id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8346 Crash clearing aniso_u6 deepto.mozumdar@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-12.2.1-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. Fatal Python error: Segmentation fault Thread 0x000000028b07f000 (most recent call first): File ""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File 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""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000286043000 (most recent call first): File ""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File 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""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py"", line 846 in _set_aniso_u6 File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/sanity_check.py"", line 12 in remove_invalid_anisou File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 667 in _anisou_sanity_check File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 636 in add_model File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 594 in __init__ File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 170 in _get_symmetry_handler File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py"", line 159 in get_symmetry_handler File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py"", line 814 in _change_selected_model File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py"", line 771 in change_selected_model File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py"", line 433 in selected_model File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py"", line 1483 in load_cryo_em_demo File ""/Users/deeptomozumdar/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/cmd/cmd.py"", line 240 in _load_demo File ""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 134 in invoke File ""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 217 in _activate File ""/private/var/folders/9_/_21z50rn1ks6pj3228lwj31c0000gn/T/AppTranslocation/33C2F0CD-F7B5-4AFD-9607-C5B91384B34C/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 186 in activate File 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240000576 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000242 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > isolde start > set selectionWidth 4 Populating font family aliases took 151 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. > isolde demo cryo_em_intro modelOnly true 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description | UniProt A B C | capsid protein VP1 | CAPSD_NVN68 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB standards. ===== Log before crash end ===== 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 OpenGL version: 4.1 Metal - 76.3 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: iMac Model Identifier: iMac21,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 7429.81.3 OS Loader Version: 7429.81.3 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 134 days 4:22 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: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 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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 }}} " defect closed normal Structure Editing duplicate Eric Pettersen Tom Goddard all ChimeraX