Unknown crash

[chimerax-bug-report@…]

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 17:18:47.00 +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":"070058CF-8793-4188-B812-9B774A9A3F3E"}
{
  "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 17:18:47.0837 +1200",
  "incident" : "070058CF-8793-4188-B812-9B774A9A3F3E",
  "pid" : 14422,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-05-29 17:18:47.0577 +1200",
  "procStartAbsTime" : 62702175650523,
  "procExitAbsTime" : 62702176231753,
  "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" : 8798,
  "sleepWakeUUID" : "0E57E789-D212-4D94-A6D4-0B31F68B7D6C",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000001, 0x00007ff7fffad9a0","rawCodes":[1,140703128279456],"type":"EXC_BREAKPOINT","signal":"SIGTRAP"},
  "termination" : {"flags":0,"code":5,"namespace":"SIGNAL","indicator":"Trace\/BPT trap: 5","byProc":"exc handler","byPid":14422},
  "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":21025583,"threadState":{"x":[{"value":0},{"value":8589934595},{"value":259845526803},{"value":3311419785731},{"value":14658723381248},{"value":3311419785217},{"value":44},{"value":0},{"value":140703128399872},{"value":0},{"value":14658723381248},{"value":140703128402321,"symbolLocation":233,"symbol":"__crashreporter_info__"},{"value":120},{"value":0},{"value":140703128304000},{"value":33},{"value":18446744073709551569},{"value":13106280503},{"value":13106286555},{"value":140703128359697},{"value":13106288272},{"value":4369739776},{"value":4},{"value":4369739776},{"value":3},{"value":1},{"value":16777223},{"value":8669159568,"symbolLocation":0,"symbol":"dyld_all_image_infos"},{"value":13106321600}],"flavor":"ARM_THREAD_STATE64","lr":{"value":140703128279448},"cpsr":{"value":1610616832},"fp":{"value":13106280688},"sp":{"value":13106280656},"esr":{"value":4060086273,"description":"(Breakpoint) brk 1"},"pc":{"value":140703128279456,"matchesCrashFrame":1},"far":{"value":13106280712}},"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" : 140703128158208,
    "size" : 196608,
    "uuid" : "6f797d84-b330-3656-9a0d-7b3dbd3f8a07",
    "path" : "\/usr\/libexec\/rosetta\/runtime",
    "name" : "runtime"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 8668487680,
    "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=8256K written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8256K(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nSTACK GUARD                       56.0M        1 \nStack                             8176K        1 \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                         28K        3 \n===========                     =======  ======= \nTOTAL                             65.3M       17 \nTOTAL, minus reserved VM space    65.3M       17 \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  

> open
> "/Users/francesca/Desktop/TRINITY_DN301_c0_g2_i2_len28037_-_TRINITY_DN7742_c0_g1_i5_len9773
> (1).fasta"

Summary of feedback from opening
/Users/francesca/Desktop/TRINITY_DN301_c0_g2_i2_len28037_-_TRINITY_DN7742_c0_g1_i5_len9773
(1).fasta  
---  
note | Alignment identifier is
TRINITY_DN301_c0_g2_i2_len28037_-_TRINITY_DN7742_c0_g1_i5_len9773 (1).fasta  
  
Opened 1 sequences from
TRINITY_DN301_c0_g2_i2_len28037_-_TRINITY_DN7742_c0_g1_i5_len9773 (1).fasta  




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, 5 hours, 48 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