id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6393	Crash in event loop	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 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 0x0000000200f34600 (most recent call first):
  File ""/Users/mengqipan/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop
  File ""/Users/mengqipan/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init
  File ""/Users/mengqipan/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in 
  File ""/Users/mengqipan/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code
  File ""/Users/mengqipan/Desktop/ChimeraX-1.3.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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  ""procRole"" : ""Foreground"",
  ""version"" : 2,
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  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro17,1"",
  ""procStartAbsTime"" : 219016499122,
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    ""build"" : ""21D62"",
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  ""incident"" : ""6804E345-EAAA-4076-9C99-454B7C4F53AF"",
  ""bug_type"" : ""309"",
  ""pid"" : 22116,
  ""procExitAbsTime"" : 238198409388,
  ""translated"" : true,
  ""cpuType"" : ""X86-64"",
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Users\/USER\/Desktop\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX"",
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  ""parentProc"" : ""launchd"",
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  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""CD8FC319-E1BF-1D62-065C-0FC3B7CAE51A"",
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  ""sleepWakeUUID"" : ""46BBC9C2-366C-42C7-AA62-B9C6F45C5D8A"",
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  ""isCorpse"" : 1,
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    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703479468032,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"",
    ""size"" : 5246976,
    ""uuid"" : ""1d1db08b-810c-316e-b9d9-eecdff8ee6e3"",
    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
    ""name"" : ""CoreFoundation"",
    ""CFBundleVersion"" : ""1856.107""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703523069952,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.AppKit"",
    ""size"" : 15278080,
    ""uuid"" : ""9d3ab204-4858-3120-b002-5c38b02edec4"",
    ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"",
    ""name"" : ""AppKit"",
    ""CFBundleVersion"" : ""2113.30.116""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703561764864,
    ""CFBundleShortVersionString"" : ""1.600.0"",
    ""CFBundleIdentifier"" : ""com.apple.SkyLight"",
    ""size"" : 3760128,
    ""uuid"" : ""eab4373e-52ca-38d7-963a-9f5bd71824e9"",
    ""path"" : ""\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight"",
    ""name"" : ""SkyLight""
  }
],
  ""sharedCache"" : {
  ""base"" : 140703475908608,
  ""size"" : 15218196480,
  ""uuid"" : ""5c9ff5db-8827-329a-8a37-2483935a9ea1""
},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 2176K        4 \nCG image                           196K       19 \nColorSync                          240K       27 \nCoreAnimation                      176K       10 \nCoreGraphics                        12K        2 \nCoreUI image data                 3948K       30 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           590.4M       85 \nMALLOC guard page                  192K        8 \nMALLOC_MEDIUM (reserved)         848.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        24K        6 \nOpenGL GLSL                        384K        5 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1628K      404 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               720K       72 \nRosetta Thread Context             720K       72 \nSTACK GUARD                         44K       11 \nStack                            146.7M       38 \nStack Guard                       56.1M       27 \nVM_ALLOCATE                      110.9M      207 \nVM_ALLOCATE (reserved)           160.1M        9         reserved VM address space (unallocated)\n__DATA                            41.2M      664 \n__DATA_CONST                      29.8M      331 \n__DATA_DIRTY                      1623K      213 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       795.0M      147 \n__OBJC_RO                         81.8M        1 \n__OBJC_RW                         3136K        2 \n__TEXT                           737.6M      659 \n__UNICODE                          588K        1 \ndyld private memory               1024K        1 \nmapped file                        5.5G     1128 \nshared memory                     3140K       28 \nunshared pmap                     10.2M        7 \n===========                     =======  ======= \nTOTAL                              9.4G     4238 \nTOTAL, minus reserved VM space     8.2G     4238 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""607844aa04477260f58a8077"",
      ""factorPackIds"" : {
        ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a""
      },
      ""deploymentId"" : 240000066
    },
    {
      ""rolloutId"" : ""60da5e84ab0ca017dace9abf"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000008
    },
    {
      ""rolloutId"" : ""602ad4dac86151000cf27e46"",
      ""factorPackIds"" : {
        ""SIRI_DICTATION_ASSETS"" : ""61fb0e87c773c43cde3bb80e""
      },
      ""deploymentId"" : 240000305
    },
    {
      ""rolloutId"" : ""60356660bbe37970735c5624"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000027
    },
    {
      ""rolloutId"" : ""601d9415f79519000ccd4b69"",
      ""factorPackIds"" : {
        ""SIRI_TEXT_TO_SPEECH"" : ""622657ce37186c771d5404ad""
      },
      ""deploymentId"" : 240000416
    },
    {
      ""rolloutId"" : ""5fc94383418129005b4e9ae0"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000274
    },
    {
      ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000123
    }
  ],
  ""experiments"" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mengqipan/Desktop/Isodle/111.pdb

Summary of feedback from opening /Users/mengqipan/Desktop/Isodle/111.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR B 90
PHE B 104 1 15  
Start residue of secondary structure not found: HELIX 2 2 LEU B 125 VAL B 129
1 5  
Start residue of secondary structure not found: HELIX 3 3 GLU B 141 PHE B 153
1 13  
Start residue of secondary structure not found: HELIX 4 4 THR B 155 ASN B 159
1 5  
Start residue of secondary structure not found: HELIX 5 5 SER B 160 ASN B 162
1 3  
55 messages similar to the above omitted  
  
Chain information for 111.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.1/B 1.1/C 1.1/D 1.1/E 1.1/H | No description available  
  

> hide #1.1 models

> hide #!1 models

> show #1.1 models

> hide #1.2 models

> close

> open /Users/mengqipan/Desktop/FinalMap/vol_combined_zflip.mrc format mrc

Opened vol_combined_zflip.mrc as #1, grid size 168,168,168, pixel 1.7, shown
at level 0.012, step 1, values float32  

> hide #!1 target m

> hide #1.1 models

> open
> /Users/mengqipan/Desktop/Isodle/TRAM_filament_map_to_model_ALPHAFOLD_cycle_1.pdb

Chain information for TRAM_filament_map_to_model_ALPHAFOLD_cycle_1.pdb #2  
---  
Chain | Description  
A | No description available  
  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mengqipan/Desktop/Isodle/Correct_AssemblyPDB_fit.pdb

Chain information for Correct_AssemblyPDB_fit.pdb #1  
---  
Chain | Description  
B C D E H | No description available  
  

> open /Users/mengqipan/Desktop/Isodle/vol_combined_zflip.mrc

Opened vol_combined_zflip.mrc as #2, grid size 168,168,168, pixel 1.7, shown
at level 0.012, step 1, values float32  




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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 8 GB

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 3:33

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: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

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