Opened 3 years ago

Closed 3 years ago

#8956 closed defect (duplicate)

Crash in removeDockWidget

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x0000000202db8140 (most recent call first):
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2301 in destroy
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2165 in _destroy
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 772 in remove_tool
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 335 in remove_tool
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 639 in close_request
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2267 in 
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 960000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "coalitionID" : 98576,
  "osVersion" : {
    "train" : "macOS 13.2.1",
    "build" : "22D68",
    "releaseType" : "User"
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  "captureTime" : "2023-05-06 15:29:53.1329 -0400",
  "incident" : "50643209-828A-4FF5-9422-E1BAEF96077B",
  "pid" : 49414,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-05-06 12:10:27.0975 -0400",
  "procStartAbsTime" : 22927884552107,
  "procExitAbsTime" : 23215069443987,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"9588A22A-EB0D-5195-965B-1DCE6BB3E267","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "998A5CF9-71C4-BB97-BD26-AE97AD750BA1",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 12001,
  "sleepWakeUUID" : "DF3AEF77-32CD-4CF5-8CD2-E85754503CFE",
  "sip" : "enabled",
  "vmRegionInfo" : "0x3e998fbc0c28 is not in any region.  Bytes after previous region: 68348226047017  Bytes before following region: 36723853882328\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x00003e998fbc0c28","rawCodes":[1,68829262384168],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00003e998fbc0c28"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n",
  "vmregioninfo" : "0x3e998fbc0c28 is not in any region.  Bytes after previous region: 68348226047017  Bytes before following region: 36723853882328\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  ...(unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV  ",
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],
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "6347054113acce15305b7b82",
      "factorPackIds" : {
        "SIRI_MEMORY_SYNC_CONFIG" : "634705e78e8be655c1316a6e"
      },
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    },
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      "factorPackIds" : {
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        "SIRI_UNDERSTANDING_MORPHUN" : "62ec7220c682040ba94e6a20"
      },
      "deploymentId" : 240000674
    }
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  "experiments" : [
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      "experimentId" : "6317d2003d24842ff850182a",
      "deploymentId" : 400000013
    },
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      "experimentId" : "64406ba83deb637ac8a04419",
      "deploymentId" : 900000005
    }
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},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MNDQTQFTERALTILTLAQKLASDHQHPQLQPIHILAAFIETPEDGSVPYLQNLIEKGRYDYDLFKKVVNRNLVRIPQQQPAPAEITPSYALGKVLQDAAKIQKQQKDSFIAQDHILFALFNDSSIQQIFKEAQVDIEAIKQQALELRGNTRIDSRGADTNTPLEYLSKYAIDMTEQARQGKLDPVIGREEEIRSTIRVLARRIKSNPCLIGEPGIGKTAIIEGVAQRIIDDDVPTILQGAKLFSLDLAALTAGAKYKGDFEERFKGVLKEIEESKTLIVLFIDEIHMLMGNGKDDAANILKPALSRGQLKVIGATTNNEYRSIVEKDGAFERRFQKIEVAEPSVRQTVAILRGLQPKYEIHHGVRILDSALVTAAQLAKRYLPYRRLPDSALDLVDISCAGVAVARDSKPEELDSKERQLQLIQVEIKALERDEDADSTTKDRLKLARQKEASLQEELEPLRQRYNEEKHGHEELTQAKKKLDELENKALDAERRYDTATAADLRYVAIPDIKKQIEKLEDQVAEEERRAGANSMIQNVVDSDTISETAARLTGIPVKKLSESEIEKLIHMERDLSSEVVGQMDAIKAVSNAVRLSRSGLANPRQPASFLFLGLSGSGKTELAKKVAGFLFNDEDMMIRVDCSELSEKYAVSKLLGTTAGYVGYDEGGFLTNQLQYKPYSVLLFDEVEKAHPDVLTVMLQMLDDGRITSGQGKTIDCSNCIVIMTSNLGAEFINSQQGSKIQESTKNLVMGAVRQHFRPEFLNRISSIVIFNKLSRKAIHKIVDIRLKEIEERFEQNDKHYKLNLTQEAKDFLAKYGYSDDMGARPLNRLIQNEILNKLALRILKNEIKDKETVNVVLKKGKSRDENVPEEAEECLEVLPNHEATIGADTLGDDDNEDSMEIDDDLD

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> open
> /Users/zoechen/Downloads/ChimeraX/AlphaFold/prediction_7_I510V_NI/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> close

> open
> /Users/zoechen/Downloads/ChimeraX/AlphaFold/prediction_7_I510V_NI/I510V_N566I.pdb

Chain information for I510V_N566I.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/zoechen/Downloads/5vy8.cif.gz

File reader requires uncompressed file; '/Users/zoechen/Downloads/5vy8.cif.gz'
is compressed  

> open /Users/zoechen/Downloads/5vy8.cif

Summary of feedback from opening /Users/zoechen/Downloads/5vy8.cif  
---  
note | Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif  
  
5vy8.cif title:  
S. cerevisiae Hsp104-ADP complex [more info...]  
  
Chain information for 5vy8.cif #2  
---  
Chain | Description | UniProt  
A B C D E F | Heat shock protein 104 | HS104_YEAST  
  
Non-standard residues in 5vy8.cif #2  
---  
ADP — adenosine-5'-diphosphate  
  

QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600002ab5b10, name="Built-in Retina Display") screenTo: QScreen(0x0)
wdgScreen: QScreen(0x600002ab5b10, name="Built-in Retina Display")
orgWdgScreen QScreen(0x600002ab5b10, name="Built-in Retina Display")  

> select #2/D

5614 atoms, 5683 bonds, 1 pseudobond, 707 residues, 2 models selected  

> hide #* target a

> show (#!2 & sel) target ab

> cartoon hide (#!2 & sel)

> cartoon (#!2 & sel)

> hide (#!2 & sel) target a

> select #1/A

7169 atoms, 7261 bonds, 908 residues, 1 model selected  

> color sel cornflower blue

> ui tool show Matchmaker

> matchmaker #1 to #2/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5vy8.cif, chain D (#2) with I510V_N566I.pdb, chain A (#1), sequence
alignment score = 3896.7  
RMSD between 255 pruned atom pairs is 1.178 angstroms; (across all 705 pairs:
5.570)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:510

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:510

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel target ab

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A #2/B #2/C #2/D #2/E #2/F

Alignment identifier is 1  

> select #2/C-E:510

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select #2/C-E:510

24 atoms, 21 bonds, 3 residues, 1 model selected  

> show sel target ab

> hide sel target a

> select #2/C-E:510

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select #2/C-E:510-511

45 atoms, 45 bonds, 6 residues, 1 model selected  

> select
> #2/A-B,F:166-171,174-181,189-202,213-232,235-240,247-253,259-274,285-289,300-309,317-334,344-364,368-383,387-409,541-562,564-580,583-601,619-638,642-646,668-678,687-704,730-737,743-765,775-796,806-819,825-847/C-E:166-171,174-181,189-202,213-232,235-240,247-253,259-274,285-289,300-309,317-334,344-364,368-383,387-433,439-525,541-562,564-580,583-601,619-638,642-646,668-678,687-704,730-737,743-765,775-796,806-819,825-847

20394 atoms, 20479 bonds, 2565 residues, 1 model selected  

> ui mousemode right select

> select clear

> select #2/D:510

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel target ab

> hide sel target a

> cartoon sel

> style sel stick

Changed 8 atom styles  

> show sel target ab

> style sel ball

Changed 8 atom styles  

> style sel stick

Changed 8 atom styles  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> view matrix models
> #1,0.62429,-0.60994,0.4881,157.9,0.46031,0.79204,0.40099,143.4,-0.63117,-0.025655,0.77522,112.92

> undo

> ui mousemode right translate

> ui mousemode right select

> ui mousemode right translate

> ui mousemode right select

> select #1/A:510

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 reveal true retainCurrent true

2 hydrogen bonds found  

> hbonds sel dashes 6 reveal true retainCurrent true

2 hydrogen bonds found  

> ui mousemode right translate

> ui mousemode right select

> select #1/A:486

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:487

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/D:486

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 8 atom styles  

> select #1/A:506

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:506

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:487

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/D:487

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 9 atom styles  

> select #2/D:506

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 11 atom styles  

> color sel byelement

> select #2/D:487

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel byelement

> select #2/D:506@NH2

1 atom, 1 residue, 1 model selected  

> select add #2/D:487@OE2

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> select #2/D:506@NH2

1 atom, 1 residue, 1 model selected  

> select add #2/D:487@OE2

2 atoms, 2 residues, 1 model selected  

> distance #2/D:506@NH2 #2/D:487@OE2

Distance between 5vy8.cif #2/D ARG 506 NH2 and GLU 487 OE2: 7.417Å  

> ~distance #2/D:506@NH2 #2/D:487@OE2

> select #2/C

5614 atoms, 5683 bonds, 1 pseudobond, 707 residues, 2 models selected  

> cartoon (#!2 & sel)

> cartoon hide (#!2 & sel)

> select #2/E

5614 atoms, 5683 bonds, 1 pseudobond, 707 residues, 2 models selected  

> cartoon (#!2 & sel)

> select #2/E:389

7 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right translate

> ui mousemode right select

> select #2/D:487

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #2/D:507

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/D:506

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel target a

> ui mousemode right translate

> ui mousemode right select

> select #1/A:506

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel target a

> select #1/A:486

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:510

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:486

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/E:426

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #2/D:507

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2/D:508

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2/E:578

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select clear

> select #2/E:426

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 7 atom styles  

> color sel byelement

> select clear

> select #2/D:507

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 12 atom styles  

> select #2/D:508

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 11 atom styles  

> select #1/A:511

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/D:511

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 7 atom styles  

> select #2/D:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:508

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #1/A:509

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:507

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel target ab

> select #2/E:426

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 reveal true retainCurrent true

3 hydrogen bonds found  

> select #2/D:515

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 9 atom styles  

> ui mousemode right clip

> ui tool show "Side View"

> ui mousemode right translate

> ui tool show Distances

> ui mousemode right select

> select clear

> select #2/D:510@CG2

1 atom, 1 residue, 1 model selected  

> select #2/D:510@CG2

1 atom, 1 residue, 1 model selected  

> select #2/E:419

11 atoms, 10 bonds, 1 residue, 1 model selected  

> ui mousemode right translate

> ui mousemode right select

> select #2/E:426@CG2

1 atom, 1 residue, 1 model selected  

> select #2/D:510@CG2

1 atom, 1 residue, 1 model selected  

> select add #2/E:426@CG2

2 atoms, 2 residues, 1 model selected  

> distance #2/D:510@CG2 #2/E:426@CG2

Distance between 5vy8.cif #2/D ILE 510 CG2 and /E VAL 426 CG2: 3.601Å  

> ui mousemode right translate

> ui mousemode right select

> select #2/E:426@CG1

1 atom, 1 residue, 1 model selected  

> select add #2/D:510@CG2

2 atoms, 2 residues, 1 model selected  

> distance #2/E:426@CG1 #2/D:510@CG2

Distance between 5vy8.cif #2/E VAL 426 CG1 and /D ILE 510 CG2: 3.998Å  
Drag select of 4 residues  

> ui mousemode right translate

> save "/Users/zoechen/Desktop/I510V:NI ADP.pdb"

> ui mousemode right select

> select #2/E:426@CG2

1 atom, 1 residue, 1 model selected  

> select add #1/A:511@CB

2 atoms, 2 residues, 2 models selected  

> distance #2/E:426@CG2 #1/A:511@CB

Distance between 5vy8.cif #2/E VAL 426 CG2 and I510V_N566I.pdb #1/A PRO 511
CB: 2.413Å  

> select #2/E:426@CG1

1 atom, 1 residue, 1 model selected  

> select #2/E:426@CG1

1 atom, 1 residue, 1 model selected  

> select subtract #2/E:426@CG1

Nothing selected  

> select #2/E:426@CG1

1 atom, 1 residue, 1 model selected  

> select add #2/D:511@CG

2 atoms, 2 residues, 1 model selected  

> distance #2/E:426@CG1 #2/D:511@CG

Distance between 5vy8.cif #2/E VAL 426 CG1 and /D PRO 511 CG: 3.722Å  

> save /Users/zoechen/Desktop/alignment/I510V_NI_ADP.pdb


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGN93LL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 47 days, 19 hours, 14 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      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: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Window Toolkit
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in removeDockWidget

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed
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