![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15799 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-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 230000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,4",
"coalitionID" : 26440,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-08-20 19:06:31.2662 +0200",
"codeSigningMonitor" : 1,
"incident" : "9C47738F-BEA2-4FEE-BB1F-7251B7A8C356",
"pid" : 58124,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-20 17:03:16.2043 +0200",
"procStartAbsTime" : 5349926543494,
"procExitAbsTime" : 5527362173327,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D91302BD-DBCE-5C53-8136-7D7F3BF49D6F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F0D674B1-5FA4-E9D0-6B9C-8D1ED9987542",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"IAAg1AAAINQAAEDUIAAg1AAAINQAAEDUIAAg1AAAINQAAEDUIAAg1A==","atPC":"AAAg1AAAQNQgACDUAAAg1AAAQNQgACDUAAAg1AAAQNQgACDUAAAg1A=="},
"wakeTime" : 27248,
"sleepWakeUUID" : "4540F693-D75C-4C0B-A521-E0BD8D4673B2",
"sip" : "enabled",
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"os_fault" : {"process":"ChimeraX"},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> graphics silhouettes true
> lighting soft
> windowsize 800 800
> ui tool hide "command line interface"
> ui tool show clix
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kelvinlau/Desktop/RhGB07-full/RBD zoomed in-more.cxs" format
> session
Opened 103_zflipped.ccp4 as #2, grid size 300,300,300, pixel 1.38, shown at
level 0.184, step 1, values float32
Opened 103_sharp_zflipped.ccp4 as #3, grid size 300,300,300, pixel 1.38, shown
at level 0.239, step 1, values float32
Opened 103_zflipped.ccp4 1 as #6.2, grid size 300,300,300, pixel 1.38, shown
at level 0.19, step 1, values float32
opened ChimeraX session
> ui tool show "Command Line Interface"
> ui tool show clix
> center #1
Unknown command: center #1
> ui tool show clix
> show #!1 models
> view list
Named views: overview
> view overview
> select clear
> show #!4 models
> hide #!1 models
> select add #7/A:64
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
182 atoms, 186 bonds, 26 residues, 1 model selected
> select up
4881 atoms, 5034 bonds, 609 residues, 1 model selected
> select up
4895 atoms, 5049 bonds, 610 residues, 1 model selected
> select up
5440 atoms, 5609 bonds, 682 residues, 1 model selected
> select up
5441 atoms, 5609 bonds, 683 residues, 1 model selected
> select up
6761 atoms, 6971 bonds, 859 residues, 1 model selected
> select down
5441 atoms, 5609 bonds, 683 residues, 1 model selected
> hide sel
> hide sel cartoons
Drag select of 147 atoms, 57 residues, 141 bonds
> select clear
> select add #7/B:436
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide (#4,7-8 & (protein|nucleic)) target a
> cartoon hide #4,7-8
> show (#4,7-8 & ((protein&@ca)|(nucleic&@p))) target ab
Drag select of 13 atoms, 11 pseudobonds
> select up
104 atoms, 102 bonds, 11 pseudobonds, 13 residues, 2 models selected
> select up
616 atoms, 627 bonds, 11 pseudobonds, 81 residues, 2 models selected
> select up
4881 atoms, 5034 bonds, 11 pseudobonds, 609 residues, 2 models selected
> hide sel
> ui tool show "Side View"
> save /Users/kelvinlau/Desktop/RhGB07-full/RBDdiff-prd0038-zoom3.tiff
> supersample 4
> hide #!7 models
> hide #!8 models
> show #!4 atoms
> show #!4 cartoons
> hide #!4 atoms
> undo
> select ::name="BMA"::name="MAN"::name="NAG"::name="ZN"
3405 atoms, 3521 bonds, 254 residues, 5 models selected
> select up
58944 atoms, 60670 bonds, 7507 residues, 5 models selected
> select down
3405 atoms, 3521 bonds, 254 residues, 5 models selected
> select add #4/A:334@CG
3406 atoms, 3521 bonds, 255 residues, 5 models selected
> select up
3408 atoms, 3522 bonds, 256 residues, 5 models selected
> select up
3421 atoms, 3537 bonds, 256 residues, 5 models selected
> invert sel
Unknown command: invert sel
> ui tool show clix
> select invert
Expected an objects specifier or a keyword
> ui tool show clix
> select ~sel & ##selected
59166 atoms, 60861 bonds, 449 pseudobonds, 7738 residues, 12 models selected
> hide sel & #!4 atoms
> select clear
> select ::name="BMA"::name="MAN"::name="NAG"::name="ZN"
3405 atoms, 3521 bonds, 254 residues, 5 models selected
Populating font family aliases took 171 ms. Replace uses of missing font
family "Poppins" with one that exists to avoid this cost.
> color sel #4ECDC4
> select clear
> color #4 byhetero
> save /Users/kelvinlau/Desktop/RhGB07-full/RBD.tiff supersample 4
> hide #!4 models
> show #!1 models
> open "/Users/kelvinlau/Library/CloudStorage/GoogleDrive-
> kelvin.lau@epfl.ch/Shared drives/new-bat-stuff-2024-uk/EM-
> Full/RealSpaceRefine_40/trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb"
Chain information for
trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb #9
---
Chain | Description
A B C | No description available
> select #9/B,C
18068 atoms, 18578 bonds, 4 pseudobonds, 2266 residues, 2 models selected
> delete sel
> hide #!1 models
> select #9
9034 atoms, 9289 bonds, 2 pseudobonds, 1133 residues, 2 models selected
> hide pbonds
> select clear
> open
> /Users/kelvinlau/Downloads/clustalo-I20240820-165439-0398-26224244-p1m.aln-
> clustal_num
Unrecognized file suffix '.aln-clustal_num'
> open
> /Users/kelvinlau/Downloads/clustalo-I20240820-165439-0398-26224244-p1m.aln
Summary of feedback from opening
/Users/kelvinlau/Downloads/clustalo-I20240820-165439-0398-26224244-p1m.aln
---
notes | Alignment identifier is clustalo-I20240820-165439-0398-26224244-p1m.aln
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain A to RhGB07_WDQ27002.1_UK with 8 mismatches
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain B to RhGB07_WDQ27002.1_UK with 8 mismatches
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain C to RhGB07_WDQ27002.1_UK with 8 mismatches
Associated 30B-RBD-only.pdb chain A to RhGB07_WDQ27002.1_UK with 4 mismatches
Associated 8u29 chain A to PRD-0038_QTJ30153.1_Rwanda with 78 mismatches
Associated 8u29 chain B to PRD-0038_QTJ30153.1_Rwanda with 78 mismatches
Associated 8u29 chain C to PRD-0038_QTJ30153.1_Rwanda with 78 mismatches
Associated 8u29 chain A to PRD-0038_QTJ30153.1_Rwanda with 78 mismatches
Associated trimer30B_real_space_refined_006-coot-1_real_space_refined_040.pdb
chain A to RhGB07_WDQ27002.1_UK with 8 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalo-I20240820-165439-0398-26224244-p1m.aln
Opened 121 sequences from clustalo-I20240820-165439-0398-26224244-p1m.aln
Traceback (most recent call last):
File "/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py",
line 203, in _on_text_changed
self._update_completion_state(False)
File "/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py",
line 45, in _update_completion_state
self._current_completion_state =
self._get_completion_list(cursor.selectedText())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py",
line 147, in _get_completion_list
return self._completion_for_chain(last_word, current_command)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py",
line 193, in _completion_for_chain
f"/{_i}" for _i in model.chains.chain_ids if _i.startswith(last_word[1:])
^^^^^^^^^^^^
AttributeError: 'PseudobondGroup' object has no attribute 'chains'
AttributeError: 'PseudobondGroup' object has no attribute 'chains'
File "/Users/kelvinlau/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/clix/widgets/main.py",
line 193, in _completion_for_chain
f"/{_i}" for _i in model.chains.chain_ids if _i.startswith(last_word[1:])
^^^^^^^^^^^^
See log for complete Python traceback.
> color byattribute seq_conservation #9 & protein range -1.5,3 noValueColor
> gray
8473 atoms, 1091 residues, atom seq_conservation range -2.5 to 0.869
> color byattribute seq_conservation #9
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> color byattribute seq_conservation #9 range -2.5,0.1
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> color byattribute seq_conservation #9 range -1,0.1
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> color byattribute seq_conservation #9 palette blue:white:red range -1,0.1
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> color byattribute seq_conservation #9 palette blue:white:red
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> select add #9/A:480
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #9/A:342
17 atoms, 16 bonds, 2 residues, 1 model selected
> select clear
> color byattribute seq_conservation #9 palette "cheer up emo kid"
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> color byattribute seq_conservation #9 palette #C44D58:#C7F464:#556270
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> color byattribute seq_conservation #9 palette #C44D58:#C7F464:#556270 range
> -2,0.5
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> color byattribute seq_conservation #9 palette #C44D58:#C7F464:#556270 range
> -1,0.1
9034 atoms, 1133 residues, atom seq_conservation range -2.5 to 0.869
> select #9/A:480
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> show #!9 surfaces
> color byattribute seq_conservation #9 palette #C44D58:#C7F464:#556270 range
> -1,0.1
9034 atoms, 1133 residues, 1 surfaces, atom seq_conservation range -2.5 to
0.869
> select ::name="BMA"::name="MAN"::name="NAG"::name="ZN"
3966 atoms, 4104 bonds, 296 residues, 6 models selected
> hide sel & #!9 atoms
> select clear
> lighting soft
> save /Users/kelvinlau/conservationsurface.cxs
> save /Users/kelvinlau/Desktop/RhGB07-full/FL_con.tiff supersample 4
> save /Users/kelvinlau/Desktop/RhGB07-full/FL_con2.tiff supersample 4
> ui tool show clix
> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1
1521 atoms, 186 residues, atom seq_conservation range -2.49 to 0.869
> hide #!9 models
> show #!4 models
> show #!4 surfaces
> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1
1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869
> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1
1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869
> hide #!4 surfaces
> select clear
Drag select of 1 atoms, 175 residues, 1 bonds
> color sel #556270
> select clear
> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1
1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869
> show #!4 surfaces
Drag select of 30B-RBD-only.pdb_A SES surface, 43263 of 188138 triangles, 1
atoms, 55 residues
> color sel #556270
> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1
1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869
> color byattribute seq_conservation #4 palette #C44D58:#C7F464:#556270 range
> -1,0.1
1521 atoms, 186 residues, 1 surfaces, atom seq_conservation range -2.49 to
0.869
> select clear
> ui mousemode right "color key"
> key blue:min white: #c44d58:max
> key blue:min #c7f464: #c44d58:max
> key #556270:min #c7f464: #c44d58:max
> key colorTreatment distinct
> key colorTreatment blended
> key pos 0.694819,0.118868 size 0.204635,0.0495277
> key #556270:min #c7f464: #c44d58:L
> key #556270:min #c7f464: #c44d58:LE
> key #556270:min #c7f464: #c44d58:LEA
> key #556270:min #c7f464: #c44d58:LEAS
> key #556270:min #c7f464: #c44d58:LEAST
> key #556270:min #c7f464: "#c44d58:LEAST "
> key #556270:min #c7f464: #c44d58:LEAST
> key #556270:min #c7f464: #c44d58:LEAS
> key #556270:min #c7f464: #c44d58:LEA
> key #556270:min #c7f464: #c44d58:LE
> key #556270:min #c7f464: #c44d58:L
> key #556270:min #c7f464: #c44d58:
> key #556270:min #c7f464: #c44d58:l
> key #556270:min #c7f464: #c44d58:
> key #556270:min #c7f464: #c44d58:L
> key #556270:min #c7f464: #c44d58:Le
> key #556270:min #c7f464: #c44d58:Lea
> key #556270:min #c7f464: #c44d58:Leas
> key #556270:min #c7f464: #c44d58:Least
> key #556270:min #c7f464: "#c44d58:Least "
> key #556270:min #c7f464: "#c44d58:Least c"
> key #556270:min #c7f464: "#c44d58:Least co"
> key #556270:min #c7f464: "#c44d58:Least con"
> key #556270:min #c7f464: "#c44d58:Least cons"
> key #556270:min #c7f464: "#c44d58:Least conse"
> key #556270:min #c7f464: "#c44d58:Least conser"
> key #556270:min #c7f464: "#c44d58:Least conserv"
> key #556270:min #c7f464: "#c44d58:Least conserve"
> key #556270:min #c7f464: "#c44d58:Least conserver"
> key #556270:min #c7f464: "#c44d58:Least conserverd"
> key #556270:min #c7f464: "#c44d58:Least c"
> key #556270:min #c7f464: "#c44d58:Least co"
> key #556270:min #c7f464: "#c44d58:Least con"
> key #556270:min #c7f464: "#c44d58:Least cons"
> key #556270:min #c7f464: "#c44d58:Least conse"
> key #556270:min #c7f464: "#c44d58:Least conser"
> key #556270:min #c7f464: "#c44d58:Least conserv"
> key #556270:min #c7f464: "#c44d58:Least conserve"
> key #556270:min #c7f464: "#c44d58:Least conserved"
> key #556270:M #c7f464: "#c44d58:Least conserved"
> key #556270:Mo #c7f464: "#c44d58:Least conserved"
> key #556270:Mos #c7f464: "#c44d58:Least conserved"
> key #556270:Most #c7f464: "#c44d58:Least conserved"
> key "#556270:Most " #c7f464: "#c44d58:Least conserved"
> key "#556270:Most c" #c7f464: "#c44d58:Least conserved"
> key "#556270:Most co" #c7f464: "#c44d58:Least conserved"
> key "#556270:Most con" #c7f464: "#c44d58:Least conserved"
> key "#556270:Most cons" #c7f464: "#c44d58:Least conserved"
> key "#556270:Most conse" #c7f464: "#c44d58:Least conserved"
> key "#556270:Most conser" #c7f464: "#c44d58:Least conserved"
> key "#556270:Most conserv" #c7f464: "#c44d58:Least conserved"
> key "#556270:Most conserve" #c7f464: "#c44d58:Least conserved"
> key "#556270:Most conserved" #c7f464: "#c44d58:Least conserved"
> ui mousemode right translate
> save /Users/kelvinlau/Desktop/RhGB07-full/RBD_con1.tiff supersample 4
> save /Users/kelvinlau/Desktop/RhGB07-full/RBD_con2.tiff supersample 4
> save /Users/kelvinlau/Desktop/RhGB07-full/RBD_con3.tiff supersample 4
> hide #!4 surfaces
> show #!8 models
> hide #!8 models
> hide #10 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!7 models
> show #!8 models
> show #!4,7-8 cartoons
> hide #!7 models
> hide #!8 models
> show #!8 models
Alignment identifier is 1
Alignment identifier is 4/A
Alignment identifier is 2
Alignment identifier is 7/A
Alignment identifier is 7/B
> select #4/A:483
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/A:483-489
46 atoms, 47 bonds, 7 residues, 1 model selected
> select clear
> select add #4/A:439
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #4/A:435
17 atoms, 16 bonds, 2 residues, 2 models selected
> select #8/A:434
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #8/A:440
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/A:435
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #4/A:436
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #4/A:437
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #4/A:466
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:466-470
34 atoms, 34 bonds, 5 residues, 1 model selected
> select clear
> show #!7 models
> select #4/A:465-466
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #4/A:465-470
38 atoms, 38 bonds, 6 residues, 1 model selected
> select #4/A:466
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:466-469
27 atoms, 27 bonds, 4 residues, 1 model selected
> select #4/A:470
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:470
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide (#!4 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!4 & sel-residues)
> show (#!4 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> hide (#4,7-8 & (protein|nucleic)) target a
> cartoon hide #4,7-8
> show (#4,7-8 & ((protein&@ca)|(nucleic&@p))) target ab
> select add #7/A:33@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
272 atoms, 278 bonds, 34 residues, 1 model selected
> select up
4881 atoms, 5034 bonds, 609 residues, 1 model selected
> hide sel
> select clear
> ui tool show "Side View"
> color #4 #556270
> select clear
> save /Users/kelvinlau/Desktop/RhGB07-full/RBDdiff-prd0038-zoom4.tiff
> supersample 4
> select #4/A:466
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:466-469
27 atoms, 27 bonds, 3 pseudobonds, 4 residues, 2 models selected
> select #4/A:470-471
16 atoms, 15 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #4/A:466-471
43 atoms, 43 bonds, 5 pseudobonds, 6 residues, 2 models selected
> select #4/A:466
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:466-470
34 atoms, 34 bonds, 4 pseudobonds, 5 residues, 2 models selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> graphics silhouettes true
> lighting soft
> windowsize 800 800
> ui tool hide "command line interface"
> ui tool show clix
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Failed to send bug report. Possibly no internet connection.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
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 Pro
Model Identifier: MacBookPro18,4
Model Number: Z15H00063SM/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 20 days, 19 hours, 41 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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-clix: 0.1.1
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: 1.8
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 , 14 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 , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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This crash is in the Qt 6.6 window toolkit on Mac. We've seen it many times and seems to happen when an external display is plugged in or unplugged or the Mac wakes from sleep. We have never seen this crash reported with Qt version 6.7 which is in the ChimeraX daily builds, so you might want to use the ChimeraX daily build. If you need to add or remove an external display or sleep and wake your computer you should save your ChimeraX work (ChimeraX command "save mystuff.cxs").