id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9089	Unknown crash	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-13.0-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.
{""app_name"":""ChimeraX"",""timestamp"":""2023-05-29 23:04:18.00 +1200"",""app_version"":""1.5.0"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.5.0.0"",""platform"":0,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.0 (22A380)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""C0AC5F9E-4A79-433F-AD55-9FDE05E5AD4E""}
{
  ""uptime"" : 2600000,
  ""procRole"" : ""Default"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookAir10,1"",
  ""coalitionID"" : 152542,
  ""osVersion"" : {
    ""train"" : ""macOS 13.0"",
    ""build"" : ""22A380"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2023-05-29 23:04:18.7634 +1200"",
  ""incident"" : ""C0AC5F9E-4A79-433F-AD55-9FDE05E5AD4E"",
  ""pid"" : 27299,
  ""translated"" : true,
  ""cpuType"" : ""X86-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2023-05-29 23:04:18.7222 +1200"",
  ""procStartAbsTime"" : 63151292711925,
  ""procExitAbsTime"" : 63151293620893,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.5.0"",""CFBundleVersion"":""1.5.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""C6B00BA1-23DF-5726-A7DB-D48356989882"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""6EA1089D-EE9E-784C-E6AB-3B8A597C7645"",
  ""wakeTime"" : 6672,
  ""sleepWakeUUID"" : ""25BF535A-3064-4F00-BD36-3F55A5403521"",
  ""sip"" : ""enabled"",
  ""exception"" : {""codes"":""0x0000000000000001, 0x00007ff7ffe629a0"",""rawCodes"":[1,140703126923680],""type"":""EXC_BREAKPOINT"",""signal"":""SIGTRAP""},
  ""termination"" : {""flags"":0,""code"":5,""namespace"":""SIGNAL"",""indicator"":""Trace\/BPT trap: 5"",""byProc"":""exc handler"",""byPid"":27299},
  ""os_fault"" : {""process"":""ChimeraX""},
  ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0},
  ""faultingThread"" : 0,
  ""threads"" : [{""triggered"":true,""id"":21177223,""threadState"":{""x"":[{""value"":0},{""value"":8589934595},{""value"":259845526803},{""value"":3311419785731},{""value"":14658723381248},{""value"":3311419785217},{""value"":44},{""value"":0},{""value"":140703127044096},{""value"":0},{""value"":14658723381248},{""value"":140703127046545,""symbolLocation"":233,""symbol"":""__crashreporter_info__""},{""value"":120},{""value"":0},{""value"":140703126948224},{""value"":33},{""value"":18446744073709551569},{""value"":13045578407},{""value"":13045584459},{""value"":140703127003921},{""value"":13045586176},{""value"":4340629504},{""value"":4},{""value"":4340629504},{""value"":3},{""value"":1},{""value"":16777223},{""value"":8637571216,""symbolLocation"":0,""symbol"":""dyld_all_image_infos""},{""value"":13045619504}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":140703126923672},""cpsr"":{""value"":1610616832},""fp"":{""value"":13045578592},""sp"":{""value"":13045578560},""esr"":{""value"":4060086273,""description"":""(Breakpoint) brk 1""},""pc"":{""value"":140703126923680,""matchesCrashFrame"":1},""far"":{""value"":13045578616}},""frames"":[{""imageOffset"":121248,""imageIndex"":0},{""imageOffset"":121320,""imageIndex"":0},{""imageOffset"":74736,""imageIndex"":0},{""imageOffset"":79024,""imageIndex"":0},{""imageOffset"":76844,""imageIndex"":0},{""imageOffset"":14608,""imageIndex"":0},{""imageOffset"":0,""imageIndex"":1}]}],
  ""usedImages"" : [
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64"",
    ""base"" : 140703126802432,
    ""size"" : 196608,
    ""uuid"" : ""6f797d84-b330-3656-9a0d-7b3dbd3f8a07"",
    ""path"" : ""\/usr\/libexec\/rosetta\/runtime"",
    ""name"" : ""runtime""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 8636899328,
    ""size"" : 622592,
    ""uuid"" : ""0f050705-2258-3d40-b7bc-f3b35a44bbea"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
  }
],
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1132K resident=0K(0%) swapped_out_or_unallocated=1132K(100%)\nWritable regions: Total=23.4M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=23.4M(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nSTACK GUARD                       56.0M        1 \nStack                             8176K        1 \nVM_ALLOCATE                       15.3M        6 \nVM_ALLOCATE (reserved)              32K        1         reserved VM address space (unallocated)\n__DATA                              80K        3 \n__DATA_CONST                        32K        1 \n__DATA_DIRTY                        16K        1 \n__LINKEDIT                         352K        4 \n__TEXT                             800K        2 \nmapped file                        6.5G       33 \n===========                     =======  ======= \nTOTAL                              6.6G       53 \nTOTAL, minus reserved VM space     6.6G       53 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {

  }
},
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""6112e3d2fc54bc3389840661"",
      ""factorPackIds"" : {
        ""SIRI_TEXT_TO_SPEECH"" : ""6407d37503b3136e9aacb281""
      },
      ""deploymentId"" : 240000447
    },
    {
      ""rolloutId"" : ""62cdf63ddb3b7109d6d765cc"",
      ""factorPackIds"" : {
        ""SIRI_UNDERSTANDING_TMDC"" : ""62cdf6dddb3b7109d6d765cd""
      },
      ""deploymentId"" : 240000007
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"",
      ""experimentId"" : ""6317d2003d24842ff850182a"",
      ""deploymentId"" : 400000005
    },
    {
      ""treatmentId"" : ""c9ac7ace-da9d-41f5-b424-a422a874751d"",
      ""experimentId"" : ""63b8ec83fd1d345f491884ba"",
      ""deploymentId"" : 400000024
    }
  ]
},
  ""reportNotes"" : [
  ""dyld_process_snapshot_get_shared_cache failed""
]
}


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: MGN63X/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 74 days, 11 hours, 33 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

}}}
"	defect	closed	normal		Core		can't reproduce		Tom Goddard				all	ChimeraX