![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18270 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-14.7.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 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 0x00000001fe844f40 (most recent call first):
File "/Applications/ChimeraX-1.10.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.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.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, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, 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, PIL._imaging, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 48)
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{
"uptime" : 780000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 71252,
"osVersion" : {
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"build" : "23H222",
"releaseType" : "User"
},
"captureTime" : "2025-07-24 13:59:56.4366 -0700",
"codeSigningMonitor" : 1,
"incident" : "51E29C57-A839-4938-8D8D-205760443059",
"pid" : 93226,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-24 12:39:47.3237 -0700",
"procStartAbsTime" : 18815774404035,
"procExitAbsTime" : 18931187812825,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"69E1CEB5-2901-54D2-AE46-772119326E71","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DA5DEA7B-E35A-7EB2-98E3-726D0D61BD2B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 11524,
"sleepWakeUUID" : "4AAA9D04-0D17-4193-A051-DE96ED7631F5",
"sip" : "enabled",
"vmRegionInfo" : "0x7b46e32f78f0 is not in any region. Bytes after previous region: 29990736328945 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000fb46e32f78f0","rawCodes":[1,276281877821680],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000fb46e32f78f0 -> 0x00007b46e32f78f0 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":93226},
"vmregioninfo" : "0x7b46e32f78f0 is not in any region. Bytes after previous region: 29990736328945 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/karthik/Desktop/Stuff/UCSF/DARPA_Project/Alpha2a_zPZd_Manuscript/Figure_7/NURefineMap_Sharpened_Flipped_MOR.mrc
Opened NURefineMap_Sharpened_Flipped_MOR.mrc as #1, grid size 360,360,360,
pixel 0.819, shown at level 0.0567, step 2, values float32
> set bgColor white
> volume #1 step 1
> volume #1 level 0.2175
> open
> /Users/karthik/Desktop/Stuff/UCSF/DARPA_Project/Alpha2a_zPZd_Manuscript/Figure_7/LocalMap_J561_Sharp_Flip.mrc
Opened LocalMap_J561_Sharp_Flip.mrc as #2, grid size 360,360,360, pixel 0.819,
shown at level 0.0647, step 2, values float32
> volume #2 step 1
> volume #2 level 0.2391
> hide #!2 models
> hide #!1 models
> show #!2 models
> open
> /Users/karthik/Desktop/Stuff/UCSF/DARPA_Project/Alpha2a_zPZd_Manuscript/Figure_7/MOR_20250228_CombinedModel6_Refined.pdb
Chain information for MOR_20250228_CombinedModel6_Refined.pdb #3
---
Chain | Description
R | No description available
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select add #2
2 models selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel orchid
> color sel thistle
> color sel violet
> color sel plum
> color sel light pink
> color sel plum
> surface dust #2 size 8.19
> ui mousemode right select
> select clear
> transparency #2-3 60
> volume #2 level 0.1724
> cartoon style helix width 1.2 thickness 0.3
> ui tool show "Side View"
> select #2
3 models selected
> select clear
> hide #!2 models
> select /R:126
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:1@C18
1 atom, 1 residue, 1 model selected
> select /A:1@C08
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
4579 atoms, 4637 bonds, 286 residues, 1 model selected
> select /A:1@C07
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel sandy brown
> color sel light salmon
> color sel salmon
> color sel byhetero
> show #!2 models
> lighting soft
> ui mousemode right "pick blobs"
> measure blob #!2.1 triangleNumber 26765 color #ce7dd6ff
Surface LocalMap_J561_Sharp_Flip.mrc #2.1 blob:
volume = 16132
area = 22495
size = 84.534 58.536 47.52
> volume #1 level 0.2794
> hide #!1 models
> ui mousemode right "contour level"
> transparency sel 60
> select add #2
38 atoms, 40 bonds, 1 residue, 5 models selected
> select add #3
4617 atoms, 4677 bonds, 287 residues, 5 models selected
> transparency (#3 & sel) 60
> close #1
> select subtract #3
4 models selected
> hide #3 models
> transparency #2.1 60
> show #3 models
> volume #2 level 0.1768
> hide #!2 models
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
4579 atoms, 4637 bonds, 286 residues, 1 model selected
> select add #2
4579 atoms, 4637 bonds, 286 residues, 3 models selected
> select add #3
4617 atoms, 4677 bonds, 287 residues, 3 models selected
> select subtract #3
2 models selected
> select subtract #2
Nothing selected
> select add #3
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> color sel byhetero
> show #!2 models
> select add #3
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #2
4 models selected
> select /A:1@C07
1 atom, 1 residue, 1 model selected
> select clear
> select #2
4 models selected
> ui tool show "Scale Bar"
> ui tool show "Volume Viewer"
> volume #2 level 0.2268
> volume #2 level 0.1768
> select #2
4 models selected
> hide #3 models
> ui tool show "Color Actions"
> color sel salmon
> show #3 models
> select #2
4 models selected
> select #2
4 models selected
> select /A:1@CL14
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> color zone #2 near sel & #3 distance 4.91
> undo
> ui tool show "Color Zone"
> color zone #2 near sel distance 0.87
> color zone #2 near sel distance 0.84
> color zone #2 near sel distance 1.03
> color zone #2 near sel distance 1
> color zone #2 near sel distance 1.7
> ui tool show "Color Actions"
> color sel plum
> color zone #2 near sel distance 1.7
> ui tool show "Side View"
> color zone #2 near sel distance 1.62
> color zone #2 near sel distance 2.46
> color zone #2 near sel distance 2.49
> color zone #2 near sel distance 1.77
> ui tool show "Measure and Color Blobs"
> measure blob #!2.1 triangleNumber 27487 outline true
Surface LocalMap_J561_Sharp_Flip.mrc #2.1 blob:
volume = 15706
area = 21938
size = 84.254 58.39 47.523
> transparency sel 60
> measure blob #!2.1 triangleNumber 15930 outline true
Surface LocalMap_J561_Sharp_Flip.mrc #2.1 blob:
volume = 15706
area = 21938
size = 84.254 58.39 47.523
> ui mousemode right select
> select clear
> select add #3
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #2
6 models selected
> transparency #2.1-3 60
> select #2
6 models selected
> select clear
> select #2
6 models selected
> select clear
> select /A:1@CL14
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> color zone #2 near sel distance 1.7
> color zone #2 near sel distance 1.73
> color zone #2 near sel distance 1.34
> hide #3 models
> show #3 models
> open
> /Users/karthik/Desktop/Stuff/UCSF/DARPA_Project/Alpha2a_zPZd_Manuscript/Figure_7/MOR_LocalMap_J561_Sharp_Flip_2.mrc
Opened MOR_LocalMap_J561_Sharp_Flip_2.mrc as #1, grid size 360,360,360, pixel
0.819, shown at level 0.0647, step 2, values float32
> hide #!2 models
> hide #3 models
> hide #!1 models
> show #3 models
> show #!1 models
> volume #1 step 1
> volume #1 level 0.187
> surface dust #1 size 8.19
> ui tool show "Map Eraser"
> volume erase #1 center 174.3,150.4,154.6 radius 19.972
Opened MOR_LocalMap_J561_Sharp_Flip_2.mrc copy as #5, grid size 360,360,360,
pixel 0.819, shown at step 1, values float32
> volume erase #5 center 159.53,137.63,151.16 radius 19.899
> volume erase #5 center 175.27,144.24,179.02 radius 57.782
> transparency sel 90
> hide #3 models
> show #3 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #2
38 atoms, 40 bonds, 1 residue, 5 models selected
> transparency (#3 & sel) 60
> select subtract #2
38 atoms, 40 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #4 models
> hide #3 models
> show #4 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!1 models
> hide #4 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> show #4 models
> select add #5
38 atoms, 40 bonds, 1 residue, 3 models selected
> transparency #5.1 90
> show #3 models
> select add #3
4617 atoms, 4677 bonds, 287 residues, 3 models selected
> select subtract #3
2 models selected
> transparency #5.1 70
> ui mousemode right select
> select clear
Drag select of 3 residues, 5 MOR_LocalMap_J561_Sharp_Flip_2.mrc copy
> select clear
> ui mousemode right "translate selected models"
> select add #4
1 model selected
> view matrix models #4,1,0,0,172.71,0,1,0,135.77,0,0,1,166.9
> volume erase #5 center 172.71,135.77,166.9 radius 57.782
> view matrix models #4,1,0,0,152.22,0,1,0,145.89,0,0,1,136.95
> view matrix models #4,1,0,0,128.26,0,1,0,154.93,0,0,1,106.59
> view matrix models #4,1,0,0,106.92,0,1,0,165.12,0,0,1,75.985
> view matrix models #4,1,0,0,101.01,0,1,0,167.89,0,0,1,67.591
> volume erase #5 center 101.01,167.89,67.591 radius 57.782
> view matrix models #4,1,0,0,81.444,0,1,0,129.52,0,0,1,118.81
> view matrix models #4,1,0,0,100.09,0,1,0,127.68,0,0,1,133.8
> volume erase #5 center 100.09,127.68,133.8 radius 42.304
> view matrix models #4,1,0,0,122.02,0,1,0,106.33,0,0,1,117.42
> view matrix models #4,1,0,0,136.65,0,1,0,105.55,0,0,1,108.65
> view matrix models #4,1,0,0,137.2,0,1,0,106.22,0,0,1,108.43
> volume erase #5 center 137.2,106.22,108.43 radius 42.304
> view matrix models #4,1,0,0,152.69,0,1,0,108.07,0,0,1,99.572
> view matrix models #4,1,0,0,166.65,0,1,0,128.26,0,0,1,87.884
> view matrix models #4,1,0,0,167.82,0,1,0,132.35,0,0,1,87.668
> volume erase #5 center 167.82,132.35,87.668 radius 39.946
> view matrix models #4,1,0,0,167.07,0,1,0,188.77,0,0,1,103.57
> volume erase #5 center 167.07,188.77,103.57 radius 39.946
> view matrix models #4,1,0,0,128.05,0,1,0,181.72,0,0,1,146.19
> view matrix models #4,1,0,0,130.59,0,1,0,185.2,0,0,1,144.39
> view matrix models #4,1,0,0,130.35,0,1,0,184.19,0,0,1,142.15
> volume erase #5 center 130.35,184.19,142.15 radius 39.946
> hide #3 models
> view matrix models #4,1,0,0,159.32,0,1,0,152.9,0,0,1,123.69
> view matrix models #4,1,0,0,148.27,0,1,0,157.94,0,0,1,122.98
> volume erase #5 center 148.27,157.94,122.98 radius 6.3383
> view matrix models #4,1,0,0,154.03,0,1,0,150.13,0,0,1,117.62
> volume erase #5 center 154.03,150.13,117.62 radius 6.3383
> view matrix models #4,1,0,0,132.59,0,1,0,145.8,0,0,1,106.41
> view matrix models #4,1,0,0,130.8,0,1,0,158.01,0,0,1,112.9
> volume erase #5 center 130.8,158.01,112.9 radius 6.3383
> view matrix models #4,1,0,0,127.38,0,1,0,145.38,0,0,1,113.48
> volume erase #5 center 127.38,145.38,113.48 radius 6.3383
> view matrix models #4,1,0,0,137.32,0,1,0,142.36,0,0,1,115.42
> view matrix models #4,1,0,0,139.27,0,1,0,148.54,0,0,1,125.57
> view matrix models #4,1,0,0,138.53,0,1,0,148.88,0,0,1,125.44
> volume erase #5 center 138.53,148.88,125.44 radius 6.3383
> view matrix models #4,1,0,0,134.97,0,1,0,147.85,0,0,1,124.78
> volume erase #5 center 134.97,147.85,124.78 radius 6.3383
> view matrix models #4,1,0,0,137.36,0,1,0,143.22,0,0,1,121.71
> volume erase #5 center 137.36,143.22,121.71 radius 6.3383
> view matrix models #4,1,0,0,134.37,0,1,0,157.94,0,0,1,119.77
> view matrix models #4,1,0,0,128.02,0,1,0,154.91,0,0,1,120.75
> volume erase #5 center 128.02,154.91,120.75 radius 6.3383
> view matrix models #4,1,0,0,124.22,0,1,0,157.49,0,0,1,121.3
> volume erase #5 center 124.22,157.49,121.3 radius 6.3383
> view matrix models #4,1,0,0,137.48,0,1,0,160.91,0,0,1,112.41
> volume erase #5 center 137.48,160.91,112.41 radius 6.3383
> view matrix models #4,1,0,0,138.7,0,1,0,160.15,0,0,1,113.51
> volume erase #5 center 138.7,160.15,113.51 radius 6.3383
> view matrix models #4,1,0,0,140.06,0,1,0,155.54,0,0,1,109.08
> volume erase #5 center 140.06,155.54,109.08 radius 6.3383
> view matrix models #4,1,0,0,141.48,0,1,0,149.57,0,0,1,114.47
> view matrix models #4,1,0,0,142.45,0,1,0,150.66,0,0,1,116.5
> view matrix models #4,1,0,0,141.56,0,1,0,150.57,0,0,1,116.02
> view matrix models #4,1,0,0,141.86,0,1,0,150.58,0,0,1,116.16
> volume erase #5 center 141.86,150.58,116.16 radius 8.2545 outside true
> hide #!5 models
> hide #4 models
> show #4 models
> show #3 models
> select subtract #4
Nothing selected
> show #!2 models
> hide #3 models
> ui tool show "Map Eraser"
> ui mousemode right select
> ui mousemode right "translate selected models"
> select add #4
1 model selected
> view matrix models #4,1,0,0,139.72,0,1,0,150.43,0,0,1,116.65
> volume erase #2 center 139.72,150.43,116.65 radius 2.0636
Opened LocalMap_J561_Sharp_Flip.mrc copy as #6, grid size 360,360,360, pixel
0.819, shown at step 1, values float32
> view matrix models #4,1,0,0,137.12,0,1,0,150.45,0,0,1,117.42
> volume erase #6 center 137.12,150.45,117.42 radius 2.0636
> view matrix models #4,1,0,0,135.14,0,1,0,150.25,0,0,1,116.99
> volume erase #6 center 135.14,150.25,116.99 radius 2.0636
> show #!5 models
> hide #!5 models
> view matrix models #4,1,0,0,139.35,0,1,0,151.88,0,0,1,116.29
> view matrix models #4,1,0,0,141.33,0,1,0,152.13,0,0,1,115.86
> view matrix models #4,1,0,0,141.47,0,1,0,151.64,0,0,1,115.92
> view matrix models #4,1,0,0,142.54,0,1,0,152.75,0,0,1,117.15
> view matrix models #4,1,0,0,142.67,0,1,0,152.15,0,0,1,117.12
> volume erase #6 center 142.67,152.15,117.12 radius 2.0636
> view matrix models #4,1,0,0,143.5,0,1,0,151.98,0,0,1,117.35
> volume erase #6 center 143.5,151.98,117.35 radius 2.0636
> view matrix models #4,1,0,0,144.85,0,1,0,151.93,0,0,1,116.44
> view matrix models #4,1,0,0,144.89,0,1,0,152.29,0,0,1,116.75
> volume erase #6 center 144.89,152.29,116.75 radius 2.0636
> view matrix models #4,1,0,0,146.31,0,1,0,152.95,0,0,1,115.64
> volume erase #6 center 146.31,152.95,115.64 radius 2.0636
> show #!5 models
> select subtract #4
Nothing selected
> close #4
> show #3 models
> hide #!5 models
> hide #3 models
> surface dust #6 size 8.19
> show #!5 models
> show #3 models
> select add #3
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select subtract #3
Nothing selected
> ui mousemode right select
> select /A:1@N10
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> color sel byhetero
> select down
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select clear
> view
> select add #6
3 models selected
> ui tool show "Color Actions"
> color sel plum
> color sel mint cream
> color sel linen
> select clear
> select #5
3 models selected
> select clear
> select /A:1@C15
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> style sel ball
Changed 38 atom styles
> select ~sel & ##selected
4579 atoms, 4637 bonds, 286 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> color sel byhetero
> select /A:1@C12
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> color sel byhetero
> select ~sel & ##selected
4579 atoms, 4637 bonds, 286 residues, 1 model selected
> color sel light salmon
> color sel sandy brown
> select clear
> select /A:1@CL14
1 atom, 1 residue, 1 model selected
> select up
38 atoms, 40 bonds, 1 residue, 1 model selected
> select up
4617 atoms, 4677 bonds, 287 residues, 1 model selected
> select down
38 atoms, 40 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
4579 atoms, 4637 bonds, 286 residues, 1 model selected
> color sel byhetero
> select #6
4 models selected
> select clear
> select #6
4 models selected
> select #6
4 models selected
> hide #!6 models
> hide #3 models
> hide #!5 models
> show #3 models
> select /R:149
12 atoms, 11 bonds, 1 residue, 1 model selected
> show #!6 models
> show #!5 models
> ui tool show "Color Actions"
> color sel gold
> color sel byhetero
> undo
> select /R:149@OD2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> hide #3 models
> hide #!6 models
> show #3 models
> hide #!5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select add /R:149@CB
1 atom, 2 bonds, 1 residue, 1 model selected
> select subtract /R:149
Nothing selected
> select add /R:149@CG
1 atom, 2 bonds, 1 residue, 1 model selected
> select /R:151
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel yellow
> undo
> select clear
> color sel yellow
> undo
> select /R:149@OD2
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel target b
> show sel target ab
> color sel dim gray
> undo
> color yellow sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel byatom yellow
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel yellow atoms
> select clear
> select /R:149@CG
1 atom, 1 residue, 1 model selected
> color sel yellow atoms
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> select /R:149
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel cyan
> undo
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: Mac14,7
Model Number: Z16R0005ULL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.41.5
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.1 (23H222)
Kernel Version: Darwin 23.6.0
Time since boot: 30 days, 1 hour, 33 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
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: 14.1.18
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
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: 1.1.2
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: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
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: 4.4.4
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
pyelftools: 0.32
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: 4.14.0
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 (4)
comment:1 by , 4 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 , 4 months ago
comment:3 by , 4 months ago
Hi Tom,
I disconnected and external display, but ChimeraX was still running (I've also done this many time without a crash in 1.10.
It was when I closed my laptop lid to put it to sleep, and then reopened later that the crash occurred. Thank you for looking into this.
Best,
Karthik (I'm a huge fan of ChimeraX!)
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, July 24, 2025 3:28 PM
To: Srinivasan, Karthik <http://Karthik.Srinivasan@ucsf.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #18270: Crash on Mac waking from sleep
!-------------------------------------------------------------------|
This Message Is From an External Sender
This message came from outside your organization.
|-------------------------------------------------------------------!
#18270: Crash on Mac waking from sleep
-------------------------------------------+-------------------------
Reporter: karthik.srinivasan@… | Owner: Tom Goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Window Toolkit | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------------+-------------------------
Comment (by Tom Goddard):
The ChimeraX bug report panel says 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 it was fixed in ChimeraX 1.10 by a new Qt version (6.8.2) but
your crash shows that is not the case.
Did it crash when you woke your Mac from sleep? Did you unplug on plug in
an external display before the crash? Anything else you can tell me that
led up to the crash?
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18270#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
Version 0, edited 4 months ago by (next)
comment:4 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Thanks for the info. Those are the steps that produced many crashes on Mac ChimeraX 1.9. We were never able to reproduce the crash, but when we updated to Qt 6.8.2 back around February 2025 we no longer got any crash reports up to our June 2025 ChimeraX 1.10 release so we thought Qt had fixed it. We will be updating the ChimeraX daily build to Qt version 6.9.1 in the next week or two and maybe that will fix it. I'm glad it doesn't happen too often for you. Just be aware that unplugging or plugging in a display while ChimeraX is running on Mac seems to sometimes lead to a crash so you might want to save a ChimeraX session to avoid losing work.
Note:
See TracTickets
for help on using tickets.
The ChimeraX bug report panel says 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 it was fixed in ChimeraX 1.10 by a new Qt version (6.8.2) but your crash shows that is not the case.
Did it crash when you woke your Mac from sleep? Did you unplug on plug in an external display before the crash? Anything else you can tell me that led up to the crash?