id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9582	Cannot find Python	davis797@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-13.5-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{""app_name"":""ChimeraX"",""timestamp"":""2023-08-14 20:07:39.00 -0400"",""app_version"":""1.5.0"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""build_version"":""1.5.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.5 (22G74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""4710711C-5F14-40D4-894C-EA7B65D6A7D5""}
{
  ""uptime"" : 350000,
  ""procRole"" : ""Default"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro18,3"",
  ""coalitionID"" : 8505,
  ""osVersion"" : {
    ""train"" : ""macOS 13.5"",
    ""build"" : ""22G74"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2023-08-14 20:07:38.8305 -0400"",
  ""incident"" : ""4710711C-5F14-40D4-894C-EA7B65D6A7D5"",
  ""pid"" : 26560,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2023-08-14 20:07:38.7631 -0400"",
  ""procStartAbsTime"" : 8547006547139,
  ""procExitAbsTime"" : 8547007420443,
  ""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"":""0E4B0D04-C11F-542E-907F-81979C299B16"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""52A405A5-600E-B7E8-BFAF-483074B0FE2A"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 0,
  ""wakeTime"" : 695,
  ""sleepWakeUUID"" : ""AF44A9E5-18E4-4675-9686-A9A0D0D17704"",
  ""sip"" : ""enabled"",
  ""exception"" : {""codes"":""0x0000000000000000, 0x0000000000000000"",""rawCodes"":[0,0],""type"":""EXC_CRASH"",""signal"":""SIGABRT""},
  ""termination"" : {""code"":1,""flags"":518,""namespace"":""DYLD"",""indicator"":""Library missing"",""details"":[""(terminated at launch; ignore backtrace)""],""reasons"":[""Library not loaded: @rpath\/Versions\/3.9\/Python"",""Referenced from:  \/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX"",""Reason: tried: '\/Applications\/ChimeraX-1.5.app\/Contents\/lib\/Versions\/3.9\/Python' (no such file), '\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python' (no such file), '\/Applications\/ChimeraX-1.5.app\/Contents\/lib\/Versions\/3.9\/Python' (no such file), '\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python' (no such file), '\/usr\/lib\/Python' (no such file, not in dyld cache)""]},
  ""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"":7475668,""threadState"":{""x"":[{""value"":6},{""value"":1},{""value"":6167783696},{""value"":102},{""value"":6167782672},{""value"":0},{""value"":0},{""value"":2896},{""value"":32},{""value"":9},{""value"":1},{""value"":10},{""value"":0},{""value"":50},{""value"":4},{""value"":32768},{""value"":521},{""value"":7051318108,""symbolLocation"":416,""symbol"":""__simple_bprintf""},{""value"":0},{""value"":0},{""value"":6167782672},{""value"":102},{""value"":6167783696},{""value"":1},{""value"":6},{""value"":8587268288,""symbolLocation"":0,""symbol"":""gProcessInfo""},{""value"":0},{""value"":0},{""value"":0}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":7051824508},""cpsr"":{""value"":4096},""fp"":{""value"":6167782624},""sp"":{""value"":6167782560},""esr"":{""value"":1442840704,""description"":"" Address size fault""},""pc"":{""value"":7051776280,""matchesCrashFrame"":1},""far"":{""value"":4299472896}},""frames"":[{""imageOffset"":471320,""symbol"":""__abort_with_payload"",""symbolLocation"":8,""imageIndex"":1},{""imageOffset"":519548,""symbol"":""abort_with_payload_wrapper_internal"",""symbolLocation"":104,""imageIndex"":1},{""imageOffset"":519600,""symbol"":""abort_with_payload"",""symbolLocation"":16,""imageIndex"":1},{""imageOffset"":43176,""symbol"":""dyld4::halt(char const*)"",""symbolLocation"":328,""imageIndex"":1},{""imageOffset"":30096,""symbol"":""dyld4::prepare(dyld4::APIs&, dyld3::MachOAnalyzer const*)"",""symbolLocation"":4184,""imageIndex"":1},{""imageOffset"":24088,""symbol"":""start"",""symbolLocation"":1964,""imageIndex"":1}]}],
  ""usedImages"" : [
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64"",
    ""base"" : 4299096064,
    ""CFBundleShortVersionString"" : ""1.5.0"",
    ""CFBundleIdentifier"" : ""edu.ucsf.cgl.ChimeraX"",
    ""size"" : 16384,
    ""uuid"" : ""a5992708-d5b4-36ec-ac0a-e525f6105b56"",
    ""path"" : ""\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX"",
    ""name"" : ""ChimeraX"",
    ""CFBundleVersion"" : ""1.5.0.0""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 7051304960,
    ""size"" : 583048,
    ""uuid"" : ""e7a99595-e0f8-34af-be8b-9347d0d658a4"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
  }
],
  ""sharedCache"" : {
  ""base"" : 7050641408,
  ""size"" : 3553361920,
  ""uuid"" : ""9c875b0a-d532-3933-b1f0-f1ea72cedde2""
},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=802.8M resident=0K(0%) swapped_out_or_unallocated=802.8M(100%)\nWritable regions: Total=8448K written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8448K(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nSTACK GUARD                       56.0M        1 \nStack                             8176K        1 \nVM_ALLOCATE                         16K        1 \n__DATA                              27K        2 \n__DATA_CONST                        38K        2 \n__DATA_DIRTY                         7K        1 \n__LINKEDIT                       802.2M        2 \n__TEXT                             588K        2 \ndyld private memory                272K        2 \n===========                     =======  ======= \nTOTAL                            867.2M       14 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {

  }
},
  ""logWritingSignature"" : ""5c3dcb0f07b1c86cfccf1a39a67eaedac6929bc2"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""60da5e84ab0ca017dace9abf"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000008
    },
    {
      ""rolloutId"" : ""63508950b3714d3622fc77f7"",
      ""factorPackIds"" : {
        ""SIRI_MEMORY_SYNC_CONFIG"" : ""63508beab3714d3622fc7808""
      },
      ""deploymentId"" : 240000004
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""a092db1b-c401-44fa-9c54-518b7d69ca61"",
      ""experimentId"" : ""64a844035c85000c0f42398a"",
      ""deploymentId"" : 400000004
    },
    {
      ""treatmentId"" : ""8ca8349c-e2bc-482c-9ca7-3907b48a5341"",
      ""experimentId"" : ""648b5a581b04c12d4127bbb6"",
      ""deploymentId"" : 400000001
    }
  ]
}
}


Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  

> cd /Users/barrettdavis/Applications/ChimeraX

Current working directory is: /Users/barrettdavis/Applications/ChimeraX  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
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: MacBookPro18,3
      Model Number: MKGR3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5 (22G74)
      Kernel Version: Darwin 22.6.0
      Time since boot: 12 days, 6 hours, 29 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP VH240a:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        HP VH240a:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    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: 1.6.1
    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: 6.6.0
    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: 3.5.0
    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: 6.3.1
    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

}}}
"	defect	feedback	normal		Platform				Tom Goddard				all	ChimeraX