Opened 3 years ago

Closed 3 years ago

#8667 closed defect (can't reproduce)

Crash in event loop

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
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 0x0000000203210140 (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 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" : 75000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "coalitionID" : 5704,
  "osVersion" : {
    "train" : "macOS 13.2.1",
    "build" : "22D68",
    "releaseType" : "User"
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  "captureTime" : "2023-03-17 22:37:31.2846 +0100",
  "incident" : "9056A900-6D42-4AEE-A9CF-C91B594D0F03",
  "pid" : 26395,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-03-17 16:53:27.3893 +0100",
  "procStartAbsTime" : 1478588229849,
  "procExitAbsTime" : 1807129935140,
  "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":"ACDA6E2F-7357-5BE1-A382-B40D2103C0F2","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "4D720C3C-A1B4-F848-8B17-10441DA6484D",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 1668,
  "sleepWakeUUID" : "97E1A760-0B59-45EF-AFD0-5F19FE96EA32",
  "sip" : "enabled",
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=2.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.9G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 4128K        5 \nCG image                          1392K       60 \nColorSync                          592K       29 \nCoreAnimation                      848K       19 \nCoreGraphics                        96K        6 \nCoreUI image data                 4144K       55 \nFoundation                          96K        3 \nImage IO                            16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                             1.6G      334 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)         776.0M        9         reserved VM address space (unallocated)\nOpenGL GLSL                        384K        4 \nSTACK GUARD                        608K       38 \nStack                            177.9M       39 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      219.5M      459 \nVM_ALLOCATE (reserved)           160.0M        4         reserved VM address space (unallocated)\n__AUTH                            1938K      362 \n__AUTH_CONST                      24.9M      590 \n__CTF                               756        1 \n__DATA                            20.1M      725 \n__DATA_CONST                      37.4M      733 \n__DATA_DIRTY                      1984K      229 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       796.4M      142 \n__OBJC_CONST                      4759K      326 \n__OBJC_RO                         65.5M        1 \n__OBJC_RW                         1988K        1 \n__TEXT                           807.2M      754 \ndyld private memory                416K        3 \nmapped file                      547.5M       90 \nshared memory                     1120K       28 \n===========                     =======  ======= \nTOTAL                              5.2G     5068 \nTOTAL, minus reserved VM space     4.3G     5068 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "61675b89201f677a9a4cbd65",
      "factorPackIds" : {
        "HEALTH_FEATURE_AVAILABILITY" : "63f8068a238e7b23a1f30123"
      },
      "deploymentId" : 240000055
    },
    {
      "rolloutId" : "62699e1ec1ff2978b47f6c3b",
      "factorPackIds" : {
        "SIRI_FIND_MY_CONFIGURATION_FILES" : "631f72d1de559130376df1fb"
      },
      "deploymentId" : 240000023
    }
  ],
  "experiments" : [

  ]
},
  "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  

> open /Users/villena/Downloads/7diy.cif format mmcif

7diy.cif title:  
Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-exoribonuclease domain
[more info...]  
  
Chain information for 7diy.cif #1  
---  
Chain | Description | UniProt  
A | nsp10 protein | R1AB_SARS2  
B | nsp14-ExoN protein | R1AB_SARS2  
  
Non-standard residues in 7diy.cif #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  
Alignment identifier is 1/A  
Alignment identifier is 1/B  

> interfaces ~solvent

1 buried areas: B A 2219  

> interfaces ~solvent

1 buried areas: B A 2219  

> interfaces ~solvent

1 buried areas: B A 2219  

> select

3249 atoms, 3298 bonds, 19 pseudobonds, 451 residues, 2 models selected  

> color (#!1 & sel) light gray

> set bgColor white

> color sel bychain

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select

3249 atoms, 3298 bonds, 19 pseudobonds, 451 residues, 2 models selected  

> select clear

> interfaces ~solvent

1 buried areas: B A 2219  

> set bgColor black

> set bgColor white

> ui dockable true "Chain Contacts"

> ui dockable false "Sequence Viewer"

> help help:user/commands/interfaces.html#diagram

> select clear

> ui dockable false "Chain Contacts"

> select /A:22

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

> select /A:22-25

27 atoms, 26 bonds, 4 residues, 1 model selected  

> select /A:21

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

> select /A:21-32

93 atoms, 94 bonds, 12 residues, 1 model selected  

> select /A:1

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

> select /A:1-18

121 atoms, 122 bonds, 18 residues, 1 model selected  

> ui dockable true "Chain Contacts"

> select /A:21

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

> select /A:21-25

34 atoms, 33 bonds, 5 residues, 1 model selected  

> select /A:36-37

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:36-40

39 atoms, 39 bonds, 5 residues, 1 model selected  

> help help:user/commands/contacts.html#residue-plot

No help found for 'help:user/commands/contacts.html#residue-plot'  

> help help:user/commands/contacts.html#residue-plot

No help found for 'help:user/commands/contacts.html#residue-plot'  

> help help:user/commands/interfaces.html#diagram

> select down

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

> select /A:1-131

955 atoms, 976 bonds, 131 residues, 1 model selected  

> select /B:3-288

2260 atoms, 2322 bonds, 286 residues, 1 model selected  

> select /B:3-288

2260 atoms, 2322 bonds, 286 residues, 1 model selected  

> show sel cartoons

> style sel stick

Changed 2260 atom styles  

> style sel stick

Changed 2260 atom styles  

> show sel cartoons

> hide sel atoms

> select /B:3-288

2260 atoms, 2322 bonds, 286 residues, 1 model selected  

> select /B:3-288

2260 atoms, 2322 bonds, 286 residues, 1 model selected  

> select /B:3-288

2260 atoms, 2322 bonds, 286 residues, 1 model selected  

> select /B:3-288

2260 atoms, 2322 bonds, 286 residues, 1 model selected  

> select /A:1-131

955 atoms, 976 bonds, 131 residues, 1 model selected  

> show sel cartoons

> style sel stick

Changed 955 atom styles  

> hide sel atoms

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> color sel byhetero

> color sel bychain

> select /A:40

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

> select /A:40-45

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

> show sel surfaces

> select /B:3-288

2260 atoms, 2322 bonds, 286 residues, 1 model selected  

> show sel surfaces

> select

3249 atoms, 3298 bonds, 19 pseudobonds, 451 residues, 2 models selected  

> show sel surfaces

> select /A:24

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

> select /A:24-25

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:22

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

> select /A:22-24

18 atoms, 17 bonds, 3 residues, 1 model selected  

> select /A:42

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

> select /A:30-42

91 atoms, 92 bonds, 13 residues, 1 model selected  

> select /A:7-19,22-33,71-80,102-104,106-114

349 atoms, 353 bonds, 47 residues, 1 model selected  

> select /A:58

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

> select /A:58-63

44 atoms, 44 bonds, 6 residues, 1 model selected  

> select /A:40

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

> select /A:40-44

38 atoms, 37 bonds, 5 residues, 1 model selected  

> select /A:45-46

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:39-46

59 atoms, 58 bonds, 8 residues, 1 model selected  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> show sel cartoons

> color sel bychain

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> color sel bychain

> select

3249 atoms, 3298 bonds, 19 pseudobonds, 451 residues, 2 models selected  

> color sel bychain

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> help help:user/commands/contacts.html#residue-plot

No help found for 'help:user/commands/contacts.html#residue-plot'  

> hide sel atoms

> color sel bychain

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> select clear

> select /B:126

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

> select /B:126-130

38 atoms, 38 bonds, 5 residues, 1 model selected  

> select /B:88

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /B:88-100

96 atoms, 97 bonds, 13 residues, 1 model selected  

> ui dockable false "Chain Contacts"

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select clear

> interfaces ~solvent

1 buried areas: B A 2219  

> interfaces ~solvent

1 buried areas: B A 2219  

> select /A:38-39

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:38-40

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select /A:39

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

> select /A:39-46

59 atoms, 58 bonds, 8 residues, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> show sel cartoons

> style sel stick

Changed 59 atom styles  

> style sel ball

Changed 59 atom styles  

> style sel stick

Changed 59 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel cartoons

> style sel stick

Changed 59 atom styles  

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> color sel bychain

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select ~sel

3241 atoms, 3289 bonds, 19 pseudobonds, 450 residues, 2 models selected  

> select clear

> color bychain

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> interfaces ~solvent

1 buried areas: B A 2219  

> select ~sel

2633 atoms, 2633 bonds, 18 pseudobonds, 374 residues, 2 models selected  

> color (#!1 & sel) light gray

> select ~sel

616 atoms, 601 bonds, 77 residues, 1 model selected  

> select ~sel

2633 atoms, 2633 bonds, 18 pseudobonds, 374 residues, 2 models selected  

> hide sel surfaces

> select

3249 atoms, 3298 bonds, 19 pseudobonds, 451 residues, 2 models selected  

> hide sel surfaces

> hide sel atoms

> show sel atoms

> hbonds sel reveal true

103 hydrogen bonds found  

> lighting soft

> lighting full

> lighting soft

> select /A:40

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

> select /A:40-46

52 atoms, 51 bonds, 1 pseudobond, 7 residues, 2 models selected  

> select ~sel

3197 atoms, 3245 bonds, 112 pseudobonds, 444 residues, 3 models selected  

> ~hbonds

> color (#!1 & sel) light gray

> select ~sel

52 atoms, 51 bonds, 7 residues, 1 model selected  

> hbonds sel reveal true

12 hydrogen bonds found  

> select /B:3-288

2260 atoms, 2322 bonds, 286 residues, 1 model selected  

> select /B:3-22

150 atoms, 152 bonds, 20 residues, 1 model selected  

> select /B:52

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

> select /B:52

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

> select
> /B:34-35,38-39,53-55,86-96,104-111,116-118,122-126,131-135,138-139,182-185,199-200,216-218,223-225,235-237,240-243

486 atoms, 485 bonds, 60 residues, 1 model selected  

> select /B:51

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

> select /B:51-52

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select /B:37

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /B:37

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /B:38

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

> select /B:38

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

> select /B:39

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

> select /B:39

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

> color sel bychain

> select /B:25

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

> select /B:25

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

> color sel bychain

> select /B:26

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

> select /B:26

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

> color sel bychain

> hide sel atoms

> select

3249 atoms, 3298 bonds, 31 pseudobonds, 451 residues, 3 models selected  

> hide sel atoms

> set bgColor gray

> set bgColor #80808000

> set bgColor white

> set bgColor #ffffff00

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> select

3249 atoms, 3298 bonds, 31 pseudobonds, 451 residues, 3 models selected  

> style sel sphere

Changed 3249 atom styles  

> style sel sphere

Changed 3249 atom styles  


===== 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 Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11B00083Y/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 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: 2 días, 10 horas y 2 minutos

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Q24h-10:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in event loop

comment:2 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: accepted → closed
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