id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17242 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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\n__DATA 32.7M 1046 \n__DATA_CONST 33.6M 1067 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 636.0M 141 \n__OBJC_RW 2374K 1 \n__TEXT 1.2G 1087 \n__TPRO_CONST 272K 2 \nmapped file 269.2M 60 \nowned unmapped memory 180.2M 1 \npage table in kernel 2554K 1 \nshared memory 3168K 25 \n=========== ======= ======= \nTOTAL 7.1G 6144 \nTOTAL, minus reserved VM space 6.9G 6144 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""209b6c5857f430762353973738dba81062e78a6c"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67648e5334a82511f4acf879"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""658361a603dc58766bab2d2a"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""6736733a26c1270f5a9ef53d"" }, ""deploymentId"" : 240000045 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_AVX29476/man_AVX29476.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for man_AVX29476.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1 --- Chain | Description A B C D E F G H I J | No description available > set bgColor white > color sequential residues > color palette alphafold Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byresidue palette alphafold Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byatom palette alphafold Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color bfactor 14610 atoms, 1900 residues, atom bfactor range 28.7 to 96.3 > color bfactor 14610 atoms, 1900 residues, atom bfactor range 28.7 to 96.3 > color bfactor palette rainbow 14610 atoms, 1900 residues, atom bfactor range 28.7 to 96.3 > color bfactor palette alphafold 14610 atoms, 1900 residues, atom bfactor range 28.7 to 96.3 > hide atoms > hide cartoons > show cartoons > color bychain > movie record > turn y 2 180 > wait 180 > movie encode /Users/susiegrigson/Desktop/movie1.mp4 Movie saved to /Users/susiegrigson/Desktop/movie1.mp4 > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_AVX29476/man_AVX29476.12_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for man_AVX29476.12_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #2 --- Chain | Description A B C D E F G H I J K L | No description available > hide #1 models > color bfactor palette alphafold 32142 atoms, 4180 residues, atom bfactor range 28.7 to 96.3 > hide #2 atoms > hide #2 cartoons > show #2 cartoons > color #2 bychain > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_EPP33044/man_EPP33044.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for man_EPP33044.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #3 --- Chain | Description A B C D E F G H I J | No description available > hide #2 models > color bfactor palette alphafold 53282 atoms, 6990 residues, atom bfactor range 11.8 to 96.3 > color #3 bychain > color bfactor palette alphafold] Fetching url http://www.colourlovers.com/api/palettes?keywords=alphafold%5D&format=json&numResults=100 failed: HTTP Error 404: Not Found > color #3 bychain > color bfactor palette alphafold 53282 atoms, 6990 residues, atom bfactor range 11.8 to 96.3 > hide #3 cartoons > hide #3 atoms > show #3 cartoons > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_EZR26891/man_EZR26891.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for man_EZR26891.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #4 --- Chain | Description A B C D E F G H I J | No description available > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_EZR26891/man_EZR26891.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for man_EZR26891.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #5 --- Chain | Description A B C D E F G H I J | No description available > hide #3 models > hide #4 models > hide #5 atoms > hide #5 cartoons > show #5 cartoons > color bfactor palette alphafold 93862 atoms, 12530 residues, atom bfactor range 10.3 to 96.3 > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_WJZ70399/man_WJZ70399.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for man_WJZ70399.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #6 --- Chain | Description A B C D E F G H I J | No description available > hide #5 models > color bfactor palette alphafold 111202 atoms, 14710 residues, atom bfactor range 1.04 to 97.1 > hide #6 atoms > hide #6 cartoons > show #6 cartoons > color #6 bychain > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_WJZ70399/man_WJZ70399.12_scores_rank_002_alphafold2_multimer_v3_model_1_seed_000.json"" Failed opening file /Users/susiegrigson/Library/CloudStorage/OneDrive- Flinders/PhD/oligomeric state/colabbatch_phlegm/man_WJZ70399/man_WJZ70399.12_scores_rank_002_alphafold2_multimer_v3_model_1_seed_000.json: Expecting value: line 1 column 33783809 (char 33783808) > hide #6 models > show #6 models > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_WJZ70399/man_WJZ70399.12_scores_rank_002_alphafold2_multimer_v3_model_1_seed_000.json"" Failed opening file /Users/susiegrigson/Library/CloudStorage/OneDrive- Flinders/PhD/oligomeric state/colabbatch_phlegm/man_WJZ70399/man_WJZ70399.12_scores_rank_002_alphafold2_multimer_v3_model_1_seed_000.json: Expecting ',' delimiter: line 1 column 41287681 (char 41287680) > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/man_WJZ70399/man_WJZ70399.12_scores_rank_005_alphafold2_multimer_v3_model_2_seed_000.json"" Failed opening file /Users/susiegrigson/Library/CloudStorage/OneDrive- Flinders/PhD/oligomeric state/colabbatch_phlegm/man_WJZ70399/man_WJZ70399.12_scores_rank_005_alphafold2_multimer_v3_model_2_seed_000.json: man_WJZ70399.12_scores_rank_005_alphafold2_multimer_v3_model_2_seed_000.json does not look like Mole Online json file, does not contain Channels. > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/phrog_106235_singleton/phrog_106235_singleton.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for phrog_106235_singleton.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #7 --- Chain | Description A B C D E F G H I J | No description available > hide #6 models > color bfactor palette alphafold 126882 atoms, 16740 residues, atom bfactor range 1.04 to 97.1 > hide #7 cartoons > hide #7 atoms > show #7 cartoons Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/susiegrigson/Library/CloudStorage/OneDrive- > Flinders/PhD/oligomeric > state/colabbatch_phlegm/phrog_106235_singleton/phrog_106235_singleton.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for phrog_106235_singleton.10_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1 --- Chain | Description A B C D E F G H I J | No description available OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: MPHE3X/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 13 days, 3 hours, 55 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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: No Connection Type: Internal HP P224: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 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: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 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 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 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-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 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: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 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: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX