![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 22 hours ago
Closed 76 minutes ago
#19535 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
The following bug report has been submitted:
Platform: macOS-15.7.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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 0x0000000206d4a140 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, lxml.builder, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 63)
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{
"uptime" : 5400,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 1700,
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"captureTime" : "2025-12-23 11:21:41.2017 +1300",
"codeSigningMonitor" : 1,
"incident" : "6A6AE09C-7429-4D43-A982-744E4F61ACA9",
"pid" : 4690,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-23 10:05:34.7779 +1300",
"procStartAbsTime" : 22251877805,
"procExitAbsTime" : 131848131777,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5E6B9D0E-B24A-5F0D-B03B-60D34F0A124C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B764343E-6690-75E4-BB9E-16AB9F8A0AF2",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "EFC49F7F-4351-4046-8320-4F37DC17BB24",
"sip" : "enabled",
"vmRegionInfo" : "0x6fd500187144 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00186fd500187144","rawCodes":[1,6878360061374788],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00186fd500187144 -> 0x00006fd500187144 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":4690},
"vmregioninfo" : "0x6fd500187144 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Master Chimerax Workspaces/PCH45
> Neck/PCH45_NeckFitting_6.cxs"
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc as #3, grid size 416,416,416, pixel
1.37, shown at level 0.236, step 1, values float32
Opened Sheath[Unrefined]_C6Ring_R4?_ as #9, grid size 416,416,416, pixel 1.37,
shown at level 0.889, step 1, values float32
Opened Unnaccounted_for_Volumes as #14, grid size 416,416,416, pixel 1.37,
shown at level 0.662, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #13, grid size 416,416,416,
pixel 1.37, shown at level 0.604, step 1, values float32
Opened Unaccounted_volumes_updated as #15, grid size 416,416,416, pixel 1.37,
shown at level 0.537, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #18, grid size 416,416,416,
pixel 1.37, shown at level 0.887, step 1, values float32
Opened Unaccounted3 as #19, grid size 416,416,416, pixel 1.37, shown at level
0.457, step 1, values float32
Opened Gp24[Adaptor]_C6Ring_R4 as #24, grid size 416,416,416, pixel 1.37,
shown at level 0.82, step 1, values float32
Opened PCH45_Rough_Segmap cry.mrc as #23, grid size 416,416,416, pixel 1.37,
shown at level 0.497, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #2, grid size 416,416,416,
pixel 1.37, shown at level 0.585, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #25, grid size 416,416,416,
pixel 1.37, shown at level 0.585, step 1, values float32
Opened PCH45_Neck_C6_3_40A_map_sharp.mrc zone as #30, grid size 416,416,416,
pixel 1.37, shown at level 0.42, step 1, values float32
Opened PCH45_Gp182_AboveSheath_.mrc as #31, grid size 405,360,416, pixel
1.37,1.37,1.37, shown at level 0.431, step 1, values float32
> view name session-start
opened ChimeraX session
> hide #27 models
> lighting simple
> ui tool show "Side View"
> hide #29 models
> show #29 models
> volume #!9,13,24-25,30-31 showOutlineBox false
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> select add #30
1177 atoms, 1199 bonds, 146 residues, 3 models selected
> select add #31
1177 atoms, 1199 bonds, 146 residues, 5 models selected
> transparency sel & #31.1 50
> select subtract #30
1177 atoms, 1199 bonds, 146 residues, 3 models selected
> show #!30 models
> hide #!30 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!9 models
> show #!9 models
> select add #9
1177 atoms, 1199 bonds, 146 residues, 5 models selected
> select subtract #5
4 models selected
> vop subtract #9 #31 minrms True
Opened volume difference as #32, grid size 416,416,416, pixel 1.37, shown at
step 1, values float32
Minimum RMS scale factor for "PCH45_Gp182_AboveSheath_.mrc #31" above level
0.43098 is 0.63051
> select add #32
6 models selected
> show #!31 models
> select subtract #31
4 models selected
> select add #31
6 models selected
> select subtract #9
4 models selected
> vop subtract #31 #32 minrms True
Opened volume difference as #33, grid size 405,360,416, pixel 1.37,1.37,1.37,
shown at step 1, values float32
Minimum RMS scale factor for "volume difference #32" above level 0.88852 is 0
> hide #!33 models
> show #!33 models
> surface dust #13 size 13.7
> surface dust #24 size 13.7
> surface dust #25 size 13.7
> surface dust #33 size 13.7
> select add #33
6 models selected
> transparency sel & #33.1 50
> rename #33 PutativeGp183_C6Map
> select clear
> select add #33
2 models selected
> volume* threshold .82
Unknown command: volume* threshold .82
> volume threshold .82
Missing or invalid "volumes" argument: invalid density maps specifier
> volume threshold* .82
Expected a density maps specifier or a keyword
> volume threshold #* .82
Expected a keyword
> show #!32 models
> volume threshold #* level .82
Expected a keyword
> volume level #* .82
Invalid "level" argument: Expected a number
> volume threshold #* 0.82
Expected a keyword
> volume #* level 0.82
> volume #* transparency 0.25
> volume #* transparency 1
> volume #* transparency 0.75
> select clear
> volume #33 level 0.4049
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #21 models
> hide #!24 models
> hide #!22 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #26 models
> show #26 models
> hide #26 models
> show #26 models
> hide #26 models
> hide #29 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> hide #11 models
> hide #!8 models
> surface dust #32 size 13.7
> surface dust #33 size 13.7
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #1 models
> select add #4
1177 atoms, 1199 bonds, 146 residues, 1 model selected
> select add #1
258897 atoms, 267139 bonds, 31925 residues, 2 models selected
> hide #4 models
> select subtract #4
257720 atoms, 265940 bonds, 31779 residues, 1 model selected
> hide #5 models
> select clear
> select add #1
257720 atoms, 265940 bonds, 31779 residues, 1 model selected
> hide #1 models
> select subtract #1
Nothing selected
> show #5 models
> show #1 models
> hide #5 models
> show #4 models
> hide #4 models
> show #4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> close #2
> hide #4 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select add #6
16068 atoms, 16236 bonds, 2208 residues, 13 models selected
> close #6
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> select add #32
2 models selected
> color #32 #ff00bbff models
> select clear
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #27 models
> hide #27 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> show #11 models
> hide #11 models
> select add #1
257720 atoms, 265940 bonds, 31779 residues, 1 model selected
> color #32 #d6d6d6ff models
> select clear
> undo
> hide #11 models
> hide #!32 models
> show #!32 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> color #32 #ff009cff models
> select clear
> show #!3 models
> volume #!3,24,32 showOutlineBox false
> select add #3
2 models selected
> select clear
> select add #3
2 models selected
> volume #* level 0.5
> select clear
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #10 models
> hide #10 models
> show #10 models
> select add #10
3715 atoms, 3815 bonds, 462 residues, 1 model selected
Alignment identifier is 10/A
> select clear
> select #10/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:1-206
1653 atoms, 1694 bonds, 206 residues, 1 model selected
> select #10/A:201
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #10/A:1-201
1609 atoms, 1648 bonds, 201 residues, 1 model selected
> hide #!32 models
> show #!32 models
> select clear
> select #10/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:1-200
1595 atoms, 1632 bonds, 200 residues, 1 model selected
> delete sel
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_0.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_0.cif #2
---
Chain | Description
A | .
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_1.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_1.cif #6
---
Chain | Description
A | .
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_2.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_2.cif #34
---
Chain | Description
A | .
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_3.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_3.cif #35
---
Chain | Description
A | .
> open "/Users/croal939/Library/CloudStorage/OneDrive-
> UniversityofOtago/PCH45/PCH45 Alphafolded
> Proteins/fold_pch45_gp25trimmed_first_1_200aa/fold_pch45_gp25trimmed_first_1_200aa_model_4.cif"
Chain information for fold_pch45_gp25trimmed_first_1_200aa_model_4.cif #36
---
Chain | Description
A | .
Computing secondary structure
> hide #2 models
> show #2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> hide #6 models
> show #6 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> close #9
> rename #10 Gp25_volzon10-coot11_200-462AA
> show #11 models
> hide #11 models
> show #11 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> show #!32 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #11 models
> show #11 models
> hide #!12 models
> show #!12 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!12 models
> show #!12 models
> hide #!32 models
> show #!32 models
> hide #!32 models
> hide #!3 models
> show #11 models
> hide #11 models
> show #!13 models
> hide #!13 models
> color #12 #002a9bff models
> show #!13 models
> hide #!13 models
> show #!13 models
> color #13 #003ba5ff models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> close #14
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!19 models
> hide #!19 models
> show #!15 models
> select add #15
2 models selected
> close #15
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #16 models
> hide #16 models
> show #16 models
> hide #!13 models
> hide #!12 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #16 models
> show #16 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #16 models
> show #16 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> select add #17
13452 atoms, 13794 bonds, 1722 residues, 7 models selected
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> close #17
> hide #16 models
> show #16 models
> select add #16
2242 atoms, 2299 bonds, 287 residues, 1 model selected
> measure center #3
Center of mass grid index for PCH45_Neck_C6_3_40A_map_sharp.mrc = (208.00,
208.00, 143.67)
Center of mass xyz scene coordinates for PCH45_Neck_C6_3_40A_map_sharp.mrc =
(284.19, 284.19, 196.30)
> sym #16 c6 center 284.19, 284.19, 196.30
Made 6 copies for Tail_tube_monomerfit symmetry c6
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> color #8 #ff009cff models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> hide #!12 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!9 models
> show #11 models
> hide #11 models
> show #11 models
> select add #11
2242 atoms, 2299 bonds, 287 residues, 2 models selected
> hide #11 models
> show #11 models
> close #11
> show #!9 models
> hide #!9 models
> show #!9 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #16 models
> hide #16 models
> select add #9
15694 atoms, 16093 bonds, 2009 residues, 8 models selected
> select subtract #9
2242 atoms, 2299 bonds, 287 residues, 1 model selected
> select add #9
15694 atoms, 16093 bonds, 2009 residues, 8 models selected
> hide #10 models
> show #10 models
> hide #!9 models
> show #!9 models
> hide #!18 models
> show #!18 models
> volume #!18,24 showOutlineBox false
> select clear
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> rename #18 TubeC6ringvolzone
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #20 models
> hide #20 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #20 models
> hide #20 models
> show #20 models
> close #20
> show #21 models
> hide #21 models
> show #21 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #21 models
> show #21 models
> show #!22 models
> color #22 #51fb86ff models
> show #!24 models
> hide #!24 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #21 models
> show #21 models
> hide #!22 models
> show #!22 models
> show #!24 models
> color #24 #00f90040 models
> color #24 #00fd92ff models
> hide #!24 models
> show #!24 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #!24 models
> show #!24 models
> color #24 #51fb86ff models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> color #23 #d783ffff models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #1 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> rename #13 Sheathring_Lowest_Volzon
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> hide #21 models
> show #21 models
> hide #21 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #34 models
> show #34 models
> hide #34 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #!9 models
> hide #10 models
> show #10 models
> show #34 models
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_0.cif, chain A (#2), sequence
alignment score = 301.2
RMSD between 69 pruned atom pairs is 0.661 angstroms; (across all 95 pairs:
3.337)
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> ui tool show Matchmaker
> matchmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_1.cif, chain A (#6), sequence
alignment score = 301.2
RMSD between 70 pruned atom pairs is 0.691 angstroms; (across all 95 pairs:
3.338)
> ui tool show Matchmaker
> matchmaker #34-36 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_2.cif, chain A (#34), sequence
alignment score = 301.2
RMSD between 71 pruned atom pairs is 0.699 angstroms; (across all 95 pairs:
3.295)
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_3.cif, chain A (#35), sequence
alignment score = 301.2
RMSD between 70 pruned atom pairs is 0.682 angstroms; (across all 95 pairs:
3.321)
Matchmaker PCH45_C6_3_40_Wholemap_output_output.cif, chain r3 (#1) with
fold_pch45_gp25trimmed_first_1_200aa_model_4.cif, chain A (#36), sequence
alignment score = 301.2
RMSD between 70 pruned atom pairs is 0.679 angstroms; (across all 95 pairs:
3.332)
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> select add #10
2120 atoms, 2182 bonds, 262 residues, 1 model selected
> select clear
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,3
Model Number: Z1C80004VX/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.1 (24G231)
Kernel Version: Darwin 24.6.0
Time since boot: 1 hour, 32 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
VN2410C:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 144.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 2 hours ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 76 minutes ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX report a bug panel said what we know about this crash:
"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."
There is a new version 1.11 of ChimeraX released last week with a newer Qt version and we have not seen this Mac multi-display wake from sleep crash in the newer version.
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Reported by Alex Crowe