id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14923 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.0-arm64-arm-64bit ChimeraX Version: 1.8.dev202403271703 (2024-03-27 17:03:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000002bcbfb000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ffaba500 (most recent call first): File 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""130776ea-444f-4cb4-8def-f71b4f47391b"", ""experimentId"" : ""66105e203b960674f9490906"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5F726.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5F726-F1-model_v4.pdb AF-Q5F726-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for multidrug transporter (Q5F726) [more info...] Chain information for AF-Q5F726-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | multidrug transporter | Q5F726_NEIG1 1-467 > movie record > turn x 2 180 > wait 180 > mlp Map values for surface ""AF-Q5F726-F1-model_v4.pdb_A SES surface"": minimum -27.22, mean -4.035, maximum 23.12 > turn x 2 180 > wait 180 > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for AF-Q5F726-F1-model_v4.pdb_A SES surface #1.1: minimum, -25.58, mean -0.11, maximum 13.39 > turn x 2 180 > wait 180 > hide surfaces > open /Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5F726.pdb SWISSMODEL_Q5F726.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for SWISSMODEL_Q5F726.pdb #2 --- Chain | Description A B C | No description available > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SWISSMODEL_Q5F726.pdb, chain A (#2) with AF-Q5F726-F1-model_v4.pdb, chain A (#1), sequence alignment score = 2207.1 RMSD between 411 pruned atom pairs is 0.711 angstroms; (across all 445 pairs: 1.403) > view clip false > turn x 2 180 > wait 180 > delete #1 > mlp Map values for surface ""SWISSMODEL_Q5F726.pdb_A SES surface"": minimum -27.89, mean -4.024, maximum 21.81 Map values for surface ""SWISSMODEL_Q5F726.pdb_B SES surface"": minimum -27.09, mean -4.004, maximum 22.34 Map values for surface ""SWISSMODEL_Q5F726.pdb_C SES surface"": minimum -27.42, mean -4, maximum 22.35 > turn x 2 180 > wait 180 > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for SWISSMODEL_Q5F726.pdb_A SES surface #2.1: minimum, -14.34, mean -0.17, maximum 14.09 Coulombic values for SWISSMODEL_Q5F726.pdb_B SES surface #2.2: minimum, -13.89, mean -0.17, maximum 13.85 Coulombic values for SWISSMODEL_Q5F726.pdb_C SES surface #2.3: minimum, -14.08, mean -0.17, maximum 13.48 > turn x 2 180 > wait 180 > movie stop > wait 5 > movie encode output > /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5F726_movie.mp4 Movie saved to /Users/diyamathai/.../Group3_Project/Q5F726_movie.mp4 > close session > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > movie record > turn x 2 180 > wait 180 > mlp Map values for surface ""AF-Q5FAG7-F1-model_v4.pdb_A SES surface"": minimum -28.43, mean -6.816, maximum 22.22 > turn x 2 180 > wait 180 > coulombic ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYD82LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0 (22A380) Kernel Version: Darwin 22.1.0 Time since boot: 38 days, 15 hours, 27 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 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ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202403271703 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 ChimeraX-ModelPanel: 1.5 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.3 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.37.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.9 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.50.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2024.2.26 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.3 matplotlib-inline: 0.1.6 msgpack: 1.0.8 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.2.0 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.0 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX