id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14680 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chenzhd@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.1.1-arm64-arm-64bit ChimeraX Version: 1.6rc202305042315 (2023-05-04 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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}, ""deploymentId"" : 240000364 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6rc202305042315 (2023-05-04) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/chenzhd/Downloads/cryosparc_P173_J430_006_volume_map_sharp.mrc Opened cryosparc_P173_J430_006_volume_map_sharp.mrc as #1, grid size 300,300,300, pixel 0.832, shown at level 0.309, step 2, values float32 > volume #1 step 1 > volume #1 level 0.4734 > volume #1 level 0.3586 > volume #1 level 0.818 > open /Users/chenzhd/Downloads/cryosparc_P89_J54_005_volume_map_sharp.mrc Opened cryosparc_P89_J54_005_volume_map_sharp.mrc as #2, grid size 340,340,340, pixel 0.82, shown at level 0.157, step 2, values float32 > volume #2 step 1 > hide #!2 models > hide #!1 models > show #!2 models > volume #2 level 0.2555 > open /Volumes/chenzhd/2024/MscS/Rv2434/Rv2434Ms_7mer2-coot-0的副本.pdb Chain information for Rv2434Ms_7mer2-coot-0的副本.pdb #3 --- Chain | Description A B C D E F G | No description available > hide cartoons > select add #3 17010 atoms, 17297 bonds, 2254 residues, 1 model selected > hide sel cartoons > show sel cartoons > hide sel atoms > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-20.047,0,1,0,-5.4799,0,0,1,-13.395 > view matrix models #3,1,0,0,-13.317,0,1,0,-17.675,0,0,1,-14.425 > view matrix models #3,1,0,0,-20.482,0,1,0,-15.767,0,0,1,-9.5186 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.99094,0.12827,0.039858,-45.92,-0.13309,0.97767,0.16261,-17.121,-0.01811,-0.16644,0.98589,22.206 > view matrix models > #3,0.99125,0.13167,0.0093697,-41.675,-0.13058,0.9677,0.21566,-24.337,0.019329,-0.21499,0.97642,25.607 > ui tool show ""Fit in Map"" > fitmap #3 inMap #2 Fit molecule Rv2434Ms_7mer2-coot-0的副本.pdb (#3) to map cryosparc_P89_J54_005_volume_map_sharp.mrc (#2) using 17010 atoms average map value = 0.2644, steps = 116 shifted from previous position = 2.42 rotated from previous position = 12.5 degrees atoms outside contour = 8438, contour level = 0.25552 Position of Rv2434Ms_7mer2-coot-0的副本.pdb (#3) relative to cryosparc_P89_J54_005_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.98864046 0.15028878 0.00182305 -42.77328462 -0.15028826 0.98864213 -0.00042367 5.50707018 -0.00186602 0.00014487 0.99999825 -6.72260640 Axis 0.00189134 0.01227237 -0.99992290 Axis point 14.49747395 285.78751202 0.00000000 Rotation angle (degrees) 8.64431869 Shift along axis 6.70877392 > volume #2 level 0.198 > color #2 #ffffb27f models > color #2 #ffffb288 models > volume #2 color #ffffb2a6 > volume #2 color #ffffb2ad > volume #2 color #b1b08aad > volume #2 color #bbba92ad > show #!1 models > select subtract #3 Nothing selected > select add #1 2 models selected > view matrix models > #1,0.90806,0.19418,0.3711,-53.854,-0.39405,0.69638,0.59982,21.315,-0.14196,-0.69091,0.70887,136.76 > view matrix models > #1,0.94967,0.018005,0.31275,-30.534,-0.018824,-0.99326,0.11434,239.76,0.3127,-0.11448,-0.94293,190.02 > view matrix models > #1,0.7943,-0.60677,0.030345,98.656,-0.60586,-0.78744,0.11346,287.94,-0.044951,-0.10851,-0.99308,239.85 > view matrix models > #1,0.81777,-0.5155,0.25597,59.281,-0.45133,-0.85034,-0.27059,318.88,0.35715,0.10576,-0.92804,155.15 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.81777,-0.5155,0.25597,67.591,-0.45133,-0.85034,-0.27059,333.54,0.35715,0.10576,-0.92804,202.94 > view matrix models > #1,0.81777,-0.5155,0.25597,68.139,-0.45133,-0.85034,-0.27059,339.63,0.35715,0.10576,-0.92804,200.62 > volume #1 level 0.5689 > view matrix models > #1,0.81777,-0.5155,0.25597,64.129,-0.45133,-0.85034,-0.27059,340.29,0.35715,0.10576,-0.92804,199.91 > view matrix models > #1,0.81777,-0.5155,0.25597,63.099,-0.45133,-0.85034,-0.27059,342.99,0.35715,0.10576,-0.92804,211.71 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.78421,-0.61397,-0.089743,121.39,-0.61587,-0.75256,-0.23314,346.96,0.075603,0.2381,-0.96829,235.48 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.78421,-0.61397,-0.089743,130.68,-0.61587,-0.75256,-0.23314,346.73,0.075603,0.2381,-0.96829,230.93 > fitmap #1 inMap #2 Fit map cryosparc_P173_J430_006_volume_map_sharp.mrc in map cryosparc_P89_J54_005_volume_map_sharp.mrc using 117931 points correlation = 0.8405, correlation about mean = 0.3656, overlap = 4.963e+04 steps = 196, shift = 6.63, angle = 14.5 degrees Position of cryosparc_P173_J430_006_volume_map_sharp.mrc (#1) relative to cryosparc_P89_J54_005_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.78531891 -0.61909144 0.00002604 118.65801571 -0.61909143 -0.78531891 -0.00009722 314.68114785 0.00008064 0.00006023 -1.00000000 272.60456063 Axis 0.94480643 -0.32762907 0.00002884 Axis point 0.00000000 177.90799202 136.30747220 Rotation angle (degrees) 179.99522598 Shift along axis 9.01802865 > select subtract #1 Nothing selected > select add #2 2 models selected > select subtract #2 Nothing selected > hide #!2 models > show #!2 models > hide #3 models > volume guassian #1 sdev 2 Expected a density maps specifier or a keyword > volume gaussian #1 sDev 2 Opened cryosparc_P173_J430_006_volume_map_sharp.mrc gaussian as #4, grid size 300,300,300, pixel 0.832, shown at step 1, values float32 > hide #!2 models > show #!2 models > volume #4 level 0.1178 > volume #4 color #8fb2b3b5 > show #3 models > hide #3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > show #3 models > hide #!2 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.1677 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.1997 > hide #!4 models > show atoms > hide atoms > show cartoons > style stick Changed 17010 atom styles > style stick Changed 17010 atom styles > style ball Changed 17010 atom styles > hide cartoons > show cartoons > show atoms > style stick Changed 17010 atom styles > hide atoms > volume #2 level 0.2201 > show #!4 models > hide #!4 models > show #!1 models > color #1 #b2b2b281 models > color #1 #b2b2b28d models > color #1 #b2b2b2a7 models > color #1 #b2b2b2a6 models > hide #!2 models > show #!2 models > show #!4 models > hide #!4 models > hide #!1 models > show atoms > style ball Changed 17010 atom styles > style ball Changed 17010 atom styles > style stick Changed 17010 atom styles > hide #3 models > show #3 models > hide #!2 models > hide atoms > show #!2 models > volume #2 level 0.1318 > volume #2 level 0.159 > hide #!2 models > show #!1 models > volume #1 level 0.2785 > volume #1 level 0.9405 > hide #!1 models > show #!2 models > volume #2 level 0.254 Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6rc202305042315 (2023-05-04) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/chenzhd/Downloads/cryosparc_P89_J77_005_volume_map_sharp.mrc Opened cryosparc_P89_J77_005_volume_map_sharp.mrc as #1, grid size 160,160,160, pixel 1.64, shown at level 0.474, step 1, values float32 OpenGL version: 4.1 Metal - 88 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: MLXX3CH/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1.1 (23B81) Kernel Version: Darwin 23.1.0 Time since boot: 5天10小时18分钟 Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 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 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-Clipper: 0.21.0 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: 1.6rc202305042315 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-ISOLDE: 1.6.0 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 Tom Goddard all ChimeraX