![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16021 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-x86_64-i386-64bit
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 0x0000000204a8e240 (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.surface._surface, 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.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.chem_group._chem_group, chimerax.atom_search.ast, chimerax.coulombic._esp, chimerax.mlp._mlp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 63)
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{
"uptime" : 1000000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 166650,
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"build" : "23G93",
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"captureTime" : "2024-09-25 20:22:03.7500 +0100",
"codeSigningMonitor" : 1,
"incident" : "8CDB7D00-EED0-41DA-A6B2-781A24C4B2F8",
"pid" : 88455,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-25 11:29:54.5205 +0100",
"procStartAbsTime" : 24079284145589,
"procExitAbsTime" : 24577915846215,
"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":"EDD8B610-D200-5890-8C1B-29D609195B52","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "ECED8795-F73E-B1B9-01B1-947CFD465E40",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 1,
"sleepWakeUUID" : "86C7C461-B75B-4121-A4E7-A7DC84BC428A",
"sip" : "enabled",
"vmRegionInfo" : "0x3deb4ade88f8 is not in any region. Bytes after previous region: 67599746369785 Bytes before following region: 37472333559560\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00003deb4ade88f8","rawCodes":[1,68080782706936],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00003deb4ade88f8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":88455},
"vmregioninfo" : "0x3deb4ade88f8 is not in any region. Bytes after previous region: 67599746369785 Bytes before following region: 37472333559560\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/GOLPH3 3kn1.pdb"
GOLPH3 3kn1.pdb title:
Crystal structure of golgi phosphoprotein 3 N-term truncation variant [more
info...]
Chain information for GOLPH3 3kn1.pdb #1
---
Chain | Description | UniProt
A | golgi phosphoprotein 3 | GOLP3_HUMAN 52-298
Non-standard residues in GOLPH3 3kn1.pdb #1
---
SO4 — sulfate ion
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select sulfate
30 atoms, 24 bonds, 6 residues, 1 model selected
> hide sel atoms
> select clear
Alignment identifier is 1/A
> select clear
> select /A:59-297
1895 atoms, 1926 bonds, 239 residues, 1 model selected
> hide sel atoms
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ARG 59
/A ARG 112
/A GLN 211
/A ARG 231
/A LYS 266
/A LYS 282
/A ASN 284
/A THR 297
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for GOLPH3 3kn1.pdb_A SES surface #1.1: minimum, -23.22, mean
-2.15, maximum 13.32
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select ::name="HOH"
9 atoms, 9 residues, 1 model selected
> hide sel atoms
> select clear
> set bgColor white
> set bgColor black
> save /Users/sean/Desktop/image1.png supersample 3
> set bgColor white
> save /Users/sean/Desktop/image2.png supersample 3
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> save /Users/sean/Desktop/image3.png supersample 3
> lighting soft
> save /Users/sean/Desktop/image4.png supersample 3
> lighting simple
> save /Users/sean/Desktop/image5.png supersample 3
> lighting flat
> save /Users/sean/Desktop/image6.png supersample 3
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> save /Users/sean/Desktop/image7.png supersample 3
> lighting soft
> save /Users/sean/Desktop/image8.png supersample 3
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> save /Users/sean/Desktop/image9.png supersample 3
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> mlp
Map values for surface "GOLPH3 3kn1.pdb_A SES surface": minimum -27.57, mean
-4.444, maximum 36.64
To also show corresponding color key, enter the above mlp command and add key
true
> save /Users/sean/Desktop/image10.png supersample 3
> lighting simple
> save /Users/sean/Desktop/image11.png supersample 3
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> save /Users/sean/Desktop/image12.png supersample 3
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> lighting full
> lighting flat
> coulombic
Coulombic values for GOLPH3 3kn1.pdb_A SES surface #1.1: minimum, -23.22, mean
-2.15, maximum 13.32
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Unsupported scale factor (0.000000) detected on Display1
> hide surfaces
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/sean/Desktop/image1.png supersample 3
> graphics silhouettes true
> save /Users/sean/Desktop/image2.png supersample 3
> select ::name="GLN"
77 atoms, 68 bonds, 9 residues, 1 model selected
> show sel atoms
> undo
> show sel atoms
> hide sel atoms
> select ::name="GLU"
171 atoms, 153 bonds, 19 residues, 1 model selected
> show sel atoms
> select ::name="ASP"
112 atoms, 98 bonds, 14 residues, 1 model selected
> show sel atoms
> select clear
> save /Users/sean/Desktop/image3.png supersample 3
> graphics silhouettes false
> save /Users/sean/Desktop/image4.png supersample 3
> select /A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:154,159
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:83,154,159
26 atoms, 23 bonds, 3 residues, 1 model selected
> select /A:83,154,159,273
34 atoms, 30 bonds, 4 residues, 1 model selected
> select /A:83,154,159,273,275
42 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:83,154,159,273,275,277
51 atoms, 45 bonds, 6 residues, 1 model selected
> select /A:83,154,159,273,275,277,279
60 atoms, 53 bonds, 7 residues, 1 model selected
> select /A:73,83,154,159,273,275,277,279
68 atoms, 60 bonds, 8 residues, 1 model selected
> select /A:73,75,83,154,159,273,275,277,279
77 atoms, 68 bonds, 9 residues, 1 model selected
> select /A:73,75,83,154,159,250,273,275,277,279
86 atoms, 76 bonds, 10 residues, 1 model selected
> select /A:73,75,83,154,159,247,250,273,275,277,279
94 atoms, 83 bonds, 11 residues, 1 model selected
> select /A:73,75,83,154,159,247,250,258-259,273,275,277,279
111 atoms, 99 bonds, 13 residues, 1 model selected
> select /A:73,75,83,154,159,247,250,258-259,262,273,275,277,279
119 atoms, 106 bonds, 14 residues, 1 model selected
> select ~sel
1815 atoms, 1818 bonds, 240 residues, 1 model selected
> hide sel atoms
> select clear
> save /Users/sean/Desktop/image5.png supersample 3
> graphics silhouettes true
> save /Users/sean/Desktop/image6.png supersample 3
> close #1
> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/20240406_leaf_fitting_v26.cxs" format session
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 ChimeraX session
> hide #!25 models
> show #!25 models
> hide #!34 models
> show #!33 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> ui tool show "Side View"
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> hide #32.1 models
> show #32.1 models
> hide #32.2 models
> show #32.2 models
> hide #!25 models
> show #!25 models
> show #!33 models
> hide #!33 models
> show #!34 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!34 models
> set bgColor white
> hide #39 models
> show #39 models
> hide #39 models
> hide #28 models
> show #28 models
> hide #26.3 models
> hide #!29 models
> show #!29 models
> hide #28 models
> show #28 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> save /Users/sean/Desktop/image1.png supersample 3
> hide #!30 models
> show #!30 models
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
> hide #32.1 models
> show #32.1 models
> hide #32.2 models
> show #32.2 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> ui tool show "Side View"
> view
> close
> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/20240406_leaf_fitting_v26.cxs" format session
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 ChimeraX session
> show #!3 models
> hide #!3 models
> show #!3 models
Unsupported scale factor (0.000000) detected on Display1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/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.
[deleted to fit within ticket limits]
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> color zone #58 near #38 distance 10.26
> hide #!1 models
> select subtract #58
Nothing selected
> color zone #58 near #38 distance 10.93
> color zone #58 near #38 distance 4.35
> color zone #58 near #38 distance 5.21
> color zone #58 near #38 distance 5.14
> color zone #58 near #39 distance 5.14
> volume splitbyzone #58
Opened relion_locres_filtered_20240326_GT.mrc 0 as #59.1, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc 1 as #59.2, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
> hide #!59.2 models
> show #!59.2 models
> hide #!59.1 models
> show #!59.1 models
> hide #!59.2 models
> show #!59.2 models
> color zone #58 near #38 distance 5.14
[Repeated 1 time(s)]
> color zone #59.1 near #38 distance 10.26
[Repeated 1 time(s)]
> color zone #59.1 near #41 distance 9.26
> color zone #59.1 near #41 distance 9.16
> color zone #59.1 near #41 distance 9.06
> color zone #59.1 near #41 distance 8.96
> color zone #59.1 near #41 distance 8.86
> color zone #59.1 near #41 distance 8.76
> color zone #59.1 near #41 distance 8.66
> color zone #59.1 near #41 distance 8.56
> color zone #59.1 near #41 distance 8.46
> color zone #59.1 near #41 distance 8.36
> color zone #59.1 near #41 distance 8.26
> color zone #59.1 near #41 distance 8.16
> color zone #59.1 near #41 distance 8.06
> color zone #59.1 near #41 distance 7.96
> color zone #59.1 near #38 distance 7.96
> help help:user/tools/colorzone.html
> close #59.1
> close #59
> show #!58 models
> color zone #58 near #38 distance 5.14
> color zone #58 near #39 distance 5.14
> combine #38 #39 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'G'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'H'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'I'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'J'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'K'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'L'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'M'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'N'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'O'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'P'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Q'
> hide #!59 models
> show #!59 models
> hide #55 models
> hide #!54 models
> hide #53 models
> hide #52 models
> hide #51 models
> hide #50 models
> hide #!49 models
> hide #48 models
> hide #47 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #42 models
> hide #41 models
> hide #39 models
> hide #38 models
> hide #!58 models
> color zone #58 near #59 distance 5.14
> show #!58 models
> hide #!59 models
> color zone #58 near #59 distance 4.97
> color zone #58 near #59 distance 4.45
> surface dust #58 size 17.1
> color zone #58 near #59 distance 4.31
> color zone #58 near #59 distance 4.7
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #58 step 1
> volume #58 level 0.005
> color zone #58 near #59 distance 5.19
> set bgColor white
> save /Users/becca/Desktop/image1.png supersample 3
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> volume #58 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
> volume #58 level 0.005
> color zone #58 near #59 distance 5.43
> color zone #58 near #59 distance 6.99
> save /Users/becca/Desktop/image1.png supersample 3
> volume #58 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
> hide #!58 models
> show #!59 models
> rename #59 combined_model_COPI_GOLPH3
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v1.cxs"
> show #!1 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v1.cxs"
> hide #!59 models
> show #!58 models
> hide #!1 models
> volume #58 level 0.005
> ui mousemode right "map eraser"
> volume erase #58 center 281.84,261.87,305.71 radius 22.725
Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> surface dust #61 size 17.1
> color zone #61 near #59 distance 10.26
> color zone #61 near #59 distance 10.16
> color zone #61 near #59 distance 6.84
> save /Users/becca/Desktop/image1.png supersample 3
> volume #61 level 0.008
> save /Users/becca/Desktop/image2.png supersample 3
> volume #61 level 0.005
> save /Users/becca/Desktop/image3.png supersample 3
> volume #61 level 0.008
> save /Users/becca/Desktop/image4.png supersample 3
> color zone #61 near #59 distance 4.76
> color zone #61 near #59 distance 4.4
> color zone #61 near #59 distance 5.99
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!61 models
> show #!1 models
> color #1 #a9a9a9a0 models
> hide #!1 models
> color #1 #a9a9a9a1 models
> show #!1 models
> show #!57 models
> hide #!57 models
> show #!59 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right select
> select #59/O:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 6 atom styles
> show #!1 models
> hide #!1 models
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #59/O:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #59/O:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #59/O:106
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #59/Q:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> select #59/Q:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #59/Q:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #59/Q:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #59/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select clear
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #59/Q:226@CB
1 atom, 1 residue, 1 model selected
> select #59/Q:226@CA
1 atom, 1 residue, 1 model selected
> select #59/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #59/O:107@NZ
1 atom, 1 residue, 1 model selected
> select #59/Q:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/O:106@CG
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #59/O:106
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #59/O:108@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> undo
> select #59/O:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #59/Q:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> select #59/M:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #59/M:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/M:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/M:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:5
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #59/M:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #59/M:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:8
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1
2 models selected
> select #59/M:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1
2 models selected
> select #1
2 models selected
> select clear
> select #1
2 models selected
> select clear
> select #59/M:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:13
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:14
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:15
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/K:255
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:254
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:250
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:249
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"
> show #!61 models
> hide #!1 models
> color zone #61 near #59 distance 5.86
> color zone #61 near #59 distance 5.55
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"
——— End of log from Tue Aug 6 15:17:45 2024 ———
opened ChimeraX session
> hide #!61 models
> show #!61 models
> hide #!59 models
> show #!59 models
> hide #!61 models
> show #!58 models
> hide #!58 models
> show #!58 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!61 models
> show #!56 models
> hide #!56 models
> show #!57 models
> close #61
> combine #1
No structures specified
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT.mrc as #60, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 2, values float32
> select add #60
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #60,1,0,0,94.293,0,1,0,59.794,0,0,1,17.203
> view matrix models #60,1,0,0,87.011,0,1,0,46.591,0,0,1,75.712
> view matrix models #60,1,0,0,62.484,0,1,0,72.607,0,0,1,72.836
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #60 inMap #1
Fit map relion_locres_filtered_20240326_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30918 points
correlation = 1, correlation about mean = 1, overlap = 3.365
steps = 92, shift = 5.1, angle = 0.971 degrees
Position of relion_locres_filtered_20240326_GT.mrc (#60) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00004012 -0.00014956 0.04461249
-0.00004012 1.00000000 0.00001176 -0.00027160
0.00014956 -0.00001176 0.99999999 -0.04335390
Axis -0.07572659 -0.96307673 -0.25835770
Axis point 275.92599265 0.00000000 302.35452588
Rotation angle (degrees) 0.00889794
Shift along axis 0.00808403
> select subtract #60
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #60 step 1
> volume #60 level 0.005
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v5.cxs"
> color #24 #98fcffff
> color #24 label_red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #24 alphav1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color name label_red #E32723
Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723
> color name label_purple #6C4896
Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896
> color name arf1v2 #EB70A8
Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8
> color name alphav1 #5786F5
Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5
> color name alphav2 #2A4B9B
Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b
> color name betapv1 #53EAF3
Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3
> color name betapv2 #759ED9
Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9
> color name betav1 #37863D
Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d
> color name betav2 #207B35
Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35
> color name deltav1 #CE8041
Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041
> color name deltav2 #E97408
Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408
> color name epsilonv1 #F06969
Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969
> color name gammav1 #2AFF3C
Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c
> color name gammav2 #61B230
Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230
> color name zetav1 #E0C819
Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819
> color name zetav2 #EFE30C
Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c
> color name arf1v1 #FF76AF
Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af
> color #24 label_red
> color #60 white models
> color #56 white models
> hide #!57 models
> hide #!58 models
> hide #!59 models
> color #38 alphav1
> show #38 models
> hide #!60 models
> show #39 models
> show #41 models
> show #42 models
> show #!43 models
> show #!44 models
> show #!45 models
> show #!46 models
> show #48 models
> show #47 models
> show #!49 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #!54 models
> color #39 alphav1
> color #41 betapv1
> color #42 betapv1
> color #43 betav1
> color #44 betav1
> color #45 betav1
> color #46 deltav1
> color #47 gammav1
> color #47 gammav2
> color #48 gammav2
> color #49 gammav2
> color #43 betav2
> color #44 betav2
> color #45 betav2
> color #50 zetav1
> color #51 arf1v1
> color #52 arf1v1
> color #53 arf1v1
> color #47 #acacacff
> color #47 gammav2
> color #47 #61db30ff
> color #47 #61c730ff
> color #47 #58c730ff
> color #47 #58de30ff
> color name gammav3 #58DE30
Color 'gammav3' is opaque: rgb(34.5%, 87.1%, 18.8%) hex: #58de30
> color #48 gammav3
> color #49 gammav3
> color #51 arf1v2
> color #52 arf1v2
> color #53 arf1v2
> color #38 alphav1
> color #38 alphav2
> color #39 alphav2
> color #54 label_purple
> color #55 label_purple
> show #55 models
> color #11 #801effff
> color #11 #801ed1ff
> color name label_purplev2 #7F1ED1
Color 'label_purplev2' is opaque: rgb(49.8%, 11.8%, 82%) hex: #7f1ed1
> color #54 label_purplev2
> color #55 label_purplev2
> combine #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54
> #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'D' in fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif
#40 to 'I'
Remapping chain ID 'E' in fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif
#40 to 'J'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_M1-S586.cif #41 to
'K'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'L'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'M'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'N'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'O'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'P'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'Q'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'R'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'S'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'T'
Remapping chain ID 'B' in 20240711_copi_golph3_beta_Arf1_.cif #51 to 'U'
Remapping chain ID 'C' in 20240711_copi_golph3_gamma_Arf1_.cif #52 to 'V'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'W'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_M1-.cif #54 to 'X'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Y'
> hide #38 models
> hide #39 models
> hide #41 models
> hide #42 models
> hide #!43 models
> hide #!44 models
> hide #!45 models
> hide #!46 models
> hide #47 models
> hide #48 models
> hide #!49 models
> hide #50 models
> hide #51 models
> hide #52 models
> hide #53 models
> hide #!54 models
> hide #55 models
> rename #59 combined_model_COPI_GOLPH3_colorset1
> rename #58 relion_locres_filtered_20240326_GT_colorset1.mrc
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!60 models
> color zone #60 near #61 distance 10.26
> color zone #60 near #61 distance 10.73
> color zone #60 near #61 distance 4.91
> volume #60 level 0.01316
> close #61
> combine #38 #39 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'G'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'H'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'I'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'J'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'K'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'L'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'M'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'N'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'O'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'P'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Q'
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #60 near #61 distance 4.91
> hide #!60 models
> ui mousemode right select
> select #61/K:255
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:254
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #61/K:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select clear
> select #61/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:250
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:249
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete sel
> show #!60 models
> color single #60
> color zone #60 near #61 distance 4.91
> volume #60 level 0.008979
> color zone #60 near #61 distance 4.85
> color zone #60 near #61 distance 6.64
> color #1 #ebebebff models
> color #1 #d6d6d6ff models
> volume #60 level 0.008
> hide #!61 models
> rename #61 combine_model_COPI_GOLPH3_colorset2
> rename #60 relion_locres_filtered_20240326_GT_colorset2.mrc
> save /Users/becca/Desktop/image1.png supersample 3
> color #1 #d6d6d6cc models
> color #1 #d6d6d69a models
> color #1 #d6d6d699 models
> show #!1 models
> hide #!60 models
> show #!61 models
> save /Users/becca/Desktop/image2.png supersample 3
> save /Users/becca/Desktop/image3.png supersample 3
> hide #!61 models
> show #!60 models
> hide #!1 models
> save /Users/becca/Desktop/image4.png supersample 3
> color #60 #ffffffb9 models
> color #60 #ffffffb7 models
> color zone #60 near #61 distance 6.64
> color #60 #ffffffb8 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v6.cxs"
> hide #!60 models
> show #!61 models
> color #61/chain Q label_purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #61/chainQ label_purple
> color #61/chainP label_purple
> color #61/chainP blue
> color #61/P blue
> undo
> color #61/Q label_purple
> color #61/R label_purple
> color #61/p label_purple
> undo
> color #61/o label_purple
> undo
> color #61/a label_purple
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32
> color #62 white models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #62 step 1
> volume #62 level 0.008
> select add #62
2 models selected
> show #!60 models
> ui mousemode right "translate selected models"
> view matrix models #62,1,0,0,82.731,0,1,0,56.524,0,0,1,33.509
> view matrix models #62,1,0,0,79.094,0,1,0,68.742,0,0,1,76.061
> view matrix models #62,1,0,0,75.329,0,1,0,66.28,0,0,1,82.958
> view matrix models #62,1,0,0,62.569,0,1,0,73.325,0,0,1,77.393
> fitmap #62 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 1, correlation about mean = 1, overlap = 21.45
steps = 52, shift = 2.4, angle = 0.977 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#62) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00001875 -0.00002627 0.01893074
0.00001875 1.00000000 -0.00002003 -0.00224731
0.00002628 0.00002003 1.00000000 0.00132667
Axis 0.52718994 -0.69167549 0.49361502
Axis point 178.51353821 0.00000000 475.91658522
Rotation angle (degrees) 0.00217651
Shift along axis 0.01218937
> select subtract #62
Nothing selected
> color zone #62 near #61 distance 10.26
> hide #!60 models
> hide #!61 models
> surface dust #62 size 17.1
> show #!60 models
> surface dust #60 size 17.1
> surface dust #62 size 17.1
> hide #!62 models
> hide #!60 models
> show #!62 models
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image6.png supersample 3
> hide #!1 models
> show #!1 models
> save /Users/becca/Desktop/image7.png supersample 3
> hide #!1 models
> hide #!61 models
> show #!62 models
> save /Users/becca/Desktop/image8.png supersample 3
> save /Users/becca/Desktop/image9.png supersample 3
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image10.png supersample 3
> hide #!1 models
> color #61/b gammav2
> color #61/c gammav2
> color #61/d gammav2
> color #61/e gammav2
> color #61/f gammav2
> color #61/g gammav2
> color #61/f betapv2
> color #61/g betapv2
> color #61/h gammav2
> color #61/i gammav2
> color #61/j gammav2
> color #61/k gammav2
> color #61/l gammav2
> color #61/m gammav2
> color #61/n gammav2
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32
> color #63 white models
> select add #63
2 models selected
> view matrix models #63,1,0,0,75.253,0,1,0,55.49,0,0,1,11.12
> view matrix models #63,1,0,0,90.631,0,1,0,59.745,0,0,1,63.045
> view matrix models #63,1,0,0,68.515,0,1,0,55.118,0,0,1,78.162
> view matrix models #63,1,0,0,66.634,0,1,0,67.567,0,0,1,67.24
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #63 step 1
> volume #63 level 0.008
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 0.5415, correlation about mean = 0.1363, overlap = 7.061
steps = 116, shift = 7.07, angle = 5.74 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99362306 0.08167924 -0.07772850 -0.92565197
-0.08058175 0.99660031 0.01715800 10.92285128
0.07886570 -0.01078508 0.99682691 -23.17442071
Axis -0.12297538 -0.68915930 -0.71409839
Axis point 213.07603457 14.21459699 0.00000000
Rotation angle (degrees) 6.52360209
Shift along axis 9.13506435
> show #!1 models
> view matrix models
> #63,0.99499,0.069158,-0.072244,60.427,-0.06889,0.99761,0.0061881,84.855,0.072498,-0.0011802,0.99737,52.494
> view matrix models
> #63,0.99499,0.069158,-0.072244,61.276,-0.06889,0.99761,0.0061881,84.838,0.072498,-0.0011802,0.99737,55.066
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> hide #!61 models
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 0.5415, correlation about mean = 0.1362, overlap = 7.06
steps = 64, shift = 3.65, angle = 0.0144 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99360075 0.08181777 -0.07786785 -0.90541724
-0.08073064 0.99659074 0.01701358 11.00212074
0.07899439 -0.01061838 0.99681851 -23.23121300
Axis -0.12141808 -0.68927119 -0.71425687
Axis point 213.54257878 14.23471065 0.00000000
Rotation angle (degrees) 6.53375156
Shift along axis 9.11954274
> view matrix models
> #63,0.99497,0.069297,-0.072381,72.42,-0.069041,0.9976,0.006042,87.797,0.072626,-0.0010144,0.99736,54.674
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 1, correlation about mean = 1, overlap = 21.46
steps = 152, shift = 9.34, angle = 6.54 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00003458 0.00000150 0.00697228
0.00003458 1.00000000 -0.00002441 0.00466924
-0.00000150 0.00002441 1.00000000 -0.01150830
Axis 0.57631042 0.03541164 0.81646330
Axis point -140.35346721 288.49393815 0.00000000
Rotation angle (degrees) 0.00242674
Shift along axis -0.00521256
> select subtract #63
Nothing selected
> hide #!1 models
> show #!62 models
> hide #!62 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> color zone #63 near #61 distance 10.26
> color zone #63 near #61 distance 10.66
> color zone #63 near #61 distance 8.31
> surface dust #63 size 17.1
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> save /Users/becca/Desktop/image1.png supersample 3
> hide #!63 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image2.png supersample 3
> save /Users/becca/Desktop/image3.png supersample 3
> hide #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!61 models
> show #!63 models
> save /Users/becca/Desktop/image4.png supersample 3
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!63 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image6.png supersample 3
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_02_final_volume.mrc"
Opened cryosparc_P126_J2191_class_02_final_volume.mrc as #64, grid size
180,180,180, pixel 2.42, shown at level 0.333, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_01_final_volume.mrc"
Opened cryosparc_P126_J2191_class_01_final_volume.mrc as #65, grid size
180,180,180, pixel 2.42, shown at level 0.333, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_00_final_volume.mrc"
Opened cryosparc_P126_J2191_class_00_final_volume.mrc as #66, grid size
180,180,180, pixel 2.42, shown at level 0.337, step 1, values float32
> close #66
> close #65
> close #64
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"
——— End of log from Fri Aug 9 13:21:55 2024 ———
opened ChimeraX session
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"
> includeMaps true
——— End of log from Wed Sep 25 22:56:27 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
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: MacBookPro18,1
Model Number: Z14V000GPB/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 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: 29 days, 9 hours, 10 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
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-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-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-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-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
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-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
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
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
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
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
pycollada: 0.8
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
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
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
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 , 13 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 , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Mac Qt window toolkit crashed in _NSViewHierarchyDidChangeBackingProperties, probably waking from sleep or connecting or disconnecting an external display. We do not have any fix for this bug that is in the Qt window toolkit (version 6.6 and 6.7) on Mac. I can only suggest you save your work before connecting or disconnecting external displays or letting the computer sleep. We hope a future Qt version will fix this.
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Reported by Sean Munro