Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#9721 closed defect (can't reproduce)

Crash handling text input

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Window Toolkit 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-12.5-arm64-arm-64bit
ChimeraX Version: 1.6rc202304202331 (2023-04-20 23:31:10 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 0x00000001044d0580 (most recent call first):
  File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX-1.6-rc2023.04.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6-rc2023.04.20.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" : 650000,
  "procLaunch" : "2023-09-07 14:49:09.3247 +0800",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "procStartAbsTime" : 15371086935902,
  "coalitionID" : 656,
  "osVersion" : {
    "train" : "macOS 12.5",
    "build" : "21G72",
    "releaseType" : "User"
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  "captureTime" : "2023-09-07 19:13:42.1454 +0800",
  "incident" : "2B0627FF-877F-47C9-A060-2DA2D32CA317",
  "bug_type" : "309",
  "pid" : 22939,
  "procExitAbsTime" : 15637382155331,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.6-rc2023.04.20.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"3AFED439-0FD2-5851-9C38-71652745F93E","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "1FE36C33-9CCF-B3F5-8006-378077B2E675",
  "wakeTime" : 2190,
  "sleepWakeUUID" : "DC4E6C9B-0BAA-4623-AE01-6E614DD4FD29",
  "sip" : "enabled",
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  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0x18 is not in any region.  Bytes before following region: 105553518919656\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
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    "path" : "\/Applications\/ChimeraX-1.6-rc2023.04.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 7077134336,
    "size" : 290816,
    "uuid" : "035d23d9-4cb5-3759-9059-1f7878f89fee",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 7164665856,
    "CFBundleShortVersionString" : "1.600.0",
    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 4046848,
    "uuid" : "73d946b4-c187-3095-bc77-59ad2d0da9bc",
    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "sharedCache" : {
  "base" : 7075676160,
  "size" : 3144695808,
  "uuid" : "ffede77c-d90b-366b-96f2-665c2f50ee59"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=2.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.6G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 2176K        4 \nCG image                          1056K       47 \nColorSync                          640K       28 \nCoreAnimation                     2992K       82 \nCoreGraphics                        32K        2 \nCoreUI image data                 4656K       32 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             1.4G      313 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)         520.0M        7         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        608K       38 \nStack                            170.4M       39 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      191.7M      398 \nVM_ALLOCATE (reserved)           160.0M        4         reserved VM address space (unallocated)\n__AUTH                            2624K      311 \n__AUTH_CONST                      20.6M      511 \n__CTF                               756        1 \n__DATA                            23.6M      661 \n__DATA_CONST                      28.0M      669 \n__DATA_DIRTY                      1804K      216 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       606.8M      157 \n__OBJC_CONST                      3665K      282 \n__OBJC_RO                         83.0M        1 \n__OBJC_RW                         3168K        1 \n__TEXT                           738.3M      687 \n__UNICODE                          592K        1 \ndyld private memory               1024K        1 \nmapped file                      195.7M       53 \nshared memory                     3184K       27 \n===========                     =======  ======= \nTOTAL                              4.3G     4600 \nTOTAL, minus reserved VM space     3.5G     4600 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
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      "deploymentId" : 240000066
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    {
      "rolloutId" : "5f72dc58705eff005a46b3a9",
      "factorPackIds" : {

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      "deploymentId" : 240000015
    }
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  "experiments" : [
    {
      "treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
      "experimentId" : "64406ba83deb637ac8a04419",
      "deploymentId" : 900000017
    }
  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/Fig1. overall structure of oleamide-bingding complex/Fig2.
> oleamide binding pocket/LPC oleamide.cxs"

opened ChimeraX session  

> open /Users/scarlettzhang/Downloads/5tgz.pdb

5tgz.pdb title:  
Crystal structure of the human cannabinoid receptor CB1 [more info...]  
  
Chain information for 5tgz.pdb #7  
---  
Chain | Description | UniProt  
A | cannabinoid receptor 1,flavodoxin,cannabinoid receptor 1 | CNR1_HUMAN
99-306 332-414, FLAV_DESVH 1002-1148  
  
Non-standard residues in 5tgz.pdb #7  
---  
FMN — flavin mononucleotide (riboflavin monophosphate)  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
PEG — di(hydroxyethyl)ether  
ZDG —
4-[4-[2-(2,4-dichlorophenyl)-4-methyl-5-(piperidin-1-ylcarbamoyl)pyrazol-3-yl]phenyl]but-3-ynyl
nitrate  
  

> ui tool show Matchmaker

> matchmaker #7 to #6

Parameters  
---  
Chain pairing | bb  
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 oleamide119, chain R (#6) with 5tgz.pdb, chain A (#7), sequence
alignment score = 367.5  
RMSD between 110 pruned atom pairs is 1.307 angstroms; (across all 279 pairs:
6.931)  
  

> hide #!5 models

> hide #!6 models

> hide #7 models

> show #7 models

> select add #7

3542 atoms, 3611 bonds, 455 residues, 1 model selected  

> hide sel atoms

> show #!6 models

> show #!5 models

> select ligand

213 atoms, 212 bonds, 8 residues, 2 models selected  

> show sel & #7 atoms

> hide #7 models

> show #7 models

> select add #7

3629 atoms, 3697 bonds, 456 residues, 2 models selected  

> select subtract #7

87 atoms, 86 bonds, 1 residue, 1 model selected  

> select add #7

3629 atoms, 3697 bonds, 456 residues, 2 models selected  

> show sel & #7 surfaces

> ui tool show "Side View"

> select clear

> select ligand

213 atoms, 212 bonds, 8 residues, 2 models selected  

> hide sel & #!7 cartoons

> hide sel & #!7 atoms

> hide sel & #!7 surfaces

> hide #!7 models

> show #!7 models

> hide sel & #!7 surfaces

> select add #7

3629 atoms, 3697 bonds, 456 residues, 3 models selected  

> hide sel & #!7 surfaces

> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/Fig2. AS structure and binding pocket/AR+AS口袋比对.cxs"

opened ChimeraX session  

> hide #!2 models

> hide #!1 models

> select #4/R:265

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #4/R:265@NE1

1 atom, 1 residue, 1 model selected  

> color (#!4 & sel) byelement

> ui tool show H-Bonds

> hbonds sel radius 0.5 restrict cross interModel false distSlop 0.5 select
> true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: AS119 #4/R PRO 69 N  

0 hydrogen bonds found  

> select #4/R:265@NE1

1 atom, 1 residue, 1 model selected  

> ui tool show Distances

> select add #3/R:401@O17

2 atoms, 2 residues, 3 models selected  

> distance #4/R:265@NE1 #3/R:401@O17

Distance between AS119 #4/R TRP 265 NE1 and AS #3/R LIG 401 O17: 3.520Å  

> select clear

> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/作图/pocket/AS pocket.cxs"

opened ChimeraX session  

> hide #1.3 models

> select /R:401@O17

1 atom, 1 residue, 1 model selected  

> select add /R:265@NE1

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance /R:401@O17 /R:265@NE1

Distance between /R LIG 401 O17 and TRP 265 NE1: 3.520Å  

> distance style color #0096ff

> distance style decimalPlaces 2

> distance style dashes 8

> distance style radius 0.05

> select clear

> select add /R:157@CZ

1 atom, 1 bond, 1 residue, 1 model selected  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> select up

3 atoms, 1 bond, 2 residues, 1 model selected  

> select up

25 atoms, 26 bonds, 2 residues, 1 model selected  

> show sel surfaces

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

18 atoms, 19 bonds, 1 residue, 1 model selected  

> show sel surfaces

> select /R:157@CD1

1 atom, 1 residue, 1 model selected  

> select add /R:265@CE2

2 atoms, 2 residues, 2 models selected  

> select up

25 atoms, 26 bonds, 2 residues, 2 models selected  

> mlp sel

Map values for surface "GRP119-AS1269574.pdb_R SES surface": minimum -26.52,
mean 0.3881, maximum 23.19  
To also show corresponding color key, enter the above mlp command and add key
true  

> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/结构/119-As-253post.mrc"

Opened 119-As-253post.mrc as #3, grid size 280,280,280, pixel 0.851, shown at
level 0.0168, step 2, values float32  

Mismatch between Cocoa '\x0' and Carbon 'w' for virtual key 13 with
QFlags(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon 'W' for virtual key 13 with
QFlags(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon 'w' for virtual key 13 with
QFlags(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon 'W' for virtual key 13 with
QFlags(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u2211' for virtual key 13 with
QFlags(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u201e' for virtual key 13 with
QFlags(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u2211' for virtual key 13 with
QFlags(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\u201e' for virtual key 13 with
QFlags(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x17' for virtual key 13 with
QFlags(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x17' for virtual key 13 with
QFlags(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x17' for virtual key 13 with
QFlags(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x17' for virtual key 13 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x17' for virtual key 13 with
QFlags(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x17' for virtual key 13 with
QFlags(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x17' for virtual key 13 with
QFlags(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x17' for virtual key 13 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  


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

Log:
UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/scarlettzhang/杂事/Ye Lab/GPCR interaction/写文章/GPR119
> AS+oleamide/结构/GRP119-AS1269574.pdb"

Chain information for GRP119-AS1269574.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
N | No description available  
R | No description available  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5 (21G72)
      Kernel Version: Darwin 21.6.0
      Time since boot: 14 days 8:11

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      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: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202304202331
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    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: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.5.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    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: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.2.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (3)

comment:1 by pett, 2 years ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash handling text input

comment:2 by pett, 2 years ago

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

Seems highly correlated with "Mismatch between Cocoa and Carbon for virtual key" messages.

comment:3 by Tom Goddard, 2 years ago

Good observation about the Mismatch warning. I tried long ago to get that Mismatch warning by pushing key combinations in various text entries but never could produce it. If we find a recipe to get that warning we might get to the bottom of this text input crash. Seems likely to be a Qt bug and make Qt 6.5 or later will fix it.

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