![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16851 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: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001ef3a8f40 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, chimerax.atomic._ribbons, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix (total: 118)
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{
"uptime" : 77000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 1692,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2025-02-12 23:42:57.8416 +0100",
"codeSigningMonitor" : 1,
"incident" : "D88BB350-C480-47BE-AE57-06200CB675AD",
"pid" : 57057,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-12 16:18:27.3559 +0100",
"procStartAbsTime" : 1387044834968,
"procExitAbsTime" : 1859103323941,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"ED62F962-88CB-52CD-B9C7-9378ADDF2FB5","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" : 15534,
"sleepWakeUUID" : "A361DBF7-8E86-4D0D-B577-D75652481D65",
"sip" : "enabled",
"vmRegionInfo" : "0x76e8fc19dad8 is not in any region. Bytes after previous region: 25185085938393 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600100000000-600120000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x000076e8fc19dad8","rawCodes":[1,130743034043096],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000076e8fc19dad8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":57057},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x76e8fc19dad8 is not in any region. Bytes after previous region: 25185085938393 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600100000000-600120000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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Thunderbolt Bus: MacBook Pro, Apple Inc.
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AirPort:
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250212_chimera_for_figures_v2.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.0066, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.124, step 1, values float32
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0053, step 1, values float32
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0054, step 1, values float32
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32
Opened relion_locres_filtered_job073_lp15.mrc as #11, grid size 292,292,292,
pixel 1.71, shown at level 0.0045, step 1, values float32
Opened relion_locres_filtered_job073_lp18.mrc as #10, grid size 292,292,292,
pixel 1.71, shown at level 0.00422, step 1, values float32
Opened postprocess_job020_lp20.mrc as #13, grid size 192,192,192, pixel 2.55,
shown at level 0.289, step 1, values float32
Opened postprocess_job020_lp25.mrc as #14, grid size 192,192,192, pixel 2.55,
shown at level 0.278, step 1, values float32
Log from Wed Feb 12 11:24:19 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250130_chimera_for_figures.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.0066, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.124, step 1, values float32
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0053, step 1, values float32
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0054, step 1, values float32
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32
Opened relion_locres_filtered_job073_lp15.mrc as #11, grid size 292,292,292,
pixel 1.71, shown at level 0.0047, step 1, values float32
Opened relion_locres_filtered_job073_lp18.mrc as #10, grid size 292,292,292,
pixel 1.71, shown at level 0.00422, step 1, values float32
Opened postprocess_job020_lp20.mrc as #13, grid size 192,192,192, pixel 2.55,
shown at level 0.289, step 1, values float32
Opened postprocess_job020_lp25.mrc as #14, grid size 192,192,192, pixel 2.55,
shown at level 0.278, step 1, values float32
Log from Thu Jan 30 11:29:53 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250101_chimera_for_figures.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.0066, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.124, step 1, values float32
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0053, step 1, values float32
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0054, step 1, values float32
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32
Opened relion_locres_filtered_job073_lp15.mrc as #11, grid size 292,292,292,
pixel 1.71, shown at level 0.0047, step 1, values float32
Opened relion_locres_filtered_job073_lp18.mrc as #10, grid size 292,292,292,
pixel 1.71, shown at level 0.00422, step 1, values float32
Opened postprocess_job020_lp20.mrc as #13, grid size 192,192,192, pixel 2.55,
shown at level 0.289, step 1, values float32
Opened postprocess_job020_lp25.mrc as #14, grid size 192,192,192, pixel 2.55,
shown at level 0.278, step 1, values float32
Log from Thu Jan 9 16:57:06 2025UCSF 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/20241218_chimera_for_figures.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.0066, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.124, step 1, values float32
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0053, step 1, values float32
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0054, step 1, values float32
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32
Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size
292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size
292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32
Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236,
pixel 2.55, shown at level 0.00478, step 1, values float32
Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size
292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32
Log from Wed Dec 18 14:00:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241212_chimera_for_figures.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00851, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.179, step 1, values float32
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0053, step 1, values float32
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0049, step 1, values float32
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32
Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size
292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size
292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32
Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236,
pixel 2.55, shown at level 0.00478, step 1, values float32
Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size
292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32
Log from Thu Dec 12 11:04:26 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/20241210_chimera_for_figures_v5.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00851, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.179, step 1, values float32
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0055, step 1, values float32
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0049, step 1, values float32
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32
Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size
292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size
292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.299, step 1, values float32
Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236,
pixel 2.55, shown at level 0.00478, step 1, values float32
Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size
292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32
Log from Tue Dec 10 13:42:08 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241207_chimera_for_figures.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.006, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.179, step 1, values float32
Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown
at level 0.36, step 1, values float32
Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown
at level 0.3, step 1, values float32
Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55,
shown at level 0.0057, step 1, values float32
Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel
1.71, shown at level 0.0055, step 1, values float32
Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel
1.71, shown at level 0.0049, step 1, values float32
Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel
1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292,
pixel 1.71, shown at level 0.0065, step 1, values float32
Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size
292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32
Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size
292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size
292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32
Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192,
pixel 2.55, shown at level 0.323, step 1, values float32
Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236,
pixel 2.55, shown at level 0.00472, step 1, values float32
Log from Sat Dec 7 12:37:17 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/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.
[deleted to fit within ticket limits]
> hide #14 models
> show #15 models
> hide #15 models
> show #15 models
> show #14 models
> show #13 models
> show #12 models
> show #11 models
> hide #15 models
> hide #14 models
> hide #13 models
> hide #12 models
> hide #11 models
> show #12 models
> hide #12 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #15 models
> hide #15 models
> close #11-15
> ui tool show Matchmaker
> matchmaker #16-20 to #1
Computing secondary structure
[Repeated 5 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_37_160_model_0.cif, chain B (#16), sequence
alignment score = 4867.7
RMSD between 886 pruned atom pairs is 0.833 angstroms; (across all 953 pairs:
1.913)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_37_160_model_1.cif, chain B (#17), sequence
alignment score = 4837.1
RMSD between 760 pruned atom pairs is 0.848 angstroms; (across all 953 pairs:
2.809)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_37_160_model_2.cif, chain B (#18), sequence
alignment score = 4849.7
RMSD between 755 pruned atom pairs is 0.945 angstroms; (across all 953 pairs:
2.826)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_37_160_model_3.cif, chain B (#19), sequence
alignment score = 4858.7
RMSD between 733 pruned atom pairs is 1.041 angstroms; (across all 953 pairs:
3.784)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_37_160_model_4.cif, chain B (#20), sequence
alignment score = 4843.1
RMSD between 767 pruned atom pairs is 0.737 angstroms; (across all 953 pairs:
4.033)
> select add #16
37356 atoms, 38057 bonds, 4699 residues, 1 model selected
> select add #17
74712 atoms, 76114 bonds, 9398 residues, 2 models selected
> select add #18
112068 atoms, 114171 bonds, 14097 residues, 3 models selected
> select add #19
149424 atoms, 152228 bonds, 18796 residues, 4 models selected
> select add #20
186780 atoms, 190285 bonds, 23495 residues, 5 models selected
> show sel cartoons
> select subtract #20
149424 atoms, 152228 bonds, 18796 residues, 4 models selected
> select subtract #19
112068 atoms, 114171 bonds, 14097 residues, 3 models selected
> select subtract #18
74712 atoms, 76114 bonds, 9398 residues, 2 models selected
> select subtract #17
37356 atoms, 38057 bonds, 4699 residues, 1 model selected
> select subtract #16
Nothing selected
> hide #20 models
> hide #19 models
> hide #18 models
> hide #17 models
> hide #16 models
> show #17 models
> hide #17 models
> show #18 models
> hide #18 models
> show #19 models
> hide #19 models
> show #20 models
> hide #20 models
> close #17-20
> ui tool show Matchmaker
> matchmaker #21-30 to #1
Computing secondary structure
[Repeated 10 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_1_160_model_0.cif, chain B (#21), sequence
alignment score = 4853.9
RMSD between 848 pruned atom pairs is 0.740 angstroms; (across all 953 pairs:
1.552)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_1_160_model_1.cif, chain B (#22), sequence
alignment score = 4829.9
RMSD between 816 pruned atom pairs is 0.748 angstroms; (across all 953 pairs:
1.465)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_1_160_model_2.cif, chain B (#23), sequence
alignment score = 4843.7
RMSD between 860 pruned atom pairs is 0.927 angstroms; (across all 953 pairs:
1.398)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_1_160_model_3.cif, chain B (#24), sequence
alignment score = 4852.7
RMSD between 825 pruned atom pairs is 0.786 angstroms; (across all 953 pairs:
1.400)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_man1b1_1_160_model_4.cif, chain B (#25), sequence
alignment score = 4874.3
RMSD between 675 pruned atom pairs is 0.979 angstroms; (across all 953 pairs:
2.784)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_model_0.cif, chain B (#26), sequence alignment
score = 4851.5
RMSD between 839 pruned atom pairs is 0.974 angstroms; (across all 953 pairs:
3.156)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_model_1.cif, chain B (#27), sequence alignment
score = 4834.1
RMSD between 533 pruned atom pairs is 1.124 angstroms; (across all 953 pairs:
3.328)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_model_2.cif, chain B (#28), sequence alignment
score = 4817.9
RMSD between 885 pruned atom pairs is 0.895 angstroms; (across all 953 pairs:
3.409)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_model_3.cif, chain B (#29), sequence alignment
score = 4861.7
RMSD between 710 pruned atom pairs is 1.062 angstroms; (across all 953 pairs:
2.629)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_model_4.cif, chain B (#30), sequence alignment
score = 4833.5
RMSD between 810 pruned atom pairs is 0.780 angstroms; (across all 953 pairs:
2.106)
> ui tool show Matchmaker
> matchmaker #31-40 to #1
Computing secondary structure
[Repeated 10 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_24_pa_model_0.cif, chain B (#31), sequence
alignment score = 4869.5
RMSD between 532 pruned atom pairs is 1.010 angstroms; (across all 953 pairs:
3.106)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_24_pa_model_1.cif, chain B (#32), sequence
alignment score = 4859.9
RMSD between 586 pruned atom pairs is 0.894 angstroms; (across all 953 pairs:
2.805)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_24_pa_model_2.cif, chain B (#33), sequence
alignment score = 4876.7
RMSD between 583 pruned atom pairs is 1.037 angstroms; (across all 953 pairs:
2.347)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_24_pa_model_3.cif, chain B (#34), sequence
alignment score = 4859.3
RMSD between 701 pruned atom pairs is 1.064 angstroms; (across all 953 pairs:
2.203)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_3gtp_24_pa_model_4.cif, chain B (#35), sequence
alignment score = 4844.3
RMSD between 705 pruned atom pairs is 1.081 angstroms; (across all 953 pairs:
2.238)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_model_0.cif, chain B (#36), sequence alignment
score = 4873.1
RMSD between 775 pruned atom pairs is 0.769 angstroms; (across all 953 pairs:
2.621)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_model_1.cif, chain B (#37), sequence alignment
score = 4840.1
RMSD between 874 pruned atom pairs is 1.023 angstroms; (across all 953 pairs:
3.184)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_model_2.cif, chain B (#38), sequence alignment
score = 4855.1
RMSD between 760 pruned atom pairs is 0.747 angstroms; (across all 953 pairs:
3.283)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_model_3.cif, chain B (#39), sequence alignment
score = 4835.3
RMSD between 872 pruned atom pairs is 0.686 angstroms; (across all 953 pairs:
1.722)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_model_4.cif, chain B (#40), sequence alignment
score = 4864.7
RMSD between 718 pruned atom pairs is 0.787 angstroms; (across all 953 pairs:
2.790)
> ui tool show Matchmaker
> matchmaker #41-80 to #1
Computing secondary structure
[Repeated 40 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_deltatrunc_golph3_fl_model_0.cif, chain B (#41), sequence
alignment score = 4862.9
RMSD between 789 pruned atom pairs is 0.655 angstroms; (across all 953 pairs:
2.194)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_deltatrunc_golph3_fl_model_1.cif, chain B (#42), sequence
alignment score = 4859.3
RMSD between 721 pruned atom pairs is 0.941 angstroms; (across all 953 pairs:
2.830)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_deltatrunc_golph3_fl_model_2.cif, chain B (#43), sequence
alignment score = 4859.9
RMSD between 758 pruned atom pairs is 0.784 angstroms; (across all 953 pairs:
2.695)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_deltatrunc_golph3_fl_model_3.cif, chain B (#44), sequence
alignment score = 4853.9
RMSD between 760 pruned atom pairs is 0.870 angstroms; (across all 953 pairs:
2.928)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_deltatrunc_golph3_fl_model_4.cif, chain B (#45), sequence
alignment score = 4850.3
RMSD between 773 pruned atom pairs is 0.728 angstroms; (across all 953 pairs:
2.378)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_0.cif, chain B (#46),
sequence alignment score = 4879.1
RMSD between 776 pruned atom pairs is 0.758 angstroms; (across all 953 pairs:
3.074)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_1.cif, chain B (#47),
sequence alignment score = 4864.7
RMSD between 713 pruned atom pairs is 0.826 angstroms; (across all 953 pairs:
2.786)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_2.cif, chain B (#48),
sequence alignment score = 4858.7
RMSD between 767 pruned atom pairs is 0.724 angstroms; (across all 953 pairs:
2.681)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_3.cif, chain B (#49),
sequence alignment score = 4859.3
RMSD between 788 pruned atom pairs is 0.696 angstroms; (across all 953 pairs:
2.331)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_4.cif, chain B (#50),
sequence alignment score = 4853.3
RMSD between 790 pruned atom pairs is 0.889 angstroms; (across all 953 pairs:
2.298)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_man1b1_model_0.cif, chain E (#51), sequence
alignment score = 4862.3
RMSD between 745 pruned atom pairs is 0.764 angstroms; (across all 953 pairs:
2.927)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_man1b1_model_1.cif, chain E (#52), sequence
alignment score = 4852.7
RMSD between 786 pruned atom pairs is 0.865 angstroms; (across all 953 pairs:
2.722)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_man1b1_model_2.cif, chain E (#53), sequence
alignment score = 4846.1
RMSD between 789 pruned atom pairs is 0.888 angstroms; (across all 953 pairs:
2.508)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_man1b1_model_3.cif, chain E (#54), sequence
alignment score = 4843.1
RMSD between 769 pruned atom pairs is 0.721 angstroms; (across all 953 pairs:
2.945)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_man1b1_model_4.cif, chain E (#55), sequence
alignment score = 4833.5
RMSD between 744 pruned atom pairs is 0.804 angstroms; (across all 953 pairs:
2.757)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt7_model_0.cif, chain E (#56), sequence
alignment score = 4850.3
RMSD between 768 pruned atom pairs is 0.753 angstroms; (across all 953 pairs:
2.885)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt7_model_1.cif, chain E (#57), sequence
alignment score = 4852.1
RMSD between 720 pruned atom pairs is 0.792 angstroms; (across all 953 pairs:
2.881)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt7_model_2.cif, chain E (#58), sequence
alignment score = 4837.1
RMSD between 889 pruned atom pairs is 0.711 angstroms; (across all 953 pairs:
2.128)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt7_model_3.cif, chain E (#59), sequence
alignment score = 4841.3
RMSD between 749 pruned atom pairs is 0.804 angstroms; (across all 953 pairs:
3.211)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt7_model_4.cif, chain E (#60), sequence
alignment score = 4828.7
RMSD between 712 pruned atom pairs is 0.875 angstroms; (across all 953 pairs:
2.880)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt2_model_0.cif, chain E (#61), sequence
alignment score = 4841.9
RMSD between 772 pruned atom pairs is 0.832 angstroms; (across all 953 pairs:
2.917)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt2_model_1.cif, chain E (#62), sequence
alignment score = 4830.5
RMSD between 767 pruned atom pairs is 1.024 angstroms; (across all 953 pairs:
2.805)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt2_model_2.cif, chain E (#63), sequence
alignment score = 4823.3
RMSD between 767 pruned atom pairs is 0.852 angstroms; (across all 953 pairs:
3.765)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt2_model_3.cif, chain E (#64), sequence
alignment score = 4799.9
RMSD between 781 pruned atom pairs is 0.886 angstroms; (across all 953 pairs:
2.678)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_galnt2_model_4.cif, chain E (#65), sequence
alignment score = 4855.1
RMSD between 649 pruned atom pairs is 0.917 angstroms; (across all 953 pairs:
2.733)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_fam3c_model_0.cif, chain E (#66), sequence
alignment score = 4826.3
RMSD between 757 pruned atom pairs is 0.870 angstroms; (across all 953 pairs:
4.009)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_fam3c_model_1.cif, chain E (#67), sequence
alignment score = 4823.3
RMSD between 791 pruned atom pairs is 0.692 angstroms; (across all 953 pairs:
1.847)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_fam3c_model_2.cif, chain E (#68), sequence
alignment score = 4846.7
RMSD between 738 pruned atom pairs is 0.788 angstroms; (across all 953 pairs:
4.195)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_fam3c_model_3.cif, chain E (#69), sequence
alignment score = 4850.3
RMSD between 764 pruned atom pairs is 0.688 angstroms; (across all 953 pairs:
3.004)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipids_fam3c_model_4.cif, chain E (#70), sequence
alignment score = 4850.3
RMSD between 748 pruned atom pairs is 0.913 angstroms; (across all 953 pairs:
2.788)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_lcs_model_0.cif, chain E (#71), sequence
alignment score = 4846.1
RMSD between 764 pruned atom pairs is 0.815 angstroms; (across all 953 pairs:
2.852)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_lcs_model_1.cif, chain E (#72), sequence
alignment score = 4843.7
RMSD between 740 pruned atom pairs is 0.878 angstroms; (across all 953 pairs:
3.021)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_lcs_model_2.cif, chain E (#73), sequence
alignment score = 4844.3
RMSD between 768 pruned atom pairs is 0.842 angstroms; (across all 953 pairs:
2.822)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_lcs_model_3.cif, chain E (#74), sequence
alignment score = 4838.3
RMSD between 762 pruned atom pairs is 0.904 angstroms; (across all 953 pairs:
3.114)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_lcs_model_4.cif, chain E (#75), sequence
alignment score = 4834.1
RMSD between 767 pruned atom pairs is 1.170 angstroms; (across all 953 pairs:
2.629)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_gpp130_model_0.cif, chain E (#76), sequence
alignment score = 4843.1
RMSD between 777 pruned atom pairs is 0.739 angstroms; (across all 953 pairs:
3.690)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_gpp130_model_1.cif, chain E (#77), sequence
alignment score = 4828.7
RMSD between 773 pruned atom pairs is 0.885 angstroms; (across all 953 pairs:
2.109)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_gpp130_model_2.cif, chain E (#78), sequence
alignment score = 4847.9
RMSD between 757 pruned atom pairs is 0.838 angstroms; (across all 953 pairs:
2.411)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_gpp130_model_3.cif, chain E (#79), sequence
alignment score = 4826.9
RMSD between 775 pruned atom pairs is 0.920 angstroms; (across all 953 pairs:
2.422)
Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with
fold_20241015_copi_golph3_lipid_gpp130_model_4.cif, chain E (#80), sequence
alignment score = 4829.3
RMSD between 750 pruned atom pairs is 0.629 angstroms; (across all 953 pairs:
2.904)
> select add #21
37603 atoms, 38310 bonds, 4735 residues, 1 model selected
> select add #22
75206 atoms, 76620 bonds, 9470 residues, 2 models selected
> select add #23
112809 atoms, 114930 bonds, 14205 residues, 3 models selected
> select add #24
150412 atoms, 153240 bonds, 18940 residues, 4 models selected
> select add #25
188015 atoms, 191550 bonds, 23675 residues, 5 models selected
> show sel cartoons
> select subtract #25
150412 atoms, 153240 bonds, 18940 residues, 4 models selected
> select subtract #24
112809 atoms, 114930 bonds, 14205 residues, 3 models selected
> select subtract #23
75206 atoms, 76620 bonds, 9470 residues, 2 models selected
> select subtract #22
37603 atoms, 38310 bonds, 4735 residues, 1 model selected
> select subtract #21
Nothing selected
> hide #24 models
> hide #25 models
> hide #23 models
> hide #22 models
> hide #21 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250212_AF3_all_results_aligned.cxs"
> show #21 models
> show #1 models
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> close #25
> select add #26
36421 atoms, 37093 bonds, 4578 residues, 1 model selected
> select add #27
72842 atoms, 74186 bonds, 9156 residues, 2 models selected
> select add #28
109263 atoms, 111279 bonds, 13734 residues, 3 models selected
> select add #29
145684 atoms, 148372 bonds, 18312 residues, 4 models selected
> select add #30
182105 atoms, 185465 bonds, 22890 residues, 5 models selected
> show sel cartoons
> select subtract #30
145684 atoms, 148372 bonds, 18312 residues, 4 models selected
> select subtract #29
109263 atoms, 111279 bonds, 13734 residues, 3 models selected
> select subtract #28
72842 atoms, 74186 bonds, 9156 residues, 2 models selected
> select subtract #27
36421 atoms, 37093 bonds, 4578 residues, 1 model selected
> select subtract #26
Nothing selected
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> show #27 models
> close #27
> close #29
> select add #31
36853 atoms, 37501 bonds, 4602 residues, 1 model selected
> select add #32
73706 atoms, 75002 bonds, 9204 residues, 2 models selected
> select add #33
110559 atoms, 112503 bonds, 13806 residues, 3 models selected
> select add #34
147412 atoms, 150004 bonds, 18408 residues, 4 models selected
> select add #35
184265 atoms, 187505 bonds, 23010 residues, 5 models selected
> show sel cartoons
> select subtract #35
147412 atoms, 150004 bonds, 18408 residues, 4 models selected
> select subtract #34
110559 atoms, 112503 bonds, 13806 residues, 3 models selected
> select subtract #33
73706 atoms, 75002 bonds, 9204 residues, 2 models selected
> select subtract #32
36853 atoms, 37501 bonds, 4602 residues, 1 model selected
> select subtract #31
Nothing selected
> hide #35 models
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> close #31-35
> select add #36
34868 atoms, 35508 bonds, 4394 residues, 1 model selected
> select add #37
69736 atoms, 71016 bonds, 8788 residues, 2 models selected
> select add #38
104604 atoms, 106524 bonds, 13182 residues, 3 models selected
> select add #39
139472 atoms, 142032 bonds, 17576 residues, 4 models selected
> select add #40
174340 atoms, 177540 bonds, 21970 residues, 5 models selected
> show sel cartoons
> select subtract #40
139472 atoms, 142032 bonds, 17576 residues, 4 models selected
> select subtract #39
104604 atoms, 106524 bonds, 13182 residues, 3 models selected
> select subtract #38
69736 atoms, 71016 bonds, 8788 residues, 2 models selected
> select subtract #37
34868 atoms, 35508 bonds, 4394 residues, 1 model selected
> select subtract #36
Nothing selected
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> show #37 models
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> show #40 models
> hide #40 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250212_AF3_all_results_aligned_v2.cxs"
[Repeated 1 time(s)]
——— End of log from Wed Feb 12 13:50:37 2025 ———
opened ChimeraX session
> select add #41
39522 atoms, 40261 bonds, 4983 residues, 1 model selected
> select add #42
79044 atoms, 80522 bonds, 9966 residues, 2 models selected
> select add #43
118566 atoms, 120783 bonds, 14949 residues, 3 models selected
> select add #44
158088 atoms, 161044 bonds, 19932 residues, 4 models selected
> select add #45
197610 atoms, 201305 bonds, 24915 residues, 5 models selected
> show sel cartoons
> select subtract #45
158088 atoms, 161044 bonds, 19932 residues, 4 models selected
> select subtract #44
118566 atoms, 120783 bonds, 14949 residues, 3 models selected
> select subtract #43
79044 atoms, 80522 bonds, 9966 residues, 2 models selected
> select subtract #42
39522 atoms, 40261 bonds, 4983 residues, 1 model selected
> select subtract #41
Nothing selected
> hide #45 models
> hide #44 models
> hide #43 models
> hide #42 models
> hide #41 models
> select add #36
34868 atoms, 35508 bonds, 4394 residues, 1 model selected
> select add #37
69736 atoms, 71016 bonds, 8788 residues, 2 models selected
> select add #38
104604 atoms, 106524 bonds, 13182 residues, 3 models selected
> select add #39
139472 atoms, 142032 bonds, 17576 residues, 4 models selected
> select add #40
174340 atoms, 177540 bonds, 21970 residues, 5 models selected
> select add #41
213862 atoms, 217801 bonds, 26953 residues, 6 models selected
> show #46-80 cartoons
> select subtract #36
178994 atoms, 182293 bonds, 22559 residues, 5 models selected
> select subtract #37
144126 atoms, 146785 bonds, 18165 residues, 4 models selected
> select subtract #38
109258 atoms, 111277 bonds, 13771 residues, 3 models selected
> select subtract #39
74390 atoms, 75769 bonds, 9377 residues, 2 models selected
> select subtract #40
39522 atoms, 40261 bonds, 4983 residues, 1 model selected
> select subtract #41
Nothing selected
> show #40 models
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> hide #16 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20250212_AF3_all_results_aligned_v3.cxs"
——— End of log from Wed Feb 12 15:48:26 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
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: 2 days, 3 hours, 59 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: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 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 , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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