id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14690	Crash in garbage collection	hps@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000070000dad1000 (most recent call first):
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py"", line 306 in wait
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py"", line 558 in wait
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py"", line 1252 in run
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py"", line 932 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/threading.py"", line 890 in _bootstrap

Current thread 0x00000001163dd600 (most recent call first):
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/ast.py"", line 59 in update
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/ast.py"", line 19 in __init__
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/ast.py"", line 90 in copy
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/contexts.py"", line 642 in _try
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/contextlib.py"", line 113 in __enter__
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/contexts.py"", line 665 in _option
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/contextlib.py"", line 113 in __enter__
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/_atomspec.py"", line 88 in _atom_specifier_
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/contexts.py"", line 497 in _invoke_rule
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/contexts.py"", line 458 in _call
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/contexts.py"", line 59 in wrapper
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/grako/contexts.py"", line 206 in parse
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/atomspec.py"", line 168 in _parse_unquoted
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/atomspec.py"", line 110 in parse
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 1270 in parse
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2447 in _parse_arg
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2588 in _process_positional_arguments
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2812 in run
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/run.py"", line 36 in run
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/mouse_modes/std_modes.py"", line 222 in select_pick
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/mouse_modes/std_modes.py"", line 191 in mouse_select
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/mouse_modes/std_modes.py"", line 59 in mouse_up
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/mouse_modes/mousemodes.py"", line 537 in _dispatch_mouse_event
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/mouse_modes/mousemodes.py"", line 639 in 
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/graphics.py"", line 57 in event
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 293 in event_loop
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py"", line 866 in init
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py"", line 1015 in 
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py"", line 87 in _run_code
  File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py"", line 194 in _run_module_as_main


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  ""procRole"" : ""Foreground"",
  ""version"" : 2,
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  ""incident"" : ""FFF03D89-7C8F-42C4-8666-3D1A161FB4D3"",
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  ""cpuType"" : ""X86-64"",
  ""procName"" : ""ChimeraX"",
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  ""crashReporterKey"" : ""7576620B-5893-30DB-4044-C978254392A9"",
  ""bridgeVersion"" : {""build"":""21P54212c"",""train"":""8.4""},
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  ""vmRegionInfo"" : ""0xa8 is not in any region.  Bytes before following region: 140737487675224\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      VM_ALLOCATE              7ffffff5a000-7ffffff5b000 [    4K] r-x\/r-x SM=ALI  "",
  ""isCorpse"" : 1,
  ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a8"",""rawCodes"":[1,168],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a8""},
  ""ktriageinfo"" : ""VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n"",
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Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4212.5.3,0)
      OS Loader Version: 540.120.3~37

Software:

    System Software Overview:

      System Version: macOS 12.7.3 (21H1015)
      Kernel Version: Darwin 21.6.0
      Time since boot: 4 days 22:19

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG HDR 4K:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 30.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort

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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 22.1.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    Send2Trash: 1.8.0
    SEQCROW: 1.6.1
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

}}}
"	defect	closed	normal		Core		duplicate		Tom Goddard				all	ChimeraX