![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17402 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-15.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Bus error
Current thread 0x0000000202968c40 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, fontTools.misc.bezierTools, fontTools.varLib.iup (total: 63)
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "Mac15,7",
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"codeSigningMonitor" : 1,
"incident" : "11863913-20B9-4B06-AE98-5A9DA9ADC29C",
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"translated" : false,
"cpuType" : "ARM-64",
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"procLaunch" : "2025-04-15 20:52:41.8644 -0400",
"procStartAbsTime" : 1722266092944,
"procExitAbsTime" : 1870805046892,
"procName" : "ChimeraX",
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"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BD1308D5-7C1C-C889-AD39-6908BB6F1170",
"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=="},
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"wakeTime" : 5,
"sleepWakeUUID" : "3E9B0B12-D1CD-4DEA-93EC-1D6263D24855",
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"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":70611},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/unc_prep.cxs
opened ChimeraX session
> select add #1.2
2060 atoms, 262 residues, 1 model selected
> select add #1.3
4647 atoms, 588 residues, 2 models selected
> select subtract #1.3
2060 atoms, 262 residues, 3 models selected
> select add #1.4
4101 atoms, 521 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5ftt_A SES surface #1.2: minimum, -29.28, mean -1.94,
maximum 15.08
Coulombic values for 5ftt_E SES surface #1.4: minimum, -20.65, mean -1.89,
maximum 15.52
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select add #1.3
2587 atoms, 326 residues, 1 model selected
> select subtract #1.3
1 model selected
> select add #1.5
2641 atoms, 332 residues, 1 model selected
> color #1.5 #d8ffe400
> view sel
> select add #1
9449 atoms, 9669 bonds, 1195 residues, 3 models selected
> select subtract #1
4 models selected
> select add #1.2
2060 atoms, 262 residues, 1 model selected
> select subtract #1.2
1 model selected
> select add #1.5
2641 atoms, 332 residues, 1 model selected
> select clear
> select add #1
9449 atoms, 9669 bonds, 1195 residues, 3 models selected
> select subtract #1
4 models selected
> ui tool show "Side View"
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> coloring palette
Unknown command: coloring palette
> view
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5ftt_A SES surface #1.2: minimum, -29.28, mean -1.94,
maximum 15.08
Coulombic values for 5ftt_B SES surface #1.3: minimum, -14.25, mean -1.65,
maximum 12.12
Coulombic values for 5ftt_E SES surface #1.4: minimum, -20.65, mean -1.89,
maximum 15.52
Coulombic values for 5ftt_F SES surface #1.5: minimum, -14.46, mean -1.37,
maximum 14.73
To also show corresponding color key, enter the above coulombic command and
add key true
> hide surfaces
> select /B
2601 atoms, 2657 bonds, 327 residues, 1 model selected
> save
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/unc_prep_2.cxs
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /F
2655 atoms, 2713 bonds, 333 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> view
> select /A/E
4157 atoms, 4271 bonds, 525 residues, 1 model selected
> save
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/UNC5D_dimer.pdb
> selectedOnly true relModel #1
> select /A
2088 atoms, 2145 bonds, 264 residues, 1 model selected
> select /E
2069 atoms, 2126 bonds, 261 residues, 1 model selected
> select /A
2088 atoms, 2145 bonds, 264 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /E
2069 atoms, 2126 bonds, 261 residues, 1 model selected
> save
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/UNC5D_monomer.pdb
> selectedOnly true relModel #1
> select clear
> close session
> open 7ZA2
Summary of feedback from opening 7ZA2 fetched from pdb
---
note | Fetching compressed mmCIF 7za2 from http://files.rcsb.org/download/7za2.cif
7za2 title:
GPC3-Unc5D octamer structure and role in cell migration [more info...]
Chain information for 7za2 #1
---
Chain | Description | UniProt
A B C D | Glypican-3 | GPC3_MOUSE 31-482
E F G H | Netrin receptor UNC5D | UNC5D_RAT 46-307
Non-standard residues in 7za2 #1
---
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> show cartoons
> hide atoms
> select /A:61-476
5631 atoms, 5685 bonds, 4 pseudobonds, 351 residues, 2 models selected
> select /B:61-476
5630 atoms, 5684 bonds, 4 pseudobonds, 351 residues, 2 models selected
> select /C:61-476
5631 atoms, 5685 bonds, 4 pseudobonds, 351 residues, 2 models selected
> select /D:61-476
5631 atoms, 5685 bonds, 4 pseudobonds, 351 residues, 2 models selected
> select /C:61-476
5631 atoms, 5685 bonds, 4 pseudobonds, 351 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /D:61-476
5631 atoms, 5685 bonds, 4 pseudobonds, 351 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /A:61-476
5631 atoms, 5685 bonds, 4 pseudobonds, 351 residues, 2 models selected
> select /E:51-301
3904 atoms, 3956 bonds, 251 residues, 1 model selected
> select /F:51-301
3904 atoms, 3956 bonds, 251 residues, 1 model selected
> select /G:51-301
3904 atoms, 3956 bonds, 251 residues, 1 model selected
> select /H:51-301
3905 atoms, 3957 bonds, 251 residues, 1 model selected
> close session
> open 7ZA2
7za2 title:
GPC3-Unc5D octamer structure and role in cell migration [more info...]
Chain information for 7za2 #1
---
Chain | Description | UniProt
A B C D | Glypican-3 | GPC3_MOUSE 31-482
E F G H | Netrin receptor UNC5D | UNC5D_RAT 46-307
Non-standard residues in 7za2 #1
---
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide atoms
> show cartoons
> select /E:51-301
3904 atoms, 3956 bonds, 251 residues, 1 model selected
> select /F:51-301
3904 atoms, 3956 bonds, 251 residues, 1 model selected
> select /H:51-301
3905 atoms, 3957 bonds, 251 residues, 1 model selected
> select /G:51-301
3904 atoms, 3956 bonds, 251 residues, 1 model selected
> select clear
> interfaces ~solvent
12 buried areas: C E 797, D F 763, B H 761, A G 755, F H 455, E G 450, F G
435, C G 428, E H 423, A E 383, B F 326, D H 303
> select /F:51-301
3904 atoms, 3956 bonds, 251 residues, 1 model selected
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> select /F:51-301
3904 atoms, 3956 bonds, 251 residues, 1 model selected
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> delete atoms sel
> delete bonds sel
> interfaces ~solvent
8 buried areas: C E 797, B H 761, A G 755, E G 450, C G 428, E H 423, A E 383,
D H 303
> delete atoms sel
> delete bonds sel
> interfaces ~solvent
5 buried areas: C E 797, A G 755, E G 450, C G 428, A E 383
> delete atoms sel
> delete bonds sel
> select /D
5687 atoms, 5743 bonds, 4 pseudobonds, 353 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> interfaces ~solvent
5 buried areas: C E 797, A G 755, E G 450, C G 428, A E 383
> show sel surfaces
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> show surfaces
> interfaces ~solvent
5 buried areas: C E 797, A G 755, E G 450, C G 428, A E 383
> delete atoms sel
> delete bonds sel
> interfaces ~solvent
5 buried areas: C E 797, A G 755, E G 450, C G 428, A E 383
> hide surfaces
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> interfaces ~solvent
5 buried areas: C E 797, A G 755, E G 450, C G 428, A E 383
> close session
> open 7ZA2 format mmcif fromDatabase pdb
7za2 title:
GPC3-Unc5D octamer structure and role in cell migration [more info...]
Chain information for 7za2 #1
---
Chain | Description | UniProt
A B C D | Glypican-3 | GPC3_MOUSE 31-482
E F G H | Netrin receptor UNC5D | UNC5D_RAT 46-307
Non-standard residues in 7za2 #1
---
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> show atoms
> hide atoms
> show cartoons
> interfaces ~solvent
12 buried areas: C E 797, D F 763, B H 761, A G 755, F H 455, E G 450, F G
435, C G 428, E H 423, A E 383, B F 326, D H 303
> select /D
5687 atoms, 5743 bonds, 4 pseudobonds, 353 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /B
5686 atoms, 5742 bonds, 4 pseudobonds, 353 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /F
3982 atoms, 4037 bonds, 254 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /H
3933 atoms, 3986 bonds, 252 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> interfaces ~solvent
5 buried areas: C E 797, A G 755, E G 450, C G 428, A E 383
> delete atoms sel
> delete bonds sel
> interfaces ~solvent
5 buried areas: C E 797, A G 755, E G 450, C G 428, A E 383
> color sel red
> color sel hot pink
> save
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/UNC5D_GPC3/UNC5d_GPC3.cxs
> save /Users/nirakar.basnet/Desktop/image3.png supersample 3
> save /Users/nirakar.basnet/Desktop/image4.png supersample 3
> color sel red
> color sel hot pink
> save
> /Users/nirakar.basnet/Documents/Projects/Baker_lab/UNC5D_2/UNC5D_GPC3/UNC5d_GPC3_2.cxs
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 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 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,7
Model Number: Z1AK0014ELL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4 (24E248)
Kernel Version: Darwin 24.4.0
Time since boot: 2 days, 10 hours, 8 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
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
DELL P2417H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
27B2:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 months 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
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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.
The ChimeraX daily build uses a newer Qt version 6.8.2 where we have not seen this crash. You may want to try it.