id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19404 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x0000000204fba0c0 (most recent call first): File ""/private/var/folders/kd/pqrypdnj0xx7712vrj2r_7p40000gn/T/AppTranslocation/6B72E370-76AA-401A-A91A-FD318EDC31DC/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/private/var/folders/kd/pqrypdnj0xx7712vrj2r_7p40000gn/T/AppTranslocation/6B72E370-76AA-401A-A91A-FD318EDC31DC/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File ""/private/var/folders/kd/pqrypdnj0xx7712vrj2r_7p40000gn/T/AppTranslocation/6B72E370-76AA-401A-A91A-FD318EDC31DC/d/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension 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""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6824656896, ""size"" : 636280, ""uuid"" : ""3247e185-ced2-36ff-9e29-47a77c23e004"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" } ], ""sharedCache"" : { ""base"" : 6823821312, ""size"" : 5040898048, ""uuid"" : ""4c1223e5-cace-3982-a003-6110a7a8a25c"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=617.4M resident=0K(0%) swapped_out_or_unallocated=617.4M(100%)\nWritable regions: Total=3.6G written=88.5M(2%) resident=1960K(0%) swapped_out=86.6M(2%) unallocated=3.6G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1920K 50 \nColorSync 624K 33 \nCoreAnimation 4752K 143 \nCoreGraphics 48K 3 \nCoreImage 160K 5 \nCoreUI image data 5344K 40 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.9G 113 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 640K 40 \nStack 193.9M 41 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/shuichitakeda/Library/Mobile > Documents/com~apple~CloudDocs/Linh/Tubulin/251120/Heimcurrentmodels/HeimMT1mi.mrc"" > format mrc Opened HeimMT1mi.mrc as #1, grid size 200,200,200, pixel 1.51, shown at level 0.0289, step 1, values float32 > open ""/Users/shuichitakeda/Library/Mobile > Documents/com~apple~CloudDocs/Linh/Tubulin/251120/Heimcurrentmodels/HeimMT1model.pdb"" > format pdb Summary of feedback from opening /Users/shuichitakeda/Library/Mobile Documents/com~apple~CloudDocs/Linh/Tubulin/251120/Heimcurrentmodels/HeimMT1model.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 11 GLU A 28 1 18 Start residue of secondary structure not found: HELIX 2 2 MET A 69 ASP A 77 1 9 Start residue of secondary structure not found: HELIX 3 3 PRO A 84 TYR A 86 1 3 Start residue of secondary structure not found: HELIX 4 4 TRP A 98 TYR A 102 1 5 Start residue of secondary structure not found: HELIX 5 5 GLY A 104 GLY A 107 1 4 202 messages similar to the above omitted Chain information for HeimMT1model.pdb --- Chain | Description 2.4/A 2.1/C 2.2/E 2.3/G | No description available 2.8/B 2.5/D 2.6/F 2.7/H | No description available Computing secondary structure > sequence chain #2.4/A#2.1/C#2.2/E#2.3/G Alignment identifier is 1 > color #2.1 #00f900ff > color #2.2 #00f900ff > color #2.3 #00f900ff > color #2.4 #00f900ff > transparency 50 > color #1 white models > color #1 black models > color #1 white models > color #1 #bfbfbfff models > color #1 white models > transparency 50 > hide #!1 models > hide #!2 models > hide #2.1 models > hide #2.2 models > hide #2.3 models > hide #2.4 models > hide #2.5 models > hide #2.6 models > hide #2.7 models > hide #2.8 models > open ""/Users/shuichitakeda/Library/Mobile > Documents/com~apple~CloudDocs/Linh/Tubulin/251120/Heimcurrentmodels/HeimMT2model.pdb"" Chain information for HeimMT2model.pdb --- Chain | Description 3.4/A 3.1/C 3.2/E 3.3/G | No description available 3.8/B 3.5/D 3.6/F 3.7/H | No description available > open ""/Users/shuichitakeda/Library/Mobile > Documents/com~apple~CloudDocs/Linh/Tubulin/251120/Heimcurrentmodels/HeimMT2mi.mrc"" Opened HeimMT2mi.mrc as #4, grid size 200,200,200, pixel 1.51, shown at level 0.024, step 1, values float32 > sequence chain #3.4/A#3.1/C#3.2/E#3.3/G Alignment identifier is 2 > color #3.1 #ff9300ff > color #3.2 #ff9300ff > color #3.3 #ff9300ff > color #3.4 #ff9300ff > transparency #3-4 50 > surface hidePatches #3-4 > color #3.1 #00fdffff > color #3.1 #0433ffff > color #3.2 #0433ffff > color #3.3 #0433ffff > color #3.4 #0433ffff > color #3.5 #aa7942ff > color #3.6 #aa7942ff > color #3.7 #aa7942ff > color #3.8 #aa7942ff > color #4 white models > transparency #3-4 80 > set bgColor white > color #4 #bfbfbfff models > transparency #3-4 80 > hide #!3 models > hide #!4 models > hide #4.1 models > show #!1 models > show #!2 models > show #2.1 models > show #2.2 models > show #2.3 models > show #2.4 models > show #2.5 models > show #2.6 models > show #2.7 models > show #2.8 models > hide #2.2 models > hide #2.3 models > hide #2.1 models > hide #!2 models > hide #!1 models > hide #2.4 models > hide #2.5 models > hide #2.6 models > hide #2.7 models > hide #2.8 models > show #!3 models > show #!4 models > show #4.1 models > hide #!3 models > hide #!4 models > hide #4.1 models > show #!1 models > show #!2 models > show #2.1 models > show #2.2 models > show #2.3 models > show #2.4 models > show #2.5 models > show #2.6 models > show #2.7 models > show #2.8 models > hide #2.2 models > hide #2.3 models > hide #2.4 models > hide #2.5 models > hide #2.6 models > hide #2.7 models > hide #2.8 models > show #!3 models > hide #2.1 models > hide #!2 models > hide #!1 models > show #!4 models > show #4.1 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: Z17L000BHJ/A Chip: Apple M2 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 15日 2時間 8分 Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 19 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U4025QW: Resolution: 7680 x 3240 UI Looks like: 3840 x 1620 @ 120.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX