0.068173,0.21783,-0.9736,417.72,-0.71944,0.66536,0.19924,253.4,0.6912,0.71403,0.11136,-131.07
> view matrix models
> #2,-0.07803,0.22552,-0.97111,417.51,-0.72434,0.65647,0.21065,253.86,0.68501,0.71985,0.11213,-131.24
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.07803,0.22552,-0.97111,605.87,-0.72434,0.65647,0.21065,289.74,0.68501,0.71985,0.11213,-8.4516
> view matrix models
> #2,-0.07803,0.22552,-0.97111,534.39,-0.72434,0.65647,0.21065,325.87,0.68501,0.71985,0.11213,2.9277
> view matrix models
> #2,-0.07803,0.22552,-0.97111,604.94,-0.72434,0.65647,0.21065,292.49,0.68501,0.71985,0.11213,24.568
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97374,0.14663,0.17415,81.319,-0.18321,0.95879,0.21713,86.78,-0.13513,-0.24334,0.96048,242.57
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.97374,0.14663,0.17415,29.188,-0.18321,0.95879,0.21713,88.592,-0.13513,-0.24334,0.96048,259.92
> view matrix models
> #2,0.97374,0.14663,0.17415,-20.202,-0.18321,0.95879,0.21713,71.59,-0.13513,-0.24334,0.96048,178.44
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #2 inMap #1
Fit molecule CopI_Golph_AF3_TEMPyReff_FF.pdb (#2) to map
relion_locres_filtered_20240326_GT.mrc (#1) using 35468 atoms
average map value = 0.01005, steps = 128
shifted from previous position = 6.59
rotated from previous position = 19.5 degrees
atoms outside contour = 17045, contour level = 0.008
Position of CopI_Golph_AF3_TEMPyReff_FF.pdb (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999995 -0.00024332 0.00013426 0.03612248
0.00024337 0.99999990 -0.00033935 0.03885805
-0.00013417 0.00033938 0.99999992 -0.12979950
Axis 0.77368602 0.30599038 0.55477908
Axis point 0.00000000 329.89751172 143.43354143
Rotation angle (degrees) 0.02513175
Shift along axis -0.03217240
> select subtract #2
Nothing selected
> hide #!61 models
> color #2/A alphav2
> color #2/A label_purple
> color #2/b Arf1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #2/b arf1v2
> color #2/c arf1v2
> color #2/d alphav2
> color #2/e betapv2
> color #2/e betav2
> color #2/f betapv2
> color #2/g deltav2
> color #2/f gammav3
> color #2/g zetav2
> color #2/g deltav2
> color #2/h red
> color #2/h gammav3
> color #2/i gammav3
> color #2/i zetav2
> color #2/j zetav2
> color #2/f betapv2\
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #2/f betapv2
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!61 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!61 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #2 models
> close #2
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241113_for_figures.cxs"
> volume #1 level 0.005
> volume #1 level 0.006
> volume #1 level 0.0055
> save /Users/becca/Desktop/image1.png supersample 3
[Repeated 1 time(s)]
> save /Users/becca/Desktop/image2.png supersample 3
> volume #1 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
> volume #1 level 0.005298
> volume #1 level 0.0055
> save /Users/becca/Desktop/image2.png supersample 3
> volume #1 level 0.008
> save /Users/becca/Desktop/image3.png supersample 3
> volume #1 level 0.005
> save /Users/becca/Desktop/image4.png supersample 3
> volume #1 level 0.008
> save /Users/becca/Desktop/image5.png supersample 3
> volume #1 level 0.005
> save /Users/becca/Desktop/image6.png supersample 3
> volume #1 level 0.008
> save /Users/becca/Desktop/image7.png supersample 3
> volume #1 level 0.005
> save /Users/becca/Desktop/image1.png supersample 3
> volume #1 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
[Repeated 2 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting simple
> save /Users/becca/Desktop/image1.png supersample 3
> volume #1 level 0.005
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> scene 1
Unknown command: scene 1
> view 1
Expected an objects specifier or a view name or a keyword
> view view1
Expected an objects specifier or a view name or a keyword
> view save view1
Expected an objects specifier or a view name or a keyword
> view name view1
> volume #1 level 0.008
> view name view2
> view name view3
> view name view4
> view name view5
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241114.cxs"
> view view1
> view view2
> view view1
> volume #1 level 0.005
> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov"
Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov
> save overview_w_membrane.png supersample 3 transparentBackground true
> volume #1 level 0.008
> save overview_wout_membrane.png supersample 3 transparentBackground true
> view view1
> view view2
> view view3
> ui mousemode right select
> select clear
> select #61/M:11
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 2 residues
Drag select of 6 residues
> select up
180 atoms, 182 bonds, 23 residues, 1 model selected
> select down
55 atoms, 6 residues, 1 model selected
> delete sel
Drag select of 2 residues
> select clear
Drag select of 2 residues
> delete sel
> select clear
> select #61/M:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/M:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #61/M:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> select #61/M:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #61/M:13
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select #61/M:14
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select clear
> select #61/M:15
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select #61/M:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> view 3
Expected an objects specifier or a view name or a keyword
> view view3
> select clear
> ui mousemode right select
> ui mousemode right "translate selected models"
> save zoomed_view_no_bkgd.png supersample 3 transparentBackground true
> view view4
> save zoomed_view_with_bkgd.png supersample 3 transparentBackground true
> view view5
> view view4
> view view5
> save zoomed_view_with_full_bkgd.png supersample 3 transparentBackground true
> view view2
> save overview_wout_membrane_v2.png supersample 3 transparentBackground true
> color list
19 custom colors: alphav1
, alphav2
, arf1v1
, arf1v2
, betapv1
, betapv2
, betav1
, betav2
, deltav1
, deltav2
, epsilonv1
, gammav1
, gammav2
, gammav3
, label_purple
, label_purplev2
, label_red
, zetav1
, and zetav2
.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241114_v2.cxs"
——— End of log from Thu Nov 14 15:28:36 2024 ———
opened ChimeraX session
> select add #38
4763 atoms, 4880 bonds, 591 residues, 1 model selected
> show #38 models
> hide #!1 models
> hide #!61 models
> color sel alphav3
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color alphav3 sel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color list
19 custom colors: alphav1
, alphav2
, arf1v1
, arf1v2
, betapv1
, betapv2
, betav1
, betav2
, deltav1
, deltav2
, epsilonv1
, gammav1
, gammav2
, gammav3
, label_purple
, label_purplev2
, label_red
, zetav1
, and zetav2
.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color name alphav3 #57679E
Color 'alphav3' is opaque: rgb(34.1%, 40.4%, 62%) hex: #57679e
> color name betapv3 #7ACADA
Color 'betapv3' is opaque: rgb(47.8%, 79.2%, 85.5%) hex: #7acada
> color name betav3 #447A57
Color 'betav3' is opaque: rgb(26.7%, 47.8%, 34.1%) hex: #447a57
> color name gammav3 #ADE57C
Color 'gammav3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c
> color name deltav3 #E5AF76
Color 'deltav3' is opaque: rgb(89.8%, 68.6%, 46.3%) hex: #e5af76
> color name epsilonv3 #EB8675
Color 'epsilonv3' is opaque: rgb(92.2%, 52.5%, 45.9%) hex: #eb8675
> color name zetav3 #F0E07B
Color 'zetav3' is opaque: rgb(94.1%, 87.8%, 48.2%) hex: #f0e07b
> color name arf1v3 #EB8BCA
Color 'arf1v3' is opaque: rgb(92.2%, 54.5%, 79.2%) hex: #eb8bca
> color name label_red_v3 #E51A16
Color 'label_red_v3' is opaque: rgb(89.8%, 10.2%, 8.63%) hex: #e51a16
> color name label_purple_v3 #691099
Color 'label_purple_v3' is opaque: rgb(41.2%, 6.27%, 60%) hex: #691099
> color name lable_purple_v4 #9057AD
Color 'lable_purple_v4' is opaque: rgb(56.5%, 34.1%, 67.8%) hex: #9057ad
> color name label_purple_v4 #9057AD
Color 'label_purple_v4' is opaque: rgb(56.5%, 34.1%, 67.8%) hex: #9057ad
> color sel alphav3
> hide #38 models
> select subtract #38
Nothing selected
> select add #39
1856 atoms, 1891 bonds, 233 residues, 1 model selected
> show #39 models
> color sel alphav3
[Repeated 1 time(s)]
> select subtract #39
Nothing selected
> hide #39 models
> show #41 models
> select add #41
4686 atoms, 4798 bonds, 586 residues, 1 model selected
> color sel betapv3
> show #42 models
> select add #42
6695 atoms, 6846 bonds, 838 residues, 2 models selected
> color sel betapv3
> select subtract #42
4686 atoms, 4798 bonds, 586 residues, 1 model selected
> select subtract #41
Nothing selected
> hide #41 models
> hide #42 models
> show #!43 models
> show #!44 models
> show #!45 models
> select add #45
2879 atoms, 2928 bonds, 1 pseudobond, 362 residues, 2 models selected
> select add #44
5367 atoms, 5446 bonds, 2 pseudobonds, 675 residues, 4 models selected
> select add #43
7239 atoms, 7350 bonds, 2 pseudobonds, 918 residues, 5 models selected
> color sel betav3
> select subtract #45
4360 atoms, 4422 bonds, 1 pseudobond, 556 residues, 3 models selected
> select subtract #44
1872 atoms, 1904 bonds, 243 residues, 1 model selected
> select subtract #43
Nothing selected
> hide #!45 models
> show #!45 models
> hide #!44 models
> hide #!43 models
> hide #!45 models
> show #!46 models
> color sel deltav3
> select add #46
1681 atoms, 1700 bonds, 1 pseudobond, 209 residues, 2 models selected
> color sel deltav3
> select subtract #46
Nothing selected
> hide #!46 models
> show #47 models
> show #48 models
> show #!49 models
> color sel gammav3
> select add #47
1163 atoms, 1177 bonds, 149 residues, 1 model selected
> select add #48
3496 atoms, 3549 bonds, 448 residues, 2 models selected
> select add #49
4560 atoms, 4629 bonds, 1 pseudobond, 583 residues, 4 models selected
> color sel gammav3
> select subtract #49
3496 atoms, 3549 bonds, 448 residues, 2 models selected
> select subtract #48
1163 atoms, 1177 bonds, 149 residues, 1 model selected
> select subtract #47
Nothing selected
> hide #47 models
> hide #48 models
> hide #!49 models
> show #50 models
> color sel zetav3
> select add #50
1200 atoms, 1218 bonds, 150 residues, 1 model selected
> color sel zetav3
> select subtract #50
Nothing selected
> hide #50 models
> show #51 models
> show #52 models
> show #53 models
> select add #53
1350 atoms, 1373 bonds, 167 residues, 1 model selected
> select add #52
2700 atoms, 2746 bonds, 334 residues, 2 models selected
> select add #51
4050 atoms, 4119 bonds, 501 residues, 3 models selected
> color sel arf1v3
> select subtract #51
2700 atoms, 2746 bonds, 334 residues, 2 models selected
> select subtract #52
1350 atoms, 1373 bonds, 167 residues, 1 model selected
> select subtract #53
Nothing selected
> hide #53 models
> hide #52 models
> hide #51 models
> show #!54 models
> show #55 models
> color sel label_purple_v3
> select add #54
229 atoms, 228 bonds, 31 residues, 1 model selected
> select add #55
2200 atoms, 2230 bonds, 275 residues, 2 models selected
> color sel label_purple_v3
> select subtract #55
229 atoms, 228 bonds, 31 residues, 1 model selected
> select subtract #54
Nothing selected
> hide #!54 models
> hide #55 models
> show #!57 models
> color #57/a alphav3
> color #57/b betav3
> color #57/c betapv3
> color #57/d deltav3
> color #57/e gammav3
> color #57/f gammav3
> color #57/f arf1v3
> color #57/g arf1v3
> color #57/g gammav3
> color #57/h arf1v3
> color #57/i arf1v3
> color #57/j arf1v3
> color #57/k arf1v3
> color #57/k gammav3
> color #57/l zetav3
> color #57/m zetav3
> color #57/m arf1v3
> color #57/n arf1v3
> color #57/o arf1v3
> color #57/p arf1v3
> color #57/q arf1v3
> color #57/r arf1v3
> color #57/a zetav3
> undo
> color #57/z zetav3
> hide #!57 models
> show #!61 models
> color #58/d alphav3
> color #61/d alphav3
> color #61/e alphav3
> color #61/f betapv3
> color #61/g betapv3
> color #61/h betav3
> color #61/i betav3
> color #61/j betav3
> color #61/k deltav3
> color #61/l gammav3
> color #61/m gammav3
> color #61/n gammav3
> color #61/o zetav3
> color #61/p arf1v3
> color #61/q arf1v3
> color #61/q label_purple_v3
> color #61/a label_purple_v3
> color #61/b arf1v3
> color #61/c arf1v3
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> color zone #63 near #61 distance 8.31
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1/20241114_v3.cxs"
> show #!1 models
> color #1 #d6d6d680 models
> color #1 #d6d6d669 models
> view view1
[Repeated 4 time(s)]
> view view2
> volume #1 level 0.005
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1"
Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure1
> volume #1 level 0.008
> save overview_wout_membrane_v3.png supersample 3 transparentBackground true
> view view2
[Repeated 1 time(s)]
> volume #1 level 0.005
> save overview_w_membrane_v2.png supersample 3 transparentBackground true
> volume #1 level 0.008
> save overview_w_membrane_v3.png supersample 3 transparentBackground true
> view view3
[Repeated 1 time(s)]
> save zoomed_view_with_no_bkgd_v2.png supersample 3 transparentBackground
> true
> view view4
> save zoomed_view_with_bkgd_v2.png supersample 3 transparentBackground true
> view view5
> save zoomed_view_with_full_bkgd_v2.png supersample 3 transparentBackground
> true
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241122_chimera_for_figures.cxs"
——— End of log from Fri Nov 22 15:12:25 2024 ———
opened ChimeraX session
> view view5
> view
> view view5
> ui tool show "Side View"
> view name view6
> view view6
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view name view7
> view view5
> hide #!1 models
> show #!43 models
> hide #!43 models
> hide #!61 models
> show #!43 models
> show #!40 models
> hide #!43 models
> hide #!40 models
> show #!61 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view view5
> view view6
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1"
Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure1
> save zoomed_view_GOLPH3_alpha.png supersample 3 transparentBackground true
> hide #!1 models
> ui mousemode right select
> select #61/D:136
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #61/D:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/D:136
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #61/D:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel byhetero
> select #61/D:136
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #61/D:137
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel byhetero
> select clear
> select #61/D:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #61/Q:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #61/D:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #61/D:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/D:291
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #61/D:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #61/Q:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #61/Q:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> color sel byhetero
> show sel atoms
> select #61/Q:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #61/Q:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #61/Q:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #61/Q:167
10 atoms, 10 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #61/Q:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #61/Q:176
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #61/Q:175
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 9 atom styles
> select clear
> view view6
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 1 residues
> select #61/D:243
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.005
> hide #!1 models
> volume #1 level 0.008
> select clear
> select #61/Q:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #61/D:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> view name view8
> select clear
> select #61/D:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> view view8
> select clear
> select #61/D:211
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> view name view9
> view view9
> view view8
> show #!1 models
> view name view10
> save zoomed_view_GOLPH3_alpha_residues.png supersample 3
> transparentBackground true
> volume #1 level 0.005
> volume #1 level 0.006
> save zoomed_view_GOLPH3_alpha_G-K56_A-290-292.png supersample 3
> transparentBackground true
> save zoomed_view_GOLPH3_alpha_G-K56_A-290-292_v2.png supersample 3
> transparentBackground true
> view view8
> view view9
> hide #!1 models
> select #61/Q:175
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> view view9
> show #!1 models
> volume #1 level 0.0065
> volume #1 level 0.006
> volume #1 level 0.007
> volume #1 level 0.006
> save zoomed_view_GOLPH3_alpha_G-K56_A-290-292_v3.png supersample 3
> transparentBackground true
> volume #1 level 0.008
> hide #!1 models
> select #61/D:94@CB
1 atom, 1 residue, 1 model selected
> select #61/D:94@CB
1 atom, 1 residue, 1 model selected
> select #61/D:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/D:93
8 atoms, 7 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #61/D:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/D:94@CB
1 atom, 1 residue, 1 model selected
> select #61/Q:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #61/D:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> show #!1 models
> select #1
4 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> select clear
> select #61/Q:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> select #61/Q:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #61/Q:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/Q:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #61/Q:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/Q:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!1 models
> select clear
[Repeated 1 time(s)]
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 3 time(s)]
> volume #63 color #ffffff00
> volume #1 color #ebebeb
> volume #1 color #ebebeb00
> volume #1 color #ebebeb22
> volume #1 color #ebebeb23
> volume #1 color #ebebeb32
> volume #1 color #ebebeb40
> volume #1 color white
> volume #1 color #ffffff00
> lighting simple
> volume #1 color #ffffff4d
> ui tool show "Side View"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #61/D:135
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> hide sel atoms
> show #!1 models
> save zoomed_view_GOLPH3_alpha_G-T189_K191_T200_A-136-137.png supersample 3
> transparentBackground true
> select clear
> save zoomed_view_GOLPH3_alpha_G-T189_K191_T200_A-136-137.png supersample 3
> transparentBackground true
> view view10
> volume #1 level 0.006
> view view5
> save zoomed_view_GOLPH3_alpha_G-K56_A-290-292_v4.png supersample 3
> transparentBackground true
> view view5
> view name view11
[Repeated 1 time(s)]
> save zoomed_view_GOLPH3_alpha_G-T189_K191_T200_A-136-137_v2.png supersample
> 3 transparentBackground true
> hide #!1 models
> select #61/Q:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #61/Q:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 1 residues
> hide sel atoms
> select #61/D:136@CA
1 atom, 1 residue, 1 model selected
> select #61/D:136
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #61/D:137
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #61/Q:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> view view11
> select #61/Q:199
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/D:205
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/D:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!1 models
> volume #1 level 0.008
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> save zoomed_view_GOLPH3_alpha_G-K179_A-94.png supersample 3
> transparentBackground true
> view name view12
> hide #!1 models
> view view5
> select #61/Q:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/Q:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/Q:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/Q:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/Q:191
9 atoms, 8 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #61/Q:199
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:198
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/D:137
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/D:136
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> view view5
> view view6
> view view7
> view view8
> show #!1 models
> volume #1 level 0.006
> volume #1 level 0.007
> volume #1 level 0.0067
> volume #1 level 0.0065
> select clear
> view view5
> view view11
> volume #1 level 0.008
> volume #1 level 0.008491
> volume #1 level 0.008
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from csparc/J3101/J3101_alignments_20241125.py"
Failed opening file /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/Processing/Files from csparc/J3101/J3101_alignments_20241125.py:
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene
menu item, and change the resulting dialog's "File Type" to ChimeraX.
> show #!49 models
> hide #!49 models
> view view1
> show #!49 models
> hide #!49 models
> show #48 models
> hide #48 models
> show #!56 models
> hide #!56 models
> show #!57 models
> hide #!57 models
> show #39 models
> hide #39 models
> show #39 models
> hide #!61 models
> show #38 models
> hide #39 models
> hide #38 models
> show #!61 models
> view view1
> volume #1 level 0.005
> hide #!1 models
Drag select of 57 atoms, 463 residues, 1 pseudobonds, 49 bonds
> hide sel atoms
> select clear
> view view1
> show #!1 models
> view view2
[Repeated 1 time(s)]
> view view3
[Repeated 1 time(s)]
> view name view12
> hide #!1 models
> select #61/Q:81
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select #61/Q:90
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #61/Q:171
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #61/Q:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select #61/Q:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 8 atom styles
> color sel byhetero
> view view12
> select #61/Q:81
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> view view12
> show #!1 models
> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure 2"
Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure 2
> save zoomed_view_GOLPH3_membrane_PI4P_site_sticks_v1.png supersample 3
> transparentBackground true
> volume #1 level 0.008
> view view12
> volume #1 level 0.005
> volume #1 level 0.008
> hide #!61 models
> show #55 models
> hide #!1 models
> show #!61 models
> select #55/A:171
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #55/A:175
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #55/A:175
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #55/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select #61/Q:173
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #55/A:173
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #55/A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #55/A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select add #61
34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected
> select subtract #61
Nothing selected
> select add #61
34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected
> select subtract #61
Nothing selected
> hide #!61 models
> select #55/A:172
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select add #55
1971 atoms, 2002 bonds, 244 residues, 1 model selected
> show #!61 models
> select #61/Q:90
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #61
34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected
> hide #!61 models
> select #55/A:90
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select add #55
1971 atoms, 2002 bonds, 244 residues, 1 model selected
> select subtract #55
Nothing selected
> hide #55 models
> select add #61
34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected
> show #!61 models
> hide sel atoms
> select subtract #61
Nothing selected
> hide #!61 models
> show #!61 models
> show #!1 models
> show #55 models
> view view12
> volume #1 level 0.005
> hide #55 models
> save zoomed_view_GOLPH3_membrane_PI4P_site_v2.png supersample 3
> transparentBackground true
> show #55 models
> volume #1 level 0.008
> hide #!61 models
> view name view13
> view view13
> view name view14
> save zoomed_view_GOLPH3_membrane_PI4P_site_rotate_v4.png supersample 3
> transparentBackground true
> view view13
> save zoomed_view_GOLPH3_membrane_PI4P_site_rotate_v3.png supersample 3
> transparentBackground true
> volume #1 level 0.005
> view name view15
> save zoomed_view_GOLPH3_membrane_PI4P_site_rotate_wmembrane_v5.png
> supersample 3 transparentBackground true
> view view14
> volume #1 level 0.008
> volume #1 level 0.006
> volume #1 level 0.005
> volume #1 level 0.008
> color #1 #ffffff23 models
> color #1 #ffffff24 models
> color #1 #ffffff26 models
> view name view16
> save zoomed_view_GOLPH3_membrane_PI4P_site_rotate_zoomed_v6.png supersample
> 3 transparentBackground true
> hide #!1 models
> view view1
> show #!1 models
> hide #55 models
> show #!61 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select ~sel & ##selected
Nothing selected
> view view2
> view view3
> view view4
> view view5
> view view6
> view view7
> view view8
> view view9
> view view10
> view view11
> view view10
> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure 3"
Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure 3
> color #1 #ffffff4c models
> color #1 #ffffff4d models
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> volume #1 level 0.006
> volume #1 level 0.007
> volume #1 level 0.008
> save zoomed_view_GOLPH3_alpha_overview.png supersample 3
> transparentBackground true
> view name view17
> hide #!1 models
> select #61/Q:56
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/D:290
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/D:291
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #61/D:292
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> volume #1 level 0.006
[Repeated 1 time(s)]
> color #1 #ffffff22 models
> color #1 #ffffff23 models
> color #1 #ffffff24 models
> color #1 #ffffff26 models
> lighting soft
> lighting simple
> color #1 #ffffff34 models
> color #1 #ffffff37 models
> color #1 #ffffff48 models
> color #1 #ffffff51 models
> color #1 #ffffff4e models
> color #1 #ffffff4d models
> color #1 white models
> select clear
> save zoomed_view_GOLPH3_alpha_K56-D290D292_v5.png supersample 3
> transparentBackground true
> hide #!1 models
> view view7
> show #!1 models
> hide #!1 models
> select #61/O:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel byhetero
> select #61/O:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #61/O:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #61/O:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select #61/O:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #61/Q:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #61/Q:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> select #61/Q:222
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/Q:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select #61/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #61/Q:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel bynucleotide
> color sel byhetero
> show sel atoms
> select clear
> select #61/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/Q:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> view view7
> show #!1 models
> hide #!1 models
> select #61/Q:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> view view7
> save zoomed_view_GOLPH3_zewta.png supersample 3 transparentBackground true
[Repeated 1 time(s)]
> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure4"
Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure4
> save zoomed_view_GOLPH3_zeta.png supersample 3 transparentBackground true
> select clear
> save zoomed_view_GOLPH3_zeta_v2.png supersample 3 transparentBackground true
[Repeated 1 time(s)]
> hide #!1 models
> view view5
> show #!1 models
> volume #1 level 0.008
> hide #!1 models
> select #61/A:14
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel byhetero
> select clear
> select #61/A:14
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> save zoomed_view_GOLPH3_beta_gamma.png supersample 3 transparentBackground
> true
> hide #!1 models
> select #61/A:14
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #61/L:445
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #61/L:447
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> show sel atoms
> show #!1 models
> select clear
> volume #1 level 0.007
> volume #1 level 0.008
> save zoomed_view_GOLPH3_gamma_sticks.png supersample 3 transparentBackground
> true
> view view7
> hide #!1 models
> select #61/Q:228
8 atoms, 7 bonds, 1 residue, 1 model selected
> view view7
> view view1
> show #!1 models
> volume #1 level 0.005
> volume #1 level 0.008
> volume #1 level 0.005
> volume #1 level 0.008
> volume #1 level 0.007
> volume #1 level 0.006
> volume #1 level 0.005
> volume #1 level 0.004
> volume #1 level 0.008
> volume #1 level 0.007
> volume #1 level 0.006
> lighting simple
> volume #1 level 0.004772
> volume #1 level 0.00428
> view view13
> select add #61
34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected
> select subtract #61
Nothing selected
> hide #!61 models
> show #55 models
> show #!61 models
> view view13
> volume #1 level 0.004
> volume #1 level 0.007
> view view5
> volume #1 level 0.008
> volume #1 level 0.007
> volume #1 level 0.008
> volume #1 level 0.005
> volume #1 level 0.008
> volume #1 level 0.005
> volume #1 level 0.008
> volume #1 level 0.005
> view view13
> view view14
> view view15
> view view16
> view view5
> volume #1 level 0.004
> volume #1 level 0.005
> view view5
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241125_chimera_for_figures.cxs"
——— End of log from Tue Nov 26 17:24:46 2024 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #61
34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected
> hide sel atoms
> select subtract #61
Nothing selected
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!63 models
> show #!63 models
> hide #!1 models
> hide #!63 models
> show #!63 models
> volume #63 level 0.004
> ui tool show "Side View"
> ui tool show "Map Filter"
> volume gaussian #63 sDev 1.5
Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32
> color #2 white models
> color #2 #ffffff00 models
> graphics silhouettes false
> graphics silhouettes true
> volume gaussian #63 sDev 2.1 modelId #2
Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32
> volume gaussian #63 sDev 2.79 modelId #2
Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32
> volume gaussian #63 sDev 3.55 modelId #2
Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32
> color #2 #ffffff8c models
> volume gaussian #63 sDev 3.5 modelId #2
Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32
> color #2 #ffffff00 models
> volume gaussian #63 sDev 1.5 modelId #2
Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #2
> show #!1 models
> volume #1 level 0.006
> hide #!61 models
> hide #55 models
> show #55 models
> hide #55 models
> show #!63 models
> hide #!63 models
> close #63
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/postprocess/relion_locres_filtered_20240325_GT.mrc"
Opened relion_locres_filtered_20240325_GT.mrc as #2, grid size 292,292,292,
pixel 1.71, shown at level 0.00475, step 2, values float32
> color #2 #ebebebff models
> color #2 darkgrey models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 step 1
> select add #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,60.559,0,1,0,12.615,0,0,1,89.849
> view matrix models #2,1,0,0,60.961,0,1,0,65.494,0,0,1,66.73
> view matrix models #2,1,0,0,60.741,0,1,0,65.531,0,0,1,66.879
> view matrix models #2,1,0,0,60.201,0,1,0,65.945,0,0,1,68.739
> view matrix models #2,1,0,0,61.693,0,1,0,68.054,0,0,1,78.697
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #2 inMap #1
Fit map relion_locres_filtered_20240325_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 247574 points
correlation = 0.5776, correlation about mean = 0.1585, overlap = 12.09
steps = 104, shift = 3.7, angle = 3.43 degrees
Position of relion_locres_filtered_20240325_GT.mrc (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99906191 0.00800065 0.04255917 -16.84417788
-0.00693201 0.99965844 -0.02519806 -1.48444089
-0.04274624 0.02487940 0.99877614 8.42119695
Axis 0.50058073 0.85272375 -0.14926870
Axis point 151.01302871 0.00000000 270.26195011
Rotation angle (degrees) 2.86709508
Shift along axis -10.95471000
> select subtract #2
Nothing selected
> hide #!1 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/leaf_maps/postprocess/postprocess_20231221.mrc"
Opened postprocess_20231221.mrc as #3, grid size 156,156,156, pixel 2.55,
shown at level 0.00309, step 1, values float32
> color #3 #d6d6d6ff models
> color #3 silver models
> select add #3
3 models selected
> view matrix models #3,1,0,0,112.33,0,1,0,23.983,0,0,1,141.92
> view matrix models #3,1,0,0,114.32,0,1,0,92.543,0,0,1,105.62
> view matrix models #3,1,0,0,103.11,0,1,0,95.885,0,0,1,130.81
> fitmap #3 inMap #1
Fit map postprocess_20231221.mrc in map relion_locres_filtered_20240326_GT.mrc
using 37871 points
correlation = 0.5352, correlation about mean = 0.1111, overlap = 1.056
steps = 176, shift = 20, angle = 6.83 degrees
Position of postprocess_20231221.mrc (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99751059 0.06991241 0.00921266 27.35560896
-0.06875146 0.99325284 -0.09339179 71.61173506
-0.01567974 0.09252592 0.99558681 26.73581423
Axis 0.79702261 0.10671282 -0.59444709
Axis point 0.00000000 -339.01817829 775.79602219
Rotation angle (degrees) 6.69780267
Shift along axis 13.55190198
> view matrix models
> #3,0.99819,0.058024,0.016064,86.369,-0.056065,0.99307,-0.10324,139.24,-0.021943,0.10216,0.99453,104.3
> fitmap #3 inMap #1
Fit map postprocess_20231221.mrc in map relion_locres_filtered_20240326_GT.mrc
using 37871 points
correlation = 0.5352, correlation about mean = 0.1111, overlap = 1.056
steps = 92, shift = 9.15, angle = 0.00108 degrees
Position of postprocess_20231221.mrc (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99751078 0.06990804 0.00922575 27.35667632
-0.06874570 0.99325206 -0.09340440 71.61659488
-0.01569322 0.09253767 0.99558551 26.73719253
Axis 0.79707159 0.10681931 -0.59436228
Axis point 0.00000000 -339.04603471 775.71927260
Rotation angle (degrees) 6.69827053
Shift along axis 13.56368605
> select subtract #3
Nothing selected
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.004246
> hide #!1 models
> volume #3 level 0.004102
> close #3
> show #!2 models
> volume #2 level 0.00795
> volume #2 level 0.009987
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/postprocess/COPGolph_20200121_bin2_ref9_bf300.mrc"
Opened COPGolph_20200121_bin2_ref9_bf300.mrc as #3, grid size 128,128,128,
pixel 3.4, shown at level 0.129, step 1, values float32
> select add #3
3 models selected
> select subtract #3
Nothing selected
> close #3
> view view1
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> fitmap #2 inMap #1
Fit map relion_locres_filtered_20240325_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 54122 points
correlation = 0.5268, correlation about mean = 0.1559, overlap = 7.027
steps = 44, shift = 0.309, angle = 0.235 degrees
Position of relion_locres_filtered_20240325_GT.mrc (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99902778 0.01210431 0.04239090 -17.80684422
-0.01103402 0.99961668 -0.02539190 -0.36777814
-0.04268200 0.02489947 0.99877839 8.70044806
Axis 0.49548740 0.83816672 -0.22796661
Axis point 136.08540377 -0.00000000 293.26901725
Rotation angle (degrees) 2.90897539
Shift along axis -11.11473805
> select add #2
2 models selected
> view matrix models
> #2,0.99883,-0.00024469,0.048407,49.131,0.0019347,0.99939,-0.034868,86.429,-0.048369,0.034921,0.99822,81.672
> fitmap #2 inMap #1
Fit map relion_locres_filtered_20240325_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 54122 points
correlation = 0.9995, correlation about mean = 0.9987, overlap = 22.52
steps = 60, shift = 3.01, angle = 2.92 degrees
Position of relion_locres_filtered_20240325_GT.mrc (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999997 0.00014454 -0.00020656 0.02230057
-0.00014454 0.99999999 -0.00000418 0.02620686
0.00020656 0.00000421 0.99999998 -0.02948238
Axis 0.01665653 -0.81921023 -0.57325139
Axis point 154.38656054 0.00000000 108.27488169
Rotation angle (degrees) 0.01444704
Shift along axis -0.00419666
> select subtract #2
Nothing selected
> hide #!2 models
> hide #!1 models
> show #!1 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/LocalRes_jobs_leaf/job073/relion_locres_filtered.mrc"
Opened relion_locres_filtered.mrc as #3, grid size 292,292,292, pixel 1.71,
shown at level 0.00473, step 2, values float32
> rename #3 relion_locres_filtered_job072.mrc
> color #3 silver models
> select add #3
3 models selected
> view matrix models #3,1,0,0,30.539,0,1,0,-15.667,0,0,1,78.206
> view matrix models #3,1,0,0,54.166,0,1,0,45.183,0,0,1,34.056
> view matrix models #3,1,0,0,54.587,0,1,0,50.812,0,0,1,76.198
> view matrix models #3,1,0,0,56.131,0,1,0,58.42,0,0,1,66.709
> fitmap #3 inMap #1
Fit map relion_locres_filtered_job072.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30984 points
correlation = 0.6121, correlation about mean = 0.1178, overlap = 1.264
steps = 244, shift = 12.2, angle = 2.78 degrees
Position of relion_locres_filtered_job072.mrc (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99900846 0.01613693 -0.04149329 0.32501303
-0.01436556 0.99898722 0.04264000 -14.82959067
0.04213934 -0.04200165 0.99822850 -3.51967302
Axis -0.68905437 -0.68084012 -0.24831594
Axis point 0.00000000 -27.66742894 175.53564929
Rotation angle (degrees) 3.52124839
Shift along axis 10.74661948
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #3 step 1
> volume #3 level 0.006009
> view matrix models
> #3,0.99933,0.0034134,-0.036322,74.839,-0.0022469,0.99948,0.032108,64.226,0.036413,-0.032005,0.99882,77.163
> fitmap #3 inMap #1
Fit map relion_locres_filtered_job072.mrc in map
relion_locres_filtered_20240326_GT.mrc using 104109 points
correlation = 0.9694, correlation about mean = 0.9204, overlap = 18.06
steps = 68, shift = 5.13, angle = 3.52 degrees
Position of relion_locres_filtered_job072.mrc (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999985 0.00032727 -0.00043305 0.12443189
-0.00032746 0.99999985 -0.00044412 0.17911073
0.00043290 0.00044426 0.99999981 -0.20153574
Axis 0.63330421 -0.61731536 -0.46674139
Axis point 0.00000000 388.40421450 489.76047590
Rotation angle (degrees) 0.04018615
Shift along axis 0.06230051
> select subtract #3
Nothing selected
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/LocalRes_jobs_leaf/job076/relion_locres_filtered.mrc"
Opened relion_locres_filtered.mrc as #4, grid size 292,292,292, pixel 1.71,
shown at level 0.00472, step 2, values float32
> rename #3 relion_locres_filtered_job073.mrc
> rename #4 relion_locres_filtered_job076.mrc
> select add #4
2 models selected
> view matrix models #4,1,0,0,16.92,0,1,0,24.499,0,0,1,-17.193
> view matrix models #4,1,0,0,55.723,0,1,0,11.772,0,0,1,75.251
> view matrix models #4,1,0,0,62.536,0,1,0,67.084,0,0,1,60.553
> view matrix models #4,1,0,0,67.827,0,1,0,64.316,0,0,1,70.509
> view matrix models #4,1,0,0,58.535,0,1,0,64.656,0,0,1,73.258
> fitmap #4 inMap #1
Fit map relion_locres_filtered_job076.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30955 points
correlation = 0.6078, correlation about mean = 0.1074, overlap = 1.267
steps = 64, shift = 2.8, angle = 0.688 degrees
Position of relion_locres_filtered_job076.mrc (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99988799 0.00486326 -0.01415478 -0.00653699
-0.00467298 0.99989869 0.01344490 -12.25906211
0.01421873 -0.01337725 0.99980942 -4.97528219
Axis -0.66734489 -0.70594336 -0.23726521
Axis point 191.91942423 0.00000000 461.89280026
Rotation angle (degrees) 1.15150302
Shift along axis 9.83902726
> view matrix models
> #4,0.99993,-0.0077072,-0.0086124,61.953,0.0077353,0.99996,0.0032435,68.699,0.0085871,-0.0033099,0.99996,69.366
> view matrix models
> #4,0.99993,-0.0077072,-0.0086124,56.218,0.0077353,0.99996,0.0032435,68.574,0.0085871,-0.0033099,0.99996,68.917
> fitmap #4 inMap #1
Fit map relion_locres_filtered_job076.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30955 points
correlation = 0.6108, correlation about mean = 0.1251, overlap = 1.279
steps = 104, shift = 1.78, angle = 1.12 degrees
Position of relion_locres_filtered_job076.mrc (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99997231 0.00555723 -0.00494882 -9.73830653
-0.00557589 0.99997737 -0.00376441 -1.39875088
0.00492779 0.00379190 0.99998067 -6.79486943
Axis 0.45271595 -0.59173011 -0.66701105
Axis point -157.33116793 1829.07450339 0.00000000
Rotation angle (degrees) 0.47816945
Shift along axis 0.95124929
> view matrix models
> #4,0.99998,-0.0069162,0.00080869,64.023,0.0069267,0.99988,-0.01385,78.472,-0.00071281,0.013855,0.9999,68.833
> view matrix models
> #4,0.99998,-0.0069162,0.00080869,64.971,0.0069267,0.99988,-0.01385,76.867,-0.00071281,0.013855,0.9999,73.048
> fitmap #4 inMap #1
Fit map relion_locres_filtered_job076.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30955 points
correlation = 0.982, correlation about mean = 0.9627, overlap = 2.853
steps = 84, shift = 1.03, angle = 0.447 degrees
Position of relion_locres_filtered_job076.mrc (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999991 0.00030155 -0.00029701 0.06745018
-0.00030166 0.99999988 -0.00038573 0.14319029
0.00029689 0.00038582 0.99999988 -0.16137842
Axis 0.67363056 -0.51851584 -0.52665281
Axis point 0.00000000 341.71992784 446.62796416
Rotation angle (degrees) 0.03281253
Shift along axis 0.05618047
> select subtract #4
Nothing selected
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/LocalRes_jobs_leaf/job092/relion_locres_filtered.mrc"
Opened relion_locres_filtered.mrc as #5, grid size 292,292,292, pixel 1.71,
shown at level 0.00475, step 2, values float32
> rename #5 relion_locres_filtered_job092.mrc
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #5 step 1
> select add #5
2 models selected
> color #5 darkgrey models
> view matrix models #5,1,0,0,78.04,0,1,0,9.8449,0,0,1,60.259
> view matrix models #5,1,0,0,61.825,0,1,0,76.575,0,0,1,72.243
> view matrix models #5,1,0,0,62.283,0,1,0,77.072,0,0,1,76.941
> fitmap #5 inMap #1
Fit map relion_locres_filtered_job092.mrc in map
relion_locres_filtered_20240326_GT.mrc using 247574 points
correlation = 0.9988, correlation about mean = 0.999, overlap = 29.14
steps = 88, shift = 1.22, angle = 0.968 degrees
Position of relion_locres_filtered_job092.mrc (#5) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00015944 0.00001109 -0.05484775
-0.00015944 0.99999999 0.00003740 0.02924308
-0.00001108 -0.00003741 1.00000000 0.01335645
Axis -0.22787236 0.06752846 -0.97134654
Axis point 182.74280768 341.86651106 0.00000000
Rotation angle (degrees) 0.00940494
Shift along axis 0.00149928
> select subtract #5
Nothing selected
> hide #!5 models
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/triad_maps/PostProcess_jobs_triad/job020/postprocess.mrc"
Opened postprocess.mrc as #6, grid size 192,192,192, pixel 2.55, shown at
level 0.418, step 1, values float32
> rename #6 postprocess_triad_job020.mrc
> color #6 #929292ff models
> select add #6
2 models selected
> view matrix models #6,1,0,0,104.36,0,1,0,15.431,0,0,1,0.51008
> view matrix models #6,1,0,0,93.734,0,1,0,37.225,0,0,1,90.332
> view matrix models #6,1,0,0,128.14,0,1,0,64.539,0,0,1,90.582
> view matrix models #6,1,0,0,134.94,0,1,0,70.79,0,0,1,81.862
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #6 inMap #1
Fit map postprocess_triad_job020.mrc in map
relion_locres_filtered_20240326_GT.mrc using 70711 points
correlation = 0.673, correlation about mean = 0.2053, overlap = 223.4
steps = 108, shift = 5.92, angle = 1.12 degrees
Position of postprocess_triad_job020.mrc (#6) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99982486 0.01846854 0.00302814 66.76160543
-0.01844906 0.99980970 -0.00633944 -4.37708384
-0.00314464 0.00628246 0.99997532 1.62612945
Axis 0.31953420 0.15626921 -0.93460036
Axis point -365.37120016 -3287.39016242 0.00000000
Rotation angle (degrees) 1.13169211
Shift along axis 19.12883189
> volume #6 level 0.2964
> volume #6 level 0.2721
> select add #6
3 models selected
> select subtract #6
Nothing selected
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/triad_maps/PostProcess_jobs_triad/job007/postprocess.mrc"
Opened postprocess.mrc as #7, grid size 168,168,168, pixel 3.4, shown at level
0.444, step 1, values float32
> color #7 #929292ff models
> select add #7
2 models selected
> view matrix models #7,1,0,0,91.521,0,1,0,23.197,0,0,1,24.065
> view matrix models #7,1,0,0,96.402,0,1,0,26.264,0,0,1,33.056
> fitmap #7 inMap #1
Fit map postprocess.mrc in map relion_locres_filtered_20240326_GT.mrc using
47389 points
correlation = 0.6617, correlation about mean = 0.09379, overlap = 140.4
steps = 116, shift = 4.6, angle = 1.3 degrees
Position of postprocess.mrc (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99961800 0.02680029 0.00675246 21.33370946
-0.02678389 0.99963810 -0.00250708 -42.94662361
-0.00681720 0.00232526 0.99997406 -45.51754509
Axis 0.08709040 0.24455780 -0.96571566
Axis point -1916.30172591 -708.58915302 0.00000000
Rotation angle (degrees) 1.58977516
Shift along axis 35.31203555
> select subtract #7
Nothing selected
> rename #7 postprocess_triad_job007.mrc
> hide #!6 models
> volume #7 level 0.3932
> show #!6 models
> hide #!6 models
> hide #!7 models
> hide #!4 models
> hide #!3 models
> show #!5 models
> hide #!1 models
> volume #5 level 0.008164
> volume #5 level 0.008
> volume #5 level 0.005
> volume #4 level 0.005
> show #!4 models
> volume #4 level 0.006
> hide #!4 models
> show #!3 models
> volume #3 level 0.006
> volume #3 level 0.005
> ui tool show "Side View"
> volume #2 level 0.005
> volume #4 level 0.005
> volume #4 level 0.006
> volume #3 level 0.006
> show #!6 models
> color #6 white models
> color #6 #ffffff00 models
> color #6 #ffffff54 models
> color #6 #ffffff4d models
> view view1
> view view2
> hide #!4 models
> hide #!3 models
> color #6 #ffffff00 models
> color #6 #ffffff15 models
> color #6 #ffffff11 models
> color #6 #ffffff12 models
> view view2
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> ui tool show "Map Filter"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!1 models
> show #!3 models
> volume gaussian #3 sDev 1.5
Opened relion_locres_filtered_job073.mrc gaussian as #8, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> volume #8 level 0.004637
> volume #8 level 0.004706
> volume gaussian #3 sDev 2 modelId #8
Opened relion_locres_filtered_job073.mrc gaussian as #8, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> volume #8 level 0.004247
> volume gaussian #3 sDev 2.5 modelId #8
Opened relion_locres_filtered_job073.mrc gaussian as #8, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> volume #8 level 0.004296
> volume gaussian #3 sDev 3 modelId #8
Opened relion_locres_filtered_job073.mrc gaussian as #8, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> volume #8 level 0.004258
> ui tool show "Side View"
> hide #!8 models
> show #!4 models
> volume gaussian #4 sDev 3
Opened relion_locres_filtered_job076.mrc gaussian as #9, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> volume #9 level 0.004378
> hide #!9 models
> volume gaussian #5 sDev 3
Opened relion_locres_filtered_job092.mrc gaussian as #10, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> volume #10 level 0.004746
> show #!1 models
> hide #!1 models
> hide #!10 models
> show #!6 models
> color #6 #d6d6d6ff models
> show #!1 models
> show #!61 models
> color #6 #d6d6d684 models
> color #6 #d6d6d685 models
> volume gaussian #6 sDev 3
Opened postprocess_triad_job020.mrc gaussian as #11, grid size 192,192,192,
pixel 2.55, shown at step 1, values float32
> volume #11 color #b2b2b29c
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> color #7 white models
> color #7 #ffffff3b models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> color #6 white models
> color #6 #ffffff00 models
> hide #!61 models
> show #!61 models
> hide #!61 models
> hide #!1 models
> color #6 #ffffff80 models
> hide #!6 models
> show #!7 models
> volume #7 level 0.3477
> show #!61 models
> volume #7 level 0.3337
> volume gaussian #7 sDev 3
Opened postprocess_triad_job007.mrc gaussian as #12, grid size 168,168,168,
pixel 3.4, shown at step 1, values float32
> color #12 white models
> color #12 #ffffff22 models
> color #12 #ffffff21 models
> show #!1 models
> color #1 #ffffffca models
> color #1 #ffffffc9 models
> color #1 darkgrey models
> hide #!1 models
> hide #!61 models
> show #!61 models
> view view2
> view view5
> hide #!12 models
> show #!25 models
> hide #!25 models
> hide #!61 models
> color #25.1 alphav3
> color #25.2 betav3
> color #25.3 betapv3
> color #25.4 deltav3
> color #25.5 gammav3
> color #25.6 zetav3
> color arf1v3 #25.7
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #25.7 arf1v3
> color #25.8 arf1v3
> show #!25 models
> close #25
> show #!34 models
> show #34.1 models
> show #34.2 models
> show #34.3 models
> show #34.4 models
> show #34.5 models
> show #34.6 models
> show #34.7 models
> show #34.8 models
> show #34.9 models
> color #34.1 label_purple_v3
> color #34.2 arf1v3
> color #34.3 arf1v3
> color #34.4 alphav3
> color #34.5 betav3
> color #34.6 betapv3
> color #34.7 deltav3
===== Log before crash end =====
Log:
Startup Messages
---
warning | No presets found in custom preset folder /Users/becca/Desktop/Postdoc/Computational references/ChimeraX_presets
note | available bundle cache has not been initialized yet
> color name alphav1 #5786F5
Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5
> color name alphav2 #2A4B9B
Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b
> color name betapv1 #53EAF3
Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3
> color name betapv2 #759ED9
Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9
> color name betav1 #37863D
Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d
> color name betav2 #207B35
Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35
> color name deltav1 #CE8041
Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041
> color name deltav2 #E97408
Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408
> color name epsilonv1 #F06969
Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969
> color name gammav1 #2AFF3C
Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c
> color name gammav2 #61B230
Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230
> color name zetav1 #E0C819
Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819
> color name zetav2 #EFE30C
Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c
> color name arf1v1 #FF76AF
Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af
> color name arf1v2 #EB70A8
Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8
> color name label_red #E32723
Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723
> color name label_purple #6C4896
Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896
> color name alphav3 #57679E
Color 'alphav3' is opaque: rgb(34.1%, 40.4%, 62%) hex: #57679e
> color name betapv3 #7ACADA
Color 'betapv3' is opaque: rgb(47.8%, 79.2%, 85.5%) hex: #7acada
> color name betav3 #447A57
Color 'betav3' is opaque: rgb(26.7%, 47.8%, 34.1%) hex: #447a57
> color name gammav3 #ADE57C
Color 'gammav3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c
> color name deltav3 #E5AF76
Color 'deltav3' is opaque: rgb(89.8%, 68.6%, 46.3%) hex: #e5af76
> color name epsilonv3 #EB8675
Color 'epsilonv3' is opaque: rgb(92.2%, 52.5%, 45.9%) hex: #eb8675
> color name zetav3 #F0E07B
Color 'zetav3' is opaque: rgb(94.1%, 87.8%, 48.2%) hex: #f0e07b
> color name arf1v3 #EB8BCA
Color 'arf1v3' is opaque: rgb(92.2%, 54.5%, 79.2%) hex: #eb8bca
> color name label_red_v3 #E51A16
Color 'label_red_v3' is opaque: rgb(89.8%, 10.2%, 8.63%) hex: #e51a16
> color name label_purple_v3 #691099
Color 'label_purple_v3' is opaque: rgb(41.2%, 6.27%, 60%) hex: #691099
> color name lable_purple_v4 #9057AD
Color 'lable_purple_v4' is opaque: rgb(56.5%, 34.1%, 67.8%) hex: #9057ad
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16S000N6D/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 37 days, 4 hours, 13 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2422H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
annotated-types: 0.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.4.7
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.5
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
et-xmlfile: 1.1.0
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openpyxl: 3.1.5
openvr: 1.26.701
packaging: 23.2
pandas: 2.2.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pyarrow: 16.1.0
pycollada: 0.8
pydantic: 2.8.2
pydantic-core: 2.20.1
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
seaborn: 0.13.2
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
starfile: 0.5.8
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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