Opened 3 years ago

Closed 3 years ago

#8084 closed defect (duplicate)

Crash during screen changed

Reported by: chimerax-bug-report@… 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:        Darwin-21.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
  "uptime" : 24000,
  "procLaunch" : "2022-11-25 16:23:34.5383 +0100",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 565340369,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,1",
  "procStartAbsTime" : 23503821534567,
  "coalitionID" : 3112,
  "osVersion" : {
    "train" : "macOS 12.6",
    "build" : "21G115",
    "releaseType" : "User"
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  "captureTime" : "2022-11-25 16:32:11.1347 +0100",
  "incident" : "17F7BC4A-C207-4C35-B61E-9F40207ECDE5",
  "bug_type" : "309",
  "pid" : 22947,
  "procExitAbsTime" : 24020380540464,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.1.1","CFBundleVersion":"1.1.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D36C683E-F423-2F40-D8A3-00731F1846B6",
  "wakeTime" : 8897,
  "bridgeVersion" : {"build":"19P6067","train":"6.6"},
  "sleepWakeUUID" : "4B054436-BC45-4057-8687-231061464B90",
  "sip" : "enabled",
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  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000028","rawCodes":[1,40],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000028"},
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  "faultingThread" : 0,
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    "size" : 4452352,
    "uuid" : "234d0c44-43b0-3e31-a215-9b8c6ff91ce9",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/lib\/python3.7\/site-packages\/PyQt5\/Qt\/lib\/QtWidgets.framework\/Versions\/5\/QtWidgets",
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    "arch" : "x86_64",
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    "size" : 2646016,
    "uuid" : "03c83187-2a4b-31c4-a672-eff768b4184f",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/lib\/python3.7\/site-packages\/PyQt5\/QtWidgets.so",
    "name" : "QtWidgets.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4458123264,
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    "CFBundleIdentifier" : "org.python.python",
    "size" : 2080768,
    "uuid" : "19fe2a34-09e9-309b-92d6-0b8f10faab4d",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.7\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.7.8"
  },
  {
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    "arch" : "x86_64",
    "base" : 4535955456,
    "size" : 1363968,
    "uuid" : "6a4cd3b0-d092-3178-a850-403629040e94",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/lib\/python3.7\/site-packages\/PyQt5\/QtCore.so",
    "name" : "QtCore.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4759822336,
    "size" : 5464064,
    "uuid" : "4016188b-3e53-3268-95b9-a3826de2f323",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/lib\/python3.7\/site-packages\/PyQt5\/Qt\/lib\/QtCore.framework\/Versions\/5\/QtCore",
    "name" : "QtCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703607566336,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3096576,
    "uuid" : "06fdecd6-9f69-397b-b1e2-a8226c0ba7ed",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4449505280,
    "CFBundleShortVersionString" : "1.1.1",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "ee49a5e0-ce3b-3691-8016-6b00e884a605",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/MacOS\/ChimeraX",
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    "uuid" : "71febccd-d9dc-3599-9971-2b3407c588a8",
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    "uuid" : "9914a383-f8c9-3559-bc88-b4dd28689bc5",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/lib\/python3.7\/site-packages\/numpy\/.dylibs\/libopenblasp-r0.3.7.dylib",
    "name" : "libopenblasp-r0.3.7.dylib"
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    "size" : 103034880,
    "uuid" : "ba834275-2e19-3355-abf6-dd24a3f4f3a5",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/lib\/python3.7\/site-packages\/PyQt5\/Qt\/lib\/QtWebEngineCore.framework\/Versions\/5\/QtWebEngineCore",
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    "size" : 61259776,
    "uuid" : "9914a383-f8c9-3559-bc88-b4dd28689bc5",
    "path" : "\/Applications\/ChimeraX-1.1.1.app\/Contents\/lib\/python3.7\/site-packages\/scipy\/.dylibs\/libopenblasp-r0.3.7.dylib",
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               640K        5 \nActivity Tracing                   256K        1 \nCG backing stores                 3488K        8 \nCG image                           196K       22 \nColorSync                          232K       27 \nCoreAnimation                      400K       19 \nCoreGraphics                        16K        3 \nCoreServices                       624K        2 \nCoreUI image data                 1104K       21 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           483.7M      340 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nObjC additional data                15K        1 \nOpenGL GLSL                        512K        6 \nPROTECTED_MEMORY                     4K        1 \nSTACK GUARD                        140K       35 \nStack                            160.8M       36 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      176.7M      409 \nVM_ALLOCATE (reserved)           256.0M        4         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            55.6M      761 \n__DATA_CONST                      31.5M      331 \n__DATA_DIRTY                      1576K      205 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       694.6M      208 \n__TEXT                           860.8M      724 \n__UNICODE                          592K        1 \ndyld private memory               1056K        3 \nmapped file                      429.7M       85 \nshared memory                     1332K       27 \n===========                     =======  ======= \nTOTAL                              3.4G     3301 \nTOTAL, minus reserved VM space     2.9G     3301 \n",
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}
}


Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/au612266/Aarhus Universitet/ESA-LAB - Nestor Sampedro/Aarhus
> University/Postdoc/Manuscripts/TRAP paper/Raw data/Build_Models/6-11.cxs"

Log from Fri Nov 25 16:31:55 2022UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/au612266/Aarhus Universitet/ESA-LAB - Nestor Sampedro/Aarhus
> University/Postdoc/Manuscripts/TRAP paper/Raw data/Build_Models/6-11.pdb"

Summary of feedback from opening /Users/au612266/Aarhus Universitet/ESA-LAB -
Nestor Sampedro/Aarhus University/Postdoc/Manuscripts/TRAP paper/Raw
data/Build_Models/6-11.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK - File Generated by RNA_build.pl - written by Cody Geary  
  
Ignored bad PDB record found on line 2  
REMARK - Building a total of 351 nts.  
  
Ignored bad PDB record found on line 4  
REMARK Add GNRA  
  
Ignored bad PDB record found on line 5  
REMARK Add BKL-B  
  
Ignored bad PDB record found on line 6  
REMARK Add BKL-A  
  
9 messages similar to the above omitted  
  
Chain information for 6-11.pdb #1  
---  
Chain | Description  
A | No description available  
  

> color gray

> set bgColor white

> color light gray

> color dark gray

Drag select of 10 residues, 19 shapes  

> color sel red

Drag select of 7 residues, 17 shapes  

> color sel red

> select clear

Drag select of 14 residues, 28 shapes  

> color sel red

> select clear

Drag select of 1 residues  

> color sel red

> select clear

> color sel cyan

> color sel forest green

> select clear

> color sel cyan

> select clear

Drag select of 2 residues  

> color sel cyan

> select clear

> color sel cyan

> select clear

> save "/Users/au612266/Aarhus Universitet/ESA-LAB - Nestor Sampedro/Aarhus
> University/Postdoc/Manuscripts/TRAP paper/Raw data/Build_Models/Screen Shot
> 2021-09-02 at 1.24.48 PM.png" width 1307 height 988 supersample 3

> save "/Users/au612266/Aarhus Universitet/ESA-LAB - Nestor Sampedro/Aarhus
> University/Postdoc/Manuscripts/TRAP paper/Raw data/Build_Models/6-11.cxs"

opened ChimeraX session  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0)
      OS Loader Version: 540.120.3~22

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 7:44

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    Radeon Pro 555X:

      Chipset Model: Radeon Pro 555X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00e3
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501P-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP E273q:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 6CM8181K9Z  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Adapter Firmware Version: ff.c1

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: UnassignedWindow Toolkit
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionCrash during screen changed

comment:2 by Eric Pettersen, 3 years ago

Resolution: duplicate
Status: assignedclosed
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