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Opened 3 months ago
Closed 2 months ago
#18280 closed defect (can't reproduce)
Crash in Qt waking from sleep on Mac, multiple displays
| 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-15.5-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 0x00000001f86c9f00 (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.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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 (total: 56)
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 66703,
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"build" : "24F74",
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"captureTime" : "2025-07-25 11:45:01.1847 +0200",
"codeSigningMonitor" : 1,
"incident" : "6590BFE4-6E65-4DB0-9DE3-EC6CDD71629E",
"pid" : 23248,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-25 08:10:54.4126 +0200",
"procStartAbsTime" : 11395809788939,
"procExitAbsTime" : 11704113413846,
"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":"D11F69EC-D692-5795-8D2E-E27CE963C4F6","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1A6C8CA6-7E03-1215-A189-1F1376BD7E7F",
"appleIntelligenceStatus" : {"state":"available"},
"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" : "6393956A-612E-49D6-A80E-7F60F1047023",
"wakeTime" : 13193,
"sleepWakeUUID" : "9F82B2C7-1CB5-40B6-BE63-D83D6533ADB9",
"sip" : "enabled",
"vmRegionInfo" : "0x1ae76c29ce30 is not in any region. Bytes after previous region: 29100218109489 Bytes before following region: 75971861819856\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, 0x00009ae76c29ce30","rawCodes":[1,170318742801968],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00009ae76c29ce30 -> 0x00001ae76c29ce30 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":23248},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x1ae76c29ce30 is not in any region. Bytes after previous region: 29100218109489 Bytes before following region: 75971861819856\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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===== Log before crash start =====
> buttonpanel Volume_series rows 3 columns 4
> buttonpanel Volume_series add Open_series command "open browse vseries true"
> buttonpanel Volume_series add Play_1 command "vseries play #1 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_1 command "vseries stop #1"
> buttonpanel Volume_series add Play_2 command "vseries play #2 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_2 command "vseries stop #2"
> buttonpanel Volume_series add Play_3 command "vseries play #3 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_3 command "vseries stop #3"
> buttonpanel Volume_series add Play_4 command "vseries play #4 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_4 command "vseries stop #4"
> buttonpanel Volume_series add Play_5 command "vseries play #5 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_5 command "vseries stop #5"
> buttonpanel Volume_series add Play_6 command "vseries play #6 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_6 command "vseries stop #6"
> buttonpanel Volume_series add Record command "movie record"
> buttonpanel Volume_series add Encode command "movie encode output browse"
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/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_1.cxs"
Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
> view name session-start
opened ChimeraX session
> hide #!3 models
> close #1-4
> open "/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_2.cxs"
Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
> view name session-start
opened ChimeraX session
> close #1-4
> open "/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_2.cxs" format session
Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
> view name session-start
opened ChimeraX session
> hide #!3 models
> ui tool show "Side View"
> select #1/F:81@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/F:81
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/F:74@CA
1 atom, 1 residue, 1 model selected
> select #1/F:74@CB
1 atom, 1 residue, 1 model selected
> select add #1
31580 atoms, 32552 bonds, 2 pseudobonds, 4091 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/F:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1
31580 atoms, 32552 bonds, 2 pseudobonds, 4091 residues, 2 models selected
> select subtract #1
Nothing selected
> save /Users/gyanaprakashmahapatra/Desktop/image45.png supersample 3
> save
> "/Users/gyanaprakashmahapatra/OneDrive/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_2_New.cxs" includeMaps true
> close #1-4
> open "/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_3.cxs"
Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
> view name session-start
opened ChimeraX session
> hide #!3 models
> select #1/A:653
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/A:749
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:750
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/A:749
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add #1/A:748
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #1/A:745
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add #1/A:746
37 atoms, 32 bonds, 5 residues, 1 model selected
> select add #1/A:742
48 atoms, 43 bonds, 6 residues, 1 model selected
> select add #1/A:741
54 atoms, 48 bonds, 7 residues, 1 model selected
> select add #1/A:671
62 atoms, 55 bonds, 8 residues, 1 model selected
> select add #1/A:139
71 atoms, 63 bonds, 9 residues, 1 model selected
> select add #1/A:138
79 atoms, 70 bonds, 10 residues, 1 model selected
> select add #1/A:137
83 atoms, 73 bonds, 11 residues, 1 model selected
> select add #1/A:136
92 atoms, 81 bonds, 12 residues, 1 model selected
> select add #1/A:135
103 atoms, 92 bonds, 13 residues, 1 model selected
> select add #1/A:134
107 atoms, 95 bonds, 14 residues, 1 model selected
> select add #1/A:132
111 atoms, 98 bonds, 15 residues, 1 model selected
> select add #1/A:131
118 atoms, 104 bonds, 16 residues, 1 model selected
> select add #1/A:133
122 atoms, 107 bonds, 17 residues, 1 model selected
> select add #1/A:130
130 atoms, 114 bonds, 18 residues, 1 model selected
> select add #1/A:129
134 atoms, 117 bonds, 19 residues, 1 model selected
> select add #1/A:128
142 atoms, 124 bonds, 20 residues, 1 model selected
> hide sel cartoons
> select #1/A:744
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> save /Users/gyanaprakashmahapatra/Desktop/image46.png supersample 3
> select #1/A:738
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> save /Users/gyanaprakashmahapatra/Desktop/image47.png supersample 3
> save
> "/Users/gyanaprakashmahapatra/OneDrive/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_3_New.cxs" includeMaps true
> close #1-4
> open
> "/Users/gyanaprakashmahapatra/OneDrive/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_2_New.cxs" format session
Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
> view name session-start
opened ChimeraX session
> close #1-4
> open "/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/Manuscript/Final
> Figures/Figure 3/Figure 3_A closer look_3_New.cxs"
Opened Composite Map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0208, step 1, values float32
Opened Composite Map.mrc 0 as #3.1, grid size 512,512,512, pixel 0.73, shown
at level 0.0208, step 1, values float32
Opened Composite Map.mrc 1 as #3.2, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 2 as #3.3, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 3 as #3.4, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 4 as #3.5, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 5 as #3.6, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 6 as #3.7, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 7 as #3.8, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 8 as #3.9, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 9 as #3.10, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 10 as #3.11, grid size 512,512,512, pixel 0.73, shown
at level 0.04, step 1, values float32
Opened Composite Map.mrc 11 as #3.12, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 12 as #3.13, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
Opened Composite Map.mrc 13 as #3.14, grid size 512,512,512, pixel 0.73, shown
at level 0.03, step 1, values float32
Opened Composite Map.mrc 14 as #3.15, grid size 512,512,512, pixel 0.73, shown
at level 0.045, step 1, values float32
> view name session-start
opened ChimeraX session
> close #1-4
> open
> /Users/gyanaprakashmahapatra/Downloads/cryosparc_P173_J671_map_locres.mrc
Opened cryosparc_P173_J671_map_locres.mrc as #1, grid size 512,512,512, pixel
0.73, shown at level 2.96, step 1, values float32
> volume #1 level 3.814
> close #1
> open
> /Users/gyanaprakashmahapatra/Downloads/cryosparc_P173_J671_map_locres.mrc
> format mrc
Opened cryosparc_P173_J671_map_locres.mrc as #1, grid size 512,512,512, pixel
0.73, shown at level 2.96, step 1, values float32
> open "/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/CS_PSI-
> CytC6/Jobs/J575_NU-refine_1.8Å str_Same as J458/J575_sharp map.mrc"
Opened J575_sharp map.mrc as #2, grid size 512,512,512, pixel 0.73, shown at
level 0.0459, step 1, values float32
> volume #2 level 0.09183
> ui tool show "Surface Color"
> color sample #2.1 map #1 palette #ff0000:#ffffff:#0000ff outsideColor
> #808080
Map values for surface "surface": minimum 0, mean 1.758, maximum 21.77
> volume #1 level 6.738
> hide #!1 models
> color sample #2.1 map #1 palette 1.5,#0000ff:2,#ffffff:2.5,#ff0000
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 1.758, maximum 21.77
> volume #2 level 0.08237
> color sample #2.1 map #1 palette 1.5,#0000ff:2,#00f900:2.5,#ff0000
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 1.759, maximum 23.84
===== Log before crash end =====
Log:
> buttonpanel Volume_series rows 3 columns 4
> buttonpanel Volume_series add Open_series command "open browse vseries true"
> buttonpanel Volume_series add Play_1 command "vseries play #1 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_1 command "vseries stop #1"
> buttonpanel Volume_series add Play_2 command "vseries play #2 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_2 command "vseries stop #2"
> buttonpanel Volume_series add Play_3 command "vseries play #3 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_3 command "vseries stop #3"
> buttonpanel Volume_series add Play_4 command "vseries play #4 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_4 command "vseries stop #4"
> buttonpanel Volume_series add Play_5 command "vseries play #5 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_5 command "vseries stop #5"
> buttonpanel Volume_series add Play_6 command "vseries play #6 direction
> oscillate loop true cacheFrames 20 maxFrameRate 20 normalize true"
> buttonpanel Volume_series add Stop_6 command "vseries stop #6"
> buttonpanel Volume_series add Record command "movie record"
> buttonpanel Volume_series add Encode command "movie encode output browse"
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 M1 Pro
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: MacBookPro18,1
Model Number: MK193LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 10 days, 6 hours, 44 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
BE24W:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
PA278QV:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
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-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-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 , 3 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in Qt waking from sleep on Mac, multiple displays |
comment:2 by , 2 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
No response from reporter.
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The ChimeraX bug report panel explained 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."
We thought this crash was fixed in ChimeraX 1.10 which uses a newer version of the Qt toolkit 6.8.2, but that did not fix it.
Were you waking your computer from sleep when it crashed?
We will update the ChimeraX daily build to Qt version 6.9.1 in the next few weeks and hopefully that will fix this Qt crash.