id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7289 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 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 0x0000000200cea600 (most recent call first): File ""/private/var/folders/5s/0wgsddw10t10g6vjw9d132dr0000gn/T/AppTranslocation/62D2F67E-B0F4-4533-8564-9F5EBDB7A349/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop File ""/private/var/folders/5s/0wgsddw10t10g6vjw9d132dr0000gn/T/AppTranslocation/62D2F67E-B0F4-4533-8564-9F5EBDB7A349/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 870 in init File ""/private/var/folders/5s/0wgsddw10t10g6vjw9d132dr0000gn/T/AppTranslocation/62D2F67E-B0F4-4533-8564-9F5EBDB7A349/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1021 in File 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California. All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/H/CSHL/LAb/Projects/Oct11/Oct11_Articles&PDB/Trials/cryosparc_P193_J99_class_00_00164_volume_sharp.mrc Opened cryosparc_P193_J99_class_00_00164_volume_sharp.mrc as #1, grid size 128,128,128, pixel 1.61, shown at level 0.0734, step 1, values float32 > volume #1 level 0.1952 > volume #1 step 2 > volume #1 level 0.1863 > volume #1 step 1 > volume #1 level 0.2214 > volume #1 level 0.207 > volume #1 level 0.2548 > volume #1 level 0.1736 > volume #1 step 2 > volume #1 step 4 > volume #1 step 8 > volume #1 step 2 > volume #1 level 0.1654 > volume #1 step 1 > volume #1 level 0.2339 > volume #1 level 0.2116 > volume #1 level 0.1781 > volume #1 level 0.1287 > volume #1 level 0.1574 > volume #1 level 0.1893 > open /Volumes/H/CSHL/LAb/Projects/Oct11/Oct11_Articles&PDB/Trials/1cqt.pdb 1cqt.pdb title: Crystal structure of A ternary complex containing an oca-B peptide, the oct-1 pou domain, and an octamer element [more info...] Chain information for 1cqt.pdb #2 --- Chain | Description | UniProt A | pou domain, class 2, transcription factor 1 | PO2F1_HUMAN B | pou domain, class 2, transcription factor 1 | PO2F1_HUMAN I | pou domain, class 2, associating factor 1 | OBF1_HUMAN J | pou domain, class 2, associating factor 1 | OBF1_HUMAN M | DNA (5'- D(*TP*GP*TP*ap*TP*GP*CP*ap*ap*ap*TP*ap*ap*GP*G)-3') | N | DNA (5'- D(*ap*CP*CP*TP*TP*ap*TP*TP*TP*GP*CP*ap*TP*ap*C)-3') | O | DNA (5'- D(*TP*GP*TP*ap*TP*GP*CP*ap*ap*ap*TP*ap*ap*GP*G)-3') | P | DNA (5'- D(*ap*CP*CP*TP*TP*ap*TP*TP*TP*GP*CP*ap*TP*ap*C)-3') | Drag select of 3649 atoms, 4 pseudobonds > hide sel atoms > show sel cartoons > select clear Drag select of 186 residues, 1 pseudobonds > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > ui mousemode right ""translate selected models"" Drag select of 180 residues, 3 pseudobonds > view matrix models #2,1,0,0,47.089,0,1,0,81.326,0,0,1,79.861 > transparency (#!2 & sel) 40 Drag select of 1 cryosparc_P193_J99_class_00_00164_volume_sharp.mrc > transparency #1.1 50 > view matrix models #1,1,0,0,1.3805,0,1,0,-1.3463,0,0,1,-3.4924 Drag select of 8 residues > select up 394 atoms, 398 bonds, 47 residues, 1 model selected > select up 752 atoms, 760 bonds, 94 residues, 1 model selected > select up 862 atoms, 869 bonds, 109 residues, 1 model selected > select up 1042 atoms, 1052 bonds, 129 residues, 1 model selected > select up 1800 atoms, 1880 bonds, 180 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.98634,0.14862,-0.071067,46.455,-0.15117,0.98799,-0.031918,93.113,0.06547,0.042225,0.99696,74.335 > view matrix models > #2,0.62627,-0.4241,0.65416,72.325,-0.76377,-0.16554,0.62389,149.15,-0.1563,-0.89036,-0.42759,129.19 > view matrix models > #2,0.57256,-0.40545,0.71259,75.038,-0.81209,-0.16111,0.56085,153.57,-0.11259,-0.89981,-0.4215,126.07 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.57256,-0.40545,0.71259,59.577,-0.81209,-0.16111,0.56085,154.98,-0.11259,-0.89981,-0.4215,129.79 > transparency sel 20 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule 1cqt.pdb (#2) to map cryosparc_P193_J99_class_00_00164_volume_sharp.mrc (#1) using 1800 atoms average map value = 0.2167, steps = 88 shifted from previous position = 6.73 rotated from previous position = 30.6 degrees atoms outside contour = 816, contour level = 0.18926 Position of 1cqt.pdb (#2) relative to cryosparc_P193_J99_class_00_00164_volume_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.38574486 -0.03886861 0.92178638 60.32293393 -0.86308378 -0.36825484 0.34565121 162.23192744 0.32601732 -0.92891205 -0.17559928 94.10421844 Axis -0.78166372 0.36537305 -0.50547440 Axis point 0.00000000 120.37667342 -30.30908185 Rotation angle (degrees) 125.38407791 Shift along axis -35.44434788 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. 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How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 1 day 12:56 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 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: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX