id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8681 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ 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. 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: 240000025 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000612 } ], ""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 > open ""/Users/joannavuille/Library/CloudStorage/OneDrive- > PartnersHealthCare/Joanna/Projects/HECTD4/Alphafold prediction/2. > Juan_test2_forJoanna_HECTD4/prediction_1_HECTD4(0001-1499)_cEPHA2/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description B | No description available C | No description available > color bychain > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file ""/Users/joannavuille/Library/CloudStorage/OneDrive- > PartnersHealthCare/Joanna/Projects/HECTD4/Alphafold prediction/2. > Juan_test2_forJoanna_HECTD4/prediction_1_HECTD4(0001-1499)_cEPHA2/best_model_pae.json"" > color #1/B:4-1246 lime > color #1/B:1349-1349 lime > color #1/B:1001-1001 magenta > alphafold pae #1 colorDomains true > color #1/B:352-352 lime > color #1/B:333-333 magenta > color #1/B:369-369 lime > color #1/B:685-685 magenta > color #1/B:1225-1487 lime > color bynucleotide > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1-155 1191 atoms, 1208 bonds, 155 residues, 1 model selected > color #1/B:261-261 lime > color #1/B:556-556 magenta > color #1/B:262-262 lime > color #1/B:451-451 magenta > select > /B:281-286,313-315,319-322,330-334,345-349,355-360,363-368,377-382,391-394,407-413,418-423,437-447,450-455,460-462,526-528,532-537,563-571,579-584,601-605,610-614,618-623,1065-1068,1078-1084,1090-1095,1107-1112,1119-1125,1146-1149,1152-1158,1176-1180 1344 atoms, 1356 bonds, 164 residues, 1 model selected > select /B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1-505 3853 atoms, 3927 bonds, 505 residues, 1 model selected > select /B:1071-1072 17 atoms, 18 bonds, 2 residues, 1 model selected > select /B:816-1072 1993 atoms, 2022 bonds, 257 residues, 1 model selected > select /B:1289-1290 19 atoms, 18 bonds, 2 residues, 1 model selected > select /B:914-1290 2927 atoms, 2987 bonds, 377 residues, 1 model selected > select /B:1291-1292 15 atoms, 15 bonds, 2 residues, 1 model selected > select /B:1286-1292 60 atoms, 61 bonds, 7 residues, 1 model selected > select /B:1281-1282 12 atoms, 11 bonds, 2 residues, 1 model selected > select /B:1266-1282 134 atoms, 138 bonds, 17 residues, 1 model selected > select /B:1260 7 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1238-1260 167 atoms, 173 bonds, 23 residues, 1 model selected > select /B:1236 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1216-1236 167 atoms, 167 bonds, 21 residues, 1 model selected > select /B:1187-1188 15 atoms, 14 bonds, 2 residues, 1 model selected > select /B:1178-1188 84 atoms, 83 bonds, 11 residues, 1 model selected > select /B:1232 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:1218-1232 122 atoms, 121 bonds, 15 residues, 1 model selected > select /B:1239 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1235-1239 43 atoms, 42 bonds, 5 residues, 1 model selected > select /B:1227-1228 18 atoms, 17 bonds, 2 residues, 1 model selected > select /B:811-1228 3249 atoms, 3304 bonds, 418 residues, 1 model selected > select /B:1228 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1222-1228 56 atoms, 55 bonds, 7 residues, 1 model selected > select /B:1228 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:812-1228 3241 atoms, 3296 bonds, 417 residues, 1 model selected > select /B:766-812 360 atoms, 361 bonds, 47 residues, 1 model selected > select /B:406-812 3125 atoms, 3185 bonds, 407 residues, 1 model selected > select /B:1319 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1263-1319 469 atoms, 481 bonds, 57 residues, 1 model selected > select /B:1228 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1171-1228 434 atoms, 440 bonds, 58 residues, 1 model selected > select /B:1228-1229 17 atoms, 16 bonds, 2 residues, 1 model selected > select /B:901-1229 2534 atoms, 2579 bonds, 329 residues, 1 model selected > select /B:900 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:497-900 3114 atoms, 3167 bonds, 404 residues, 1 model selected > select /B:1228 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1-1228 9430 atoms, 9604 bonds, 1228 residues, 1 model selected > select /B:1417-1418 17 atoms, 16 bonds, 2 residues, 1 model selected > select /B:1417-1422 51 atoms, 50 bonds, 6 residues, 1 model selected > select /B:1417 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1417-1499 640 atoms, 646 bonds, 83 residues, 1 model selected > close session ===== 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: MacBook Pro Model Identifier: MacBookPro17,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 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: 10 days 19:25 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: 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: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 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 UI duplicate Tom Goddard all ChimeraX