id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
8530	Crash clearing aniso_u6	21122748r@…	Tristan Croll	"{{{
The following bug report has been submitted:
Platform:        macOS-12.2-arm64-arm-64bit
ChimeraX Version: 1.6.dev202302180254 (2023-02-18 02:54:55 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
It crashed when I chose the model for ISOLDE
Fatal Python error: Segmentation fault

Current thread 0x00000001027d8580 (most recent call first):
  File ""/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py"", line 853 in _set_aniso_u6
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/sanity_check.py"", line 12 in remove_invalid_anisou
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 670 in _anisou_sanity_check
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 639 in add_model
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 597 in __init__
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 170 in _get_symmetry_handler
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/clipper/symmetry.py"", line 159 in get_symmetry_handler
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py"", line 815 in _change_selected_model
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py"", line 771 in change_selected_model
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py"", line 434 in selected_model
  File ""/Users/siqiong/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/ui/main_win.py"", line 157 in _set_selected_model
  File ""/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 284 in event_loop
  File ""/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init
  File ""/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in 
  File ""/Users/siqiong/Desktop/chimera/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code
  File ""/Users/siqiong/Desktop/chimera/ChimeraX_Daily.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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    ""CFBundleIdentifier"" : ""com.apple.QuartzCore"",
    ""size"" : 3141632,
    ""uuid"" : ""0c98ecde-c21a-3501-9c98-fc9d3dd5bb12"",
    ""path"" : ""\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore"",
    ""name"" : ""QuartzCore"",
    ""CFBundleVersion"" : ""962.63""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64e"",
    ""base"" : 6861291520,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.Foundation"",
    ""size"" : 4120576,
    ""uuid"" : ""90321a38-43a5-3767-9a9c-2c631338b9bc"",
    ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"",
    ""name"" : ""Foundation"",
    ""CFBundleVersion"" : ""1856.105""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""arm64"",
    ""base"" : 11502452736,
    ""size"" : 19300352,
    ""uuid"" : ""5431bff3-be1a-3fe5-a552-bcdbb3e0536e"",
    ""path"" : ""\/Users\/USER\/Desktop\/*\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblasp-r0.3.20.dylib"",
    ""name"" : ""libopenblasp-r0.3.20.dylib""
  },
  {
    ""size"" : 0,
    ""source"" : ""A"",
    ""base"" : 0,
    ""uuid"" : ""00000000-0000-0000-0000-000000000000""
  }
],
  ""sharedCache"" : {
  ""base"" : 6842122240,
  ""size"" : 3091218432,
  ""uuid"" : ""b90241b2-e425-3982-b3f6-26c4567cbb49""
},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=15.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=15.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 4032K        4 \nCG image                           192K       10 \nColorSync                          624K       27 \nCoreAnimation                      304K       16 \nCoreGraphics                        32K        2 \nCoreUI image data                 3760K       25 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                            12.7G      240 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         984.0M        9         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                       1008K       63 \nStack                            198.6M       64 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      309.1M      860 \nVM_ALLOCATE (reserved)           512.0M        3         reserved VM address space (unallocated)\n__AUTH                            2570K      308 \n__AUTH_CONST                      19.7M      500 \n__DATA                            27.0M      794 \n__DATA_CONST                      29.7M      784 \n__DATA_DIRTY                      1787K      215 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       623.1M      284 \n__OBJC_CONST                      3569K      273 \n__OBJC_RO                         82.1M        1 \n__OBJC_RW                         3104K        1 \n__TEXT                           777.7M      803 \n__UNICODE                          588K        1 \ndyld private memory               1072K        3 \nmapped file                      193.3M       47 \nshared memory                     3168K       26 \n===========                     =======  ======= \nTOTAL                             16.8G     5388 \nTOTAL, minus reserved VM space    15.0G     5388 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""602ad4dac86151000cf27e46"",
      ""factorPackIds"" : {
        ""SIRI_DICTATION_ASSETS"" : ""61fb0e87c773c43cde3bb80e""
      },
      ""deploymentId"" : 240000305
    },
    {
      ""rolloutId"" : ""60da5e84ab0ca017dace9abf"",
      ""factorPackIds"" : {

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      ""deploymentId"" : 240000008
    },
    {
      ""rolloutId"" : ""607844aa04477260f58a8077"",
      ""factorPackIds"" : {
        ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a""
      },
      ""deploymentId"" : 240000066
    },
    {
      ""rolloutId"" : ""601d9415f79519000ccd4b69"",
      ""factorPackIds"" : {
        ""SIRI_TEXT_TO_SPEECH"" : ""622657ce37186c771d5404ad""
      },
      ""deploymentId"" : 240000416
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      ""factorPackIds"" : {

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      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000251
    }
  ],
  ""experiments"" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.dev202302180254 (2023-02-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/siqiong/Desktop/crosslinking/2811,4.26/Crosslinking_NF5_IMP-
> FL4.26.pdb

Summary of feedback from opening
/Users/siqiong/Desktop/crosslinking/2811,4.26/Crosslinking_NF5_IMP-FL4.26.pdb  
---  
warning | Start residue of secondary structure not found: HELIX 1 1 PRO A 9
GLN A 11 1 3  
  
Chain information for Crosslinking_NF5_IMP-FL4.26.pdb  
---  
Chain | Description  
1.1/A | No description available  
1.2/A | No description available  
  

> isolde start

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

Populating font family aliases took 184 ms. Replace uses of missing font
family ""Carlito"" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.1 to IUPAC-IUB
standards.  


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

Log:
UCSF ChimeraX version: 1.6.dev202302180254 (2023-02-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
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: 6.4.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2 (21D49)
      Kernel Version: Darwin 21.3.0
      Time since boot: 1 day 12:34

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.11.0
    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: 3.0.1
    ChimeraX-AddCharge: 1.5.8
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.8
    ChimeraX-AtomicLibrary: 10.0.4
    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: 1.2.1
    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-Clipper: 0.20.0
    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.dev202302180254
    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: 1.1
    ChimeraX-DistMonitor: 1.3.3
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 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-ISOLDE: 1.6.dev0
    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: 2.0.11
    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: 1.5.8
    ChimeraX-ModelPanel: 1.3.6
    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-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.6.13
    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: 1.0
    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: 2.8.2
    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: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    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: 1.27.1
    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: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.0.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.4
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.2.0
    jupyterlab-widgets: 3.0.5
    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
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    pandas: 1.5.3
    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: 3.0.0
    prompt-toolkit: 3.0.36
    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
    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: 6.4.2
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 65.1.1
    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
    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: 1.0.2
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.5
    zipp: 3.14.0

}}}
"	defect	closed	normal		Structure Editing		fixed		Eric Pettersen Tom Goddard Zach Pearson				all	ChimeraX