![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 hours ago
Closed 17 minutes ago
#20225 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-14.3-arm64-arm-64bit
ChimeraX Version: 1.8rc202406102315 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001d9369c40 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PIL._imagingmath, chimerax.mlp._mlp (total: 65)
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{
"uptime" : 170000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 1661,
"osVersion" : {
"train" : "macOS 14.3",
"build" : "23D2057",
"releaseType" : "User"
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"captureTime" : "2026-04-26 23:15:02.2491 -0500",
"codeSigningMonitor" : 1,
"incident" : "09C3E735-2CFF-4443-B118-49FEA74222EB",
"pid" : 45672,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-04-26 02:59:55.5025 -0500",
"procStartAbsTime" : 3753384270442,
"procExitAbsTime" : 4183889873508,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.06.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"61DCCA4C-8BBE-566F-8CCC-1D1EFAE87F42","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "31D03CEA-B4B7-1878-D34B-04A35F37F001",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 6,
"sleepWakeUUID" : "6663A7AC-BDCA-47D2-9CCE-437EE572D9AF",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 105559558717079\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600180000000-6001a0000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":45672},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 105559558717079\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600180000000-6001a0000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/h_bonf_triplex.cxs
> format session
Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32
opened ChimeraX session
> lighting soft
> lighting full
> coulombic #1,10-11#!2,5-6,12,17
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for UpfC_af.pdb_9 SES surface #1.1: minimum, -8.94, mean
-0.37, maximum 7.77
Coulombic values for gp5_af.pdb_6 SES surface #10.1: minimum, -15.35, mean
-0.92, maximum 15.28
Coulombic values for gp5_af.pdb_7 SES surface #10.2: minimum, -11.39, mean
-0.89, maximum 14.28
Coulombic values for gp5_af.pdb_8 SES surface #10.3: minimum, -18.47, mean
-0.93, maximum 13.00
Coulombic values for gp6_af.pdb_3 SES surface #11.1: minimum, -15.10, mean
-0.17, maximum 14.54
Coulombic values for gp6_af.pdb_4 SES surface #11.2: minimum, -20.20, mean
-0.16, maximum 16.17
Coulombic values for gp6_af.pdb_5 SES surface #11.3: minimum, -14.77, mean
-0.17, maximum 15.83
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for gp26.cif_X SES surface #5.1: minimum, -17.97, mean -1.93,
maximum 8.40
Coulombic values for pmgA.cif_R SES surface #6.1: minimum, -18.54, mean -4.68,
maximum 6.81
Coulombic values for gp16.pdb_p SES surface #12.1: minimum, -19.32, mean
-2.22, maximum 12.53
Coulombic values for pmgG.cif_G SES surface #17.2: minimum, -14.33, mean
-1.98, maximum 8.86
Coulombic values for pmgG.cif_H SES surface #17.3: minimum, -14.49, mean
-1.97, maximum 9.31
Coulombic values for pmgG.cif_I SES surface #17.4: minimum, -14.63, mean
-1.97, maximum 8.52
Coulombic values for pmgG.cif_J SES surface #17.5: minimum, -14.51, mean
-1.97, maximum 8.67
Coulombic values for pmgG.cif_K SES surface #17.6: minimum, -14.32, mean
-1.97, maximum 10.17
Coulombic values for pmgG.cif_L SES surface #17.7: minimum, -14.45, mean
-1.96, maximum 11.02
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
> hide #!17 models
> hide #16 models
> hide #!11 models
> hide #!10 models
> hide #!5 models
> hide #!6 models
> show #!3 models
> hide #!1 models
> coulombic #!2-3,12
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for BplAplus.pdb_j SES surface #3.1: minimum, -16.70, mean
-1.85, maximum 13.05
Coulombic values for gp16.pdb_p SES surface #12.1: minimum, -19.32, mean
-2.22, maximum 12.53
To also show corresponding color key, enter the above coulombic command and
add key true
> graphics silhouettes false
> ~label #2-3,12 residues
> select #3/j:3@NZ
1 atom, 1 residue, 1 model selected
> select #12/p:55@OD1
1 atom, 1 residue, 1 model selected
> select add #3/j:3@NZ
2 atoms, 2 residues, 3 models selected
> label (#!3,12 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"
> ~label (#!3,12 & sel) residues
> label (#!3,12 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 3
> ui mousemode right "move label"
> label height 2
> select clear
> label color white
> save /Users/aninditosen/Desktop/image17.png supersample 3
> open /Users/aninditosen/Documents/P1/final_images/mocell/FigS2.tif
Opened multi-channel map FigS2.tif as #18, 3 channels, grid size 2700,3300,1,
pixel 1, shown at step 1, values uint8
> close #18.1
> close #18.2
> close #18.3
> close #9
> hide #18 models
> close #18
> hide #!12 models
> hide #!2 models
> show #!12 models
> hide #!3 models
> show #!3 models
> select add #3
7498 atoms, 7582 bonds, 8 pseudobonds, 477 residues, 3 models selected
> transparency sel 50
> hide sel cartoons
> hide sel atoms
> hide #!12 models
> show #!2 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!12 models
> select subtract #3
1 model selected
> select add #3
7498 atoms, 7582 bonds, 8 pseudobonds, 477 residues, 3 models selected
> transparency sel 0
> select subtract #3
1 model selected
> select #2/d:14@OE2
1 atom, 1 residue, 1 model selected
> select #3/j:47@NH1
1 atom, 1 residue, 1 model selected
> select add #2/d:14@OE2
2 atoms, 2 residues, 3 models selected
> label (#!2-3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #3/j:47@1HH1
1 atom, 1 residue, 1 model selected
> select add #3/j:47@NH1
2 atoms, 1 residue, 2 models selected
> select add #3/j:47@2HH1
3 atoms, 1 residue, 2 models selected
> label (#!3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> ~label (#!3 & sel) residues
> select add #3
7498 atoms, 7582 bonds, 8 pseudobonds, 477 residues, 4 models selected
> select subtract #3
1 model selected
> ~label #2-3 residues
> select #2/d:14@OE2
1 atom, 1 residue, 1 model selected
> select add #2/d:14@CG
2 atoms, 1 residue, 2 models selected
> select add #2/d:14@CD
3 atoms, 1 residue, 2 models selected
> select add #3/j:47@NH1
4 atoms, 2 residues, 3 models selected
> select subtract #3/j:47@NH1
3 atoms, 1 residue, 3 models selected
> select add #3/j:47@1HH1
4 atoms, 2 residues, 3 models selected
> select add #3/j:47@NH1
5 atoms, 2 residues, 4 models selected
> select add #3/j:47@CD
6 atoms, 2 residues, 4 models selected
> select add #3/j:47@CZ
7 atoms, 2 residues, 4 models selected
> label (#!2-3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> ui mousemode right "translate selected atoms"
> undo
> coulombic sel
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for BplAplus.pdb_j SES surface #3.1: minimum, -16.70, mean
-1.85, maximum 13.05
To also show corresponding color key, enter the above coulombic command and
add key true
> select #3/j:47@1HH1
1 atom, 1 residue, 1 model selected
> select #3/j:47@NH1
1 atom, 1 residue, 1 model selected
> select #3/j:47@CZ
1 atom, 1 residue, 1 model selected
> label (#!3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> open
> /Users/aninditosen/Documents/P1/baseplate/main_baseplate/h_bonf_triplex.cxs
> format session
Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level
0.272, step 1, values float32
opened ChimeraX session
> coulombic #1,10-11#!2,5-6,12,17
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for UpfC_af.pdb_9 SES surface #1.1: minimum, -8.94, mean
-0.37, maximum 7.77
Coulombic values for gp5_af.pdb_6 SES surface #10.1: minimum, -15.35, mean
-0.92, maximum 15.28
Coulombic values for gp5_af.pdb_7 SES surface #10.2: minimum, -11.39, mean
-0.89, maximum 14.28
Coulombic values for gp5_af.pdb_8 SES surface #10.3: minimum, -18.47, mean
-0.93, maximum 13.00
Coulombic values for gp6_af.pdb_3 SES surface #11.1: minimum, -15.10, mean
-0.17, maximum 14.54
Coulombic values for gp6_af.pdb_4 SES surface #11.2: minimum, -20.20, mean
-0.16, maximum 16.17
Coulombic values for gp6_af.pdb_5 SES surface #11.3: minimum, -14.77, mean
-0.17, maximum 15.83
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for gp26.cif_X SES surface #5.1: minimum, -17.97, mean -1.93,
maximum 8.40
Coulombic values for pmgA.cif_R SES surface #6.1: minimum, -18.54, mean -4.68,
maximum 6.81
Coulombic values for gp16.pdb_p SES surface #12.1: minimum, -19.32, mean
-2.22, maximum 12.53
Coulombic values for pmgG.cif_G SES surface #17.2: minimum, -14.33, mean
-1.98, maximum 8.86
Coulombic values for pmgG.cif_H SES surface #17.3: minimum, -14.49, mean
-1.97, maximum 9.31
Coulombic values for pmgG.cif_I SES surface #17.4: minimum, -14.63, mean
-1.97, maximum 8.52
Coulombic values for pmgG.cif_J SES surface #17.5: minimum, -14.51, mean
-1.97, maximum 8.67
Coulombic values for pmgG.cif_K SES surface #17.6: minimum, -14.32, mean
-1.97, maximum 10.17
Coulombic values for pmgG.cif_L SES surface #17.7: minimum, -14.45, mean
-1.96, maximum 11.02
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
No visible residues selected
> select add #16
43 pseudobonds, 1 model selected
> select subtract #16
Nothing selected
> hide #16 models
> hide #!17 models
> hide #!10 models
> hide #!11 models
> hide #!5 models
> hide #!6 models
> ~label #1-2,12 residues
> show #!3 models
> hide #!1 models
> show #!2-3,12 surfaces
> coulombic #!2-3,12
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BplAminus.pdb_d SES surface #2.1: minimum, -16.51, mean
-1.43, maximum 17.71
Coulombic values for BplAplus.pdb_j SES surface #3.1: minimum, -16.70, mean
-1.85, maximum 13.05
Coulombic values for gp16.pdb_p SES surface #12.1: minimum, -19.32, mean
-2.22, maximum 12.53
To also show corresponding color key, enter the above coulombic command and
add key true
> ~label #2-3,12 residues
> hide #!12 models
> lighting full
> graphics silhouettes false
> select add #2
7498 atoms, 7582 bonds, 6 pseudobonds, 477 residues, 3 models selected
> transparency sel 50
> transparency sel 0
> select subtract #2
1 model selected
> select #2/d:14@OE2
1 atom, 1 residue, 1 model selected
> select add #3/j:47@NH1
2 atoms, 2 residues, 3 models selected
> label (#!2-3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label color white
> ui mousemode right "move label"
> select add #2
7499 atoms, 7582 bonds, 6 pseudobonds, 478 residues, 8 models selected
> select subtract #2
1 atom, 1 residue, 3 models selected
> select add #3
7498 atoms, 7582 bonds, 8 pseudobonds, 477 residues, 4 models selected
> select subtract #3
1 model selected
> label height 2
> save /Users/aninditosen/Desktop/image17.png supersample 3
> select add #2
7498 atoms, 7582 bonds, 6 pseudobonds, 477 residues, 5 models selected
> transparency sel 50
> select subtract #2
1 model selected
> transparency #2.1#3.1 0
> hide #!3 models
> show #!12 models
> select add #12
4399 atoms, 4444 bonds, 10 pseudobonds, 278 residues, 2 models selected
> transparency sel 50
> select subtract #12
1 model selected
> ~label #2,12 residues
> transparency #2.1#12.1 0
> select #12/p:148@CB
1 atom, 1 residue, 1 model selected
> select add #12/p:148@2HD2
2 atoms, 1 residue, 2 models selected
> select add #12/p:148@CD2
3 atoms, 1 residue, 2 models selected
> select add #2/d:335@CE
4 atoms, 2 residues, 3 models selected
> select add #2/d:335@1HZ
5 atoms, 2 residues, 4 models selected
> select add #2/d:334@1HB
6 atoms, 3 residues, 4 models selected
> select add #2/d:335@NZ
7 atoms, 3 residues, 4 models selected
> select add #2/d:333@O
8 atoms, 4 residues, 4 models selected
> label (#!2,12 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 2
> ui mousemode right "move label"
> label color white
> select clear
> save /Users/aninditosen/Desktop/image17.png supersample 3
> select add #12
4399 atoms, 4444 bonds, 10 pseudobonds, 278 residues, 4 models selected
> transparency sel 50
> transparency sel 0
> hide #!12 models
> select subtract #12
1 model selected
> show #!3 models
> select add #2
7498 atoms, 7582 bonds, 6 pseudobonds, 477 residues, 5 models selected
> ~label (#!2 & sel) residues
> select subtract #2
1 model selected
> ~label #2-3 residues
> select #2/d:289@1HB
1 atom, 1 residue, 1 model selected
> select #2/d:289@CB
1 atom, 1 residue, 1 model selected
> select add #2/d:289@1HB
2 atoms, 1 residue, 2 models selected
> select add #2/d:282@NH1
3 atoms, 2 residues, 2 models selected
> select add #2/d:289@N
4 atoms, 2 residues, 2 models selected
> select add #3/j:217@1HD1
5 atoms, 3 residues, 3 models selected
> select add #3/j:217@CD1
6 atoms, 3 residues, 4 models selected
> select add #3/j:217@CG1
7 atoms, 3 residues, 4 models selected
> label (#!2-3 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> label color white
> label height 2
> label height 1.5
> save /Users/aninditosen/Desktop/image17.png supersample 3
> show #!12 models
> hide #!2 models
> ~label #3,12 residues
> select add #12
4399 atoms, 4444 bonds, 10 pseudobonds, 278 residues, 2 models selected
> hide #!12 models
> show #!12 models
> select clear
> select #3/j:53@OD1
1 atom, 1 residue, 1 model selected
> select add #12/p:41@NH1
2 atoms, 2 residues, 3 models selected
> select add #12/p:41@NH2
3 atoms, 2 residues, 4 models selected
> label (#!3,12 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 1.5
> label color white
> select clear
> save /Users/aninditosen/Desktop/image17.png supersample 3
> hide #!3 models
> show #4 models
> hide #4 models
> show #!3 models
> show #!2 models
> hide #!12 models
> ~label #2-3 residues
> mlp #!2-3
Map values for surface "BplAminus.pdb_d SES surface": minimum -29.61, mean
-3.276, maximum 25.53
Map values for surface "BplAplus.pdb_j SES surface": minimum -29.52, mean
-3.189, maximum 29.02
To also show corresponding color key, enter the above mlp command and add key
true
> select add #2
7498 atoms, 7582 bonds, 6 pseudobonds, 477 residues, 4 models selected
> transparency sel 50
> hide sel cartoons
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MXCU3LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D2057)
Kernel Version: Darwin 23.3.0
Time since boot: 10 days, 12 hours, 58 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 Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202406102315
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 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 , 17 minutes ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This ChimeraX crash is a bug in the Qt window toolkit. Is is fixed in newer Qt versions used by current ChimeraX 1.11. But Qt 6.9 used by ChimeraX 1.11 has some new Qt Mac crash bugs, so you might instead what to use the ChimeraX daily build which uses Qt version 6.10 which has so far (with 3 months of use) not had significant Mac crashing issues.
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Reported by Anindito Sen