![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16422 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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>
[deleted to fit within ticket limits]
> 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
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 11 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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