id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8612 Graphics crash, macOS 11.6, Intel Iris Plus Graphics 650 chimerax-bug-report@… Tom Goddard "{{{ 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. 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3.6G 3346 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } } } ===== Log before crash start ===== UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/hehl/Desktop/Structure_analysis/Dimer/step47_new_prop_and_Hulin_DSD_coot-4_27Feb2023.pdb Chain information for step47_new_prop_and_Hulin_DSD_coot-4_27Feb2023.pdb #1 --- Chain | Description A D | No description available B E | No description available F G | No description available > open /Users/hehl/Desktop/Structure_analysis/Dimer/Deep_KEM16_j197_C2sym.mrc Opened Deep_KEM16_j197_C2sym.mrc as #2, grid size 384,384,384, pixel 0.851, shown at level 0.00141, step 2, values float32 > hide atoms > show cartoons > volume #2 step 1 > volume #2 level 0.03066 > view orient > turn z 90 > view name bottomview > turn x 180 > view name topview > turn x -90 > view name frontview > turn y -90 > view name sideview > view topview > colordef acceptor #ff890a Color 'acceptor' is opaque: rgb(100%, 53.7%, 3.92%) hex: #ff890a > colordef hect #ff70a2 Color 'hect' is opaque: rgb(100%, 43.9%, 63.5%) hex: #ff70a2 > colordef imp #660024 Color 'imp' is opaque: rgb(40%, 0%, 14.1%) hex: #660024 > colordef unimp #6d545d Color 'unimp' is opaque: rgb(42.7%, 32.9%, 36.5%) hex: #6d545d > colordef donor #ffb20f Color 'donor' is opaque: rgb(100%, 69.8%, 5.88%) hex: #ffb20f > colordef uba #96525f Color 'uba' is opaque: rgb(58.8%, 32.2%, 37.3%) hex: #96525f > colordef e2 #08bec4 Color 'e2' is opaque: rgb(3.14%, 74.5%, 76.9%) hex: #08bec4 > colordef clobe #dfb5c4 Color 'clobe' is opaque: rgb(87.5%, 71%, 76.9%) hex: #dfb5c4 > colordef prop #c4918d Color 'prop' is opaque: rgb(76.9%, 56.9%, 55.3%) hex: #c4918d > colordef unimp_white #e4d2cb Color 'unimp_white' is opaque: rgb(89.4%, 82.4%, 79.6%) hex: #e4d2cb > colordef ubr #c49465 Color 'ubr' is opaque: rgb(76.9%, 58%, 39.6%) hex: #c49465 > colordef wedge #ba5aba Color 'wedge' is opaque: rgb(72.9%, 35.3%, 72.9%) hex: #ba5aba > colordef dsd #a55520 Color 'dsd' is opaque: rgb(64.7%, 33.3%, 12.5%) hex: #a55520 > colordef scaffold #f4e9e9 Color 'scaffold' is opaque: rgb(95.7%, 91.4%, 91.4%) hex: #f4e9e9 > show cartoons > color /A-B #f4e9e980 > color /A-E scaffold > color /F e2 > color /G donor > color /H acceptor > color /I uba > color /D: 1177-1245 ubr > color /E:2216-2685 hect > color /E:2686-2799 clobe > color /A: 1177-1245 ubr > color /B:2216-2685 hect > color /B:2686-2799 clobe > color /D: 0-874 prop > color /A: 0-874 prop > color /A: 496-732 grey > color /D: 496-732 grey > color /E: 2016-2072 wedge > color /B: 2016-2072 wedge > color /E: 1690-1720 dsd > color /B: 1690-1720 dsd > color /G grey > color /F grey > graphics silhouettes true > lighting full > surface dust #2 size 5 > view > lighting shadows true intensity 0.5 > set silhouettes true > set bgColor white > color zone #2 near #1 distance 10 > volume #2 transparency 0.6 > view bottomview > color #2 white > color zone #2 near #1 distance 2 > volume #2 transparency 0.4 > volume #3 transparency 0.4 No volumes specified > color zone #2 near #1 distance 3 > volume #2 transparency 0.4 > volume #2 transparency 0.6 > volume #2 transparency 0.3 > open > /Users/hehl/Desktop/Structure_analysis/Dimer/230303_difChains_HECT_DSD_HD.pdb Chain information for 230303_difChains_HECT_DSD_HD.pdb #3 --- Chain | Description A D | No description available B | No description available E | No description available F G | No description available H | No description available I | No description available J | No description available > hide #!3 models > save /Users/hehl/Desktop/Structure_analysis/221011/Dimer/UBRDens.tiff format > tiff supersample 4 width 2000 height 2000 transparentBackground true > hide #!2 models > show #!2 models > open /Users/hehl/Desktop/Structure_analysis/Dimer/221218_Apo_dimer.pdb Chain information for 221218_Apo_dimer.pdb #4 --- Chain | Description A D | No description available B E | No description available > hide #!2 models > color /A-B #f4e9e980 > color /A-E scaffold > color /F e2 > color /G donor > color /H acceptor > color /I uba > color /D: 1177-1245 ubr > color /E:2216-2685 hect > color /E:2686-2799 clobe > color /A: 1177-1245 ubr > color /B:2216-2685 hect > color /B:2686-2799 clobe > color /D: 0-874 prop > color /A: 0-874 prop > color /A: 496-732 grey > color /D: 496-732 grey > color /E: 2016-2072 wedge > color /B: 2016-2072 wedge > color /E: 1690-1720 dsd > color /B: 1690-1720 dsd > color /G grey > color /F grey > color #!1,4 byhetero > hide #!1 models > select #4 1-1146 Expected a keyword > select #4: 1-1146 7434 atoms, 7570 bonds, 10 pseudobonds, 1018 residues, 2 models selected > select #4/D: 1-1146 3714 atoms, 3785 bonds, 5 pseudobonds, 506 residues, 2 models selected > hide sel cartoons > select #4/D: 1-1176 3938 atoms, 4014 bonds, 5 pseudobonds, 536 residues, 2 models selected > hide sel cartoons > select #4/D: 1246-2000 1974 atoms, 2011 bonds, 2 pseudobonds, 254 residues, 2 models selected > hide sel cartoons > select #4/E 5467 atoms, 5592 bonds, 7 pseudobonds, 709 residues, 2 models selected > hide sel cartoons > select #4/B 5467 atoms, 5592 bonds, 7 pseudobonds, 709 residues, 2 models selected > hide sel cartoons > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > hide #!4 models > hide #!1 models > show #!1 models > ui tool show ""Side View"" > volume #2 level 0.03801 > color zone #2 near #1 distance 10 > volume #2 transparency 0.6 > color #2 white > hide #!2 models > show #!2 models > color zone #2 near #1 distance 3 > hide #!2 models > hide #!1 models > show #!4 models > save /Users/hehl/Desktop/Structure_analysis/221011/Dimer/UBR.tiff format > tiff supersample 4 width 2000 height 2000 transparentBackground true > hide #!4 models > show #!1 models > show #!2 models > select up 23784 atoms, 24278 bonds, 28 pseudobonds, 3142 residues, 2 models selected > select up 23784 atoms, 24278 bonds, 52 pseudobonds, 3142 residues, 3 models selected > select up 23784 atoms, 24278 bonds, 52 pseudobonds, 3142 residues, 3 models selected > hide #!1 atoms > color zone #2 near #1 distance 3 > color #!1 byhetero > hide #!1 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!1 models > color zone #2 near #1 distance 3 > show #!2 models > volume #2 level 0.0564 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-16.5.2 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650 OpenGL vendor: Intel Inc. 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: MacBookPro14,2 Processor Name: Dual-Core Intel Core i7 Processor Speed: 3,5 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 429.140.8.0.0 SMC Version (system): 2.44f6 Software: System Software Overview: System Version: macOS 11.6 (20G165) Kernel Version: Darwin 20.6.0 Time since boot: 2 days 19:09 Graphics/Displays: Intel Iris Plus Graphics 650: Chipset Model: Intel Iris Plus Graphics 650 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5927 Revision ID: 0x0006 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) 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-Clipper: 0.18.0 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-ISOLDE: 1.4 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-XMAS: 1.1.2 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 et-xmlfile: 1.1.0 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 openpyxl: 3.0.10 openvr: 1.16.802 packaging: 21.0 pandas: 1.5.0 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 QtRangeSlider: 0.1.5 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 seaborn: 0.12.0 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 Volume Data nonchimerax all ChimeraX