id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17418 Crash destroying OpenGL context at exit chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-64bit ChimeraX Version: 1.10.dev202504170618 (2025-04-17 06:18:02 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 0x0000000207518840 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 466 in quit File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 827 in closeEvent File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 328 in event File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 466 in quit File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 874 in file_quit_cb File 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240000008 }, { ""rolloutId"" : ""67648e5334a82511f4acf879"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.10.dev202504170618 (2025-04-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/weijiaxin/Documents/Lab/Data/Data for Chimera/Data from > Bill/HIV2_hexamer_new.pdb"" ""/Users/weijiaxin/Documents/Lab/Data/Data for > Chimera/Data from Bill/HIV2_map.mrc"" Summary of feedback from opening /Users/weijiaxin/Documents/Lab/Data/Data for Chimera/Data from Bill/HIV2_hexamer_new.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 19 LYS A 32 1 14 Start residue of secondary structure not found: HELIX 2 2 ALA A 36 LEU A 45 1 10 Start residue of secondary structure not found: HELIX 3 3 PRO A 51 ASN A 59 1 9 Start residue of secondary structure not found: HELIX 4 4 ALA A 67 ILE A 74 1 8 Start residue of secondary structure not found: HELIX 5 5 ARG B 133 MET B 146 1 14 251 messages similar to the above omitted End residue of secondary structure not found: HELIX 356 356 ASN W 23 GLU W 31 1 9 Start residue of secondary structure not found: HELIX 373 373 PRO Y 19 LYS Y 32 1 14 Start residue of secondary structure not found: HELIX 374 374 ALA Y 36 LEU Y 45 1 10 Start residue of secondary structure not found: HELIX 375 375 PRO Y 51 ASN Y 59 1 9 Start residue of secondary structure not found: HELIX 376 376 ALA Y 66 GLN Y 85 1 20 Start residue of secondary structure not found: HELIX 377 377 GLY Y 102 ILE Y 105 1 4 101 messages similar to the above omitted Chain information for HIV2_hexamer_new.pdb #1 --- Chain | Description D W X | No description available E | No description available G | No description available P | No description available Opened HIV2_map.mrc as #2, grid size 512,512,512, pixel 0.751, shown at level 0.0587, step 2, values float32 > hide #!2 models > show cartoons > style ball Changed 10250 atom styles > select 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 4 models selected > cartoon hide (#!1 & sel) > cartoon (#!1 & sel) > surface (#!1 & sel) > surface hidePatches (#!1 & sel) > hide (#!1 & sel) target a > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > select subtract #1 8 models selected > select subtract #2 Nothing selected > show #!1 models > select add #1 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 2 models selected > fitmap map Missing or invalid ""atomsOrMap"" argument: invalid objects specifier > select 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 4 models selected > select subtract #2 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 8 models selected > hide #!2 models > open ""/Users/weijiaxin/Documents/Lab/Data/Data for Chimera/Data from > Bill/HIV2_hexamer_new.pdb"" Summary of feedback from opening /Users/weijiaxin/Documents/Lab/Data/Data for Chimera/Data from Bill/HIV2_hexamer_new.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 19 LYS A 32 1 14 Start residue of secondary structure not found: HELIX 2 2 ALA A 36 LEU A 45 1 10 Start residue of secondary structure not found: HELIX 3 3 PRO A 51 ASN A 59 1 9 Start residue of secondary structure not found: HELIX 4 4 ALA A 67 ILE A 74 1 8 Start residue of secondary structure not found: HELIX 5 5 ARG B 133 MET B 146 1 14 251 messages similar to the above omitted End residue of secondary structure not found: HELIX 356 356 ASN W 23 GLU W 31 1 9 Start residue of secondary structure not found: HELIX 373 373 PRO Y 19 LYS Y 32 1 14 Start residue of secondary structure not found: HELIX 374 374 ALA Y 36 LEU Y 45 1 10 Start residue of secondary structure not found: HELIX 375 375 PRO Y 51 ASN Y 59 1 9 Start residue of secondary structure not found: HELIX 376 376 ALA Y 66 GLN Y 85 1 20 Start residue of secondary structure not found: HELIX 377 377 GLY Y 102 ILE Y 105 1 4 101 messages similar to the above omitted Chain information for HIV2_hexamer_new.pdb #3 --- Chain | Description D W X | No description available E | No description available G | No description available P | No description available > select subtract #1 6 models selected > select add #1 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 2 models selected > hide #!1 models > show #!1 models > hide #!1 models > select add #3 20500 atoms, 20942 bonds, 12 pseudobonds, 2598 residues, 10 models selected > select subtract #1 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 8 models selected > select 20500 atoms, 20942 bonds, 12 pseudobonds, 2598 residues, 6 models selected > hide (#!3 & sel) target a > show (#!3 & sel) target ab > cartoon (#!3 & sel) > hide (#!3 & sel) target a > ui tool show ""Color Actions"" > color sel cyan > hide #!3 models > select subtract #2 20500 atoms, 20942 bonds, 12 pseudobonds, 2598 residues, 10 models selected > select add #2 20500 atoms, 20942 bonds, 12 pseudobonds, 2598 residues, 12 models selected > show #!2 models > select subtract #3 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 10 models selected > select subtract #1 8 models selected > hide #!2 models > show #!2 models > ui tool show ""Color Actions"" > color sel white > color #2 #f1fdf3ff models > hide #!2 models > select subtract #2 Nothing selected > show #!1 models > select add #1 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 2 models selected > color #1 #e121fdff > color #1 #f768fdff > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > select add #3 20500 atoms, 20942 bonds, 12 pseudobonds, 2598 residues, 10 models selected > select subtract #3 10250 atoms, 10471 bonds, 6 pseudobonds, 1299 residues, 8 models selected > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.dev202504170618 (2025-04-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: 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: Mac15,6 Model Number: MRX63LL/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 45 minutes, 40 seconds Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.3.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.3 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.15 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 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: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202504170618 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 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: 2.2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.9 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: 2.7.9 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: 1.1.1 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: 1.2.0 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: 1.45.1 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.57.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.13.0 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: 8.1.6 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.14 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 4.3.7 pluggy: 1.5.0 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 pyelftools: 0.32 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: 8.3.5 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.4.0 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: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 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: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Graphics duplicate all ChimeraX