id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10169 Crash in event loop during a Qt mouse down event chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.4.1-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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All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/processing/ATPsynthase/relion_05022023/Refine3D/job380/run_it016_half1_class001.mrc Opened run_it016_half1_class001.mrc as #1, grid size 210,210,210, pixel 2.55, shown at level 0.158, step 1, values float32 > volume #1 level 0.3259 > open /Volumes/processing/ATPsynthase/warp_25012023/M/bin1.5/job380/mask.mrc Opened mask.mrc as #2, grid size 210,210,210, pixel 2.55, shown at level 1, step 1, values float32 > volume #2 level 0.9982 > volume #2 style mesh > close #1 > close #2 > open /Volumes/processing/ATPsynthase/warp_25012023/M/bin1.5/job380/mask.mrc Opened mask.mrc as #1, grid size 210,210,210, pixel 2.55, shown at level 1, step 1, values float32 > open > /Volumes/processing/ATPsynthase/warp_25012023/M/bin1.5/job380/run_ct16_half1_class001_unfil.mrc Opened run_ct16_half1_class001_unfil.mrc as #2, grid size 210,210,210, pixel 2.55, shown at level 0.382, step 1, values float32 > open > /Volumes/processing/ATPsynthase/warp_25012023/M/bin1.5/job380/run_ct16_half2_class001_unfil.mrc Opened run_ct16_half2_class001_unfil.mrc as #3, grid size 210,210,210, pixel 2.55, shown at level 0.382, step 1, values float32 > volume #3 level 0.514 > volume #2 level 0.5129 > open > /Volumes/processing/ATPsynthase/relion_05022023/Refine3D/job380/run_ct16_half1_class001_unfil.mrc Opened run_ct16_half1_class001_unfil.mrc as #4, grid size 210,210,210, pixel 2.55, shown at level 0.382, step 1, values float32 > open > /Volumes/processing/ATPsynthase/relion_05022023/Refine3D/job380/run_ct16_half2_class001_unfil.mrc Opened run_ct16_half2_class001_unfil.mrc as #5, grid size 210,210,210, pixel 2.55, shown at level 0.382, step 1, values float32 > volume #4 level 0.4905 > volume #5 level 0.5423 > volume #4 level 0.5352 > volume #5 level 0.5046 > volume #1 level 1 > volume #5 level 0.7777 > volume #1 level 0.7038 > open /Users/ledietri/Processing/starfile_convert.py Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/scripting.py"", line 83, in open_python_script code = compile(data, stream.name, 'exec') File ""/Users/ledietri/Processing/starfile_convert.py"", line 33 match current_software: ^ SyntaxError: invalid syntax Failed opening file /Users/ledietri/Processing/starfile_convert.py: Error opening python file /Users/ledietri/Processing/starfile_convert.py > close #1 > close #2 > close #3 > close #4 > close #5 > open > /Volumes/processing/ATPsynthase/coot/model_peripheral_stalk_real_space_refined_002-coot-16.pdb Chain information for model_peripheral_stalk_real_space_refined_002-coot-16.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 3 | No description available 5 | No description available 6 | No description available 8 | No description available 9 | No description available M | No description available > open /Volumes/processing/ATPsynthase/coot/ResolveCryoEM_9/denmod_map.ccp4 Opened denmod_map.ccp4 as #2, grid size 210,210,210, pixel 2.55, shown at level 0.0117, step 1, values float32 > volume #2 level 0.09276 > volume #2 level 0.04941 > hide atoms > show cartoons > ui mousemode right zoom > volume #2 level 0.04752 > volume #2 style mesh > ui tool show ""Side View"" > select /0:2-82 607 atoms, 628 bonds, 81 residues, 1 model selected > ui tool show ""Model Panel"" > lighting soft > ui tool show ""Color Key"" > ui mousemode right ""color key"" > ui mousemode right zoom > hide #3 models > ui tool show ""Basic Actions"" > select /0 607 atoms, 628 bonds, 81 residues, 1 model selected > color /0 #000000 target c > set bgColor white > color /0 #212121 target c > color /1 #212121 target c > color /5 #212121 target c > color /0 #a7a7a8 target c > color /0 #005555 target c > color /1 #005555 target c > color /3 #005555 target c > view orient > view > color /3 #ef7c00 target c > ui mousemode right select > select clear > color /M #00b1ea target c > color /9 #005555 target c > color /8 #005555 target c > color /6 #005555 target c > color /5 #005555 target c Drag select of 2 denmod_map.ccp4 > select #2 2 models selected > select clear > color /0 #006c66 target c Drag select of 141 residues, 2 denmod_map.ccp4 > select clear > ui mousemode right zoom > volume #2 color #6b6865 > graphics mesh Expected a keyword > volume #1 subdivideSurface true subdivisionLevels 2 No volumes specified > volume #2 subdivideSurface true subdivisionLevels 2 > volume #2 level 0.09276 > ui tool show ""Side View"" > surface dust #2 size 25.5 > undo > surface dust #2 size 25.5 > volume #2 level 0.05129 > volume #2 color #9e9d9b > volume #2 color #004f9f > volume #2 color #296260 > volume #2 color #7ea4a4 > volume #2 color #b3d7d5 > volume #2 color #959dab > volume #2 color #9e9d9b > set bgColor black > volume #2 color #ebebeb > volume #2 color #d6d6d6 > set bgColor white > volume #2 color #bfbfbf > volume #2 color grey > volume #2 color #9f9f9f > rock > stop > rock > stop > view orient > view > select /0 607 atoms, 628 bonds, 81 residues, 1 model selected > volume #2 color #004f9f > volume #2 color #ebebeb > volume #2 color #004f9f > volume #2 color #ebebeb > color /0 #004f9f target c > select /1 4661 atoms, 4750 bonds, 595 residues, 1 model selected > color /1 #c6d325 target c > select /3 1907 atoms, 1944 bonds, 251 residues, 1 model selected > select /3 1907 atoms, 1944 bonds, 251 residues, 1 model selected > select /5 986 atoms, 1011 bonds, 123 residues, 1 model selected > select /0 607 atoms, 628 bonds, 81 residues, 1 model selected > select /6 926 atoms, 946 bonds, 124 residues, 1 model selected > color /6 #b3d7d5 target c > ui mousemode right select > select clear > select /6 926 atoms, 946 bonds, 124 residues, 1 model selected > select /8 692 atoms, 715 bonds, 88 residues, 1 model selected > color /8 #006c66 target c > select /9 776 atoms, 802 bonds, 97 residues, 1 model selected > select /8 692 atoms, 715 bonds, 88 residues, 1 model selected > select /9 776 atoms, 802 bonds, 97 residues, 1 model selected > color /9 #796ba8 target c > select clear > select /M 1736 atoms, 1787 bonds, 230 residues, 1 model selected > select clear ===== Log before crash end ===== Log: 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 OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 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 Air Model Identifier: Mac14,2 Model Number: Z15S001DND/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4.1 (c) (22F770820d) Kernel Version: Darwin 22.5.0 Time since boot: 22 hours, 46 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2418D: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 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 can't reproduce Tom Goddard all ChimeraX