id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7148 Graphics crash, macOS 12.4, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x000000010afa7600 (most recent call first): File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 235 in swap_buffers File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 496 in swap_buffers File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 179 in draw File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in draw_new_frame File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/private/var/folders/5d/66cr647905jc0hbvqccpdbrm0000gn/T/AppTranslocation/069D8B29-1AB0-4DEA-81F8-169D19DBC2AC/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in 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""deploymentId"" : 240000137 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== > set bgColor white > cd Current working directory is: /Users/elizabethmcfadden > cd Desktop Current working directory is: /Users/elizabethmcfadden/Desktop UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/elizabethmcfadden/Desktop/negative mers mask.mrc"" format mrc Opened negative mers mask.mrc as #1, grid size 412,412,412, pixel 0.833, shown at level 0.0436, step 2, values float32 > close #1 > open ""/Users/elizabethmcfadden/Desktop/pos mers mask.mrc"" Opened pos mers mask.mrc as #1, grid size 412,412,412, pixel 0.833, shown at level 0.0225, step 2, values float32 > volume #1 level 0.0321 > vop threshold #1 minimum 0.037 set 0 Opened pos mers mask.mrc thresholded as #2, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > vop threshold #2 maximum 0.033 set 1 Opened pos mers mask.mrc thresholded as #3, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > volume #3 level 0.01165 > volume #3 level 0.0321 > save ""/Users/elizabethmcfadden/Desktop/pos bin mers mask.mrc"" models #3 > close #1 > close #2 > close #3 > open ""/Users/elizabethmcfadden/Desktop/negative mers mask.mrc"" Opened negative mers mask.mrc as #1, grid size 412,412,412, pixel 0.833, shown at level 0.0436, step 2, values float32 > volume #1 level 0.0321 > vop threshold #1 minimum 0.037 set 0 Opened negative mers mask.mrc thresholded as #2, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > vop threshold #2 maximum 0.033 set 1 Opened negative mers mask.mrc thresholded as #3, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > save ""/Users/elizabethmcfadden/Desktop/neg bin mers mask.mrc"" models #3 > close > open > /Users/elizabethmcfadden/Downloads/cryosparc_P232_J277_004_volume_map.mrc Opened cryosparc_P232_J277_004_volume_map.mrc as #1, grid size 412,412,412, pixel 0.833, shown at level 0.0496, step 2, values float32 > ui tool show ""Segment Map"" > volume #1 level 0.0321 Segmenting cryosparc_P232_J277_004_volume_map.mrc, density threshold 0.032100 Only showing 150 of 187 regions. Showing 150 of 187 region surfaces 6422 watershed regions, grouped to 187 regions Showing cryosparc_P232_J277_004_volume_map.seg - 187 regions, 150 surfaces > ui mousemode right select Grouped 6 regions Grouped 144 regions > select #2 3 models selected > ~select #2 Nothing selected > select #2.1 1 model selected > ~select #2.1 Nothing selected > select #2.1 1 model selected > hide #2.2 models > hide #!2 models > hide #!1 models > show #!2 models > show #2.2 models > hide #2.1 models > hide #!2 models > show #!2 models > show #2.1 models > hide #!2 models > show #!2 models > hide #2.2 models > show #2.2 models > select #2 3 models selected > ~select #2 Nothing selected > select #2 3 models selected > select #2.2 1 model selected > ~select #2.1 1 model selected > ~select #2 Nothing selected > select #2.1 1 model selected > ~select #2.2 1 model selected Opened cryosparc_P232_J277_004_volume_map_imasked as #3, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 Opened cryosparc_P232_J277_004_volume_map_imasked as #4, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > hide #2.2 models > hide #!2 models > hide #!4 models > hide #!3 models > show #!4 models > close #4 > close #2.1#2 > show #!3 models > close #3 > show #!1 models Segmenting cryosparc_P232_J277_004_volume_map.mrc, density threshold 0.032100 Only showing 150 of 187 regions. Showing 150 of 187 region surfaces 6422 watershed regions, grouped to 187 regions Showing cryosparc_P232_J277_004_volume_map.seg - 187 regions, 150 surfaces > hide #2.1 models > show #2.1 models > select #2.1 1 model selected > select #2.2 1 model selected > ~select #2.2 Nothing selected > select #2.3 1 model selected > ~select #2.3 Nothing selected > select #2.2 1 model selected > ~select #2.2 Nothing selected > ~select #2.1 Nothing selected > select #2.1 1 model selected > select #2.5 1 model selected > select #2.10 1 model selected > select #2.50 1 model selected > ~select #2.50 Nothing selected > select #2.57 1 model selected > ~select #2.57 Nothing selected > select #2.98 1 model selected > ~select #2.98 Nothing selected > select #2.77 1 model selected > select #2.27 1 model selected > select #2.137 1 model selected Grouped 6 regions Grouped 144 regions > select #2 3 models selected > ~select #2 Nothing selected > ~select #2.2 Nothing selected > select #2.1 1 model selected Opened cryosparc_P232_J277_004_volume_map_imasked as #3, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > select #2.2 1 model selected Opened cryosparc_P232_J277_004_volume_map_imasked as #4, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > hide #!1 models > hide #!2 models > hide #2.1 models > hide #2.2 models > select #2 3 models selected > ~select #2.2 2 models selected > ~select #2 Nothing selected > hide #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!3 models > show #!4 models > hide #!3 models > hide #!4 models > show #!4 models > close #3 > close #4 > close #2 > show #!1 models Segmenting cryosparc_P232_J277_004_volume_map.mrc, density threshold 0.032100 Only showing 150 of 187 regions. Showing 150 of 187 region surfaces 6422 watershed regions, grouped to 187 regions Showing cryosparc_P232_J277_004_volume_map.seg - 187 regions, 150 surfaces Drag select of 8407, 535 of 73732 triangles, 1 cryosparc_P232_J277_004_volume_map.mrc > select clear Grouped 6 regions > hide #!1 models Only showing 150 of 182 regions. Showing 150 of 182 region surfaces Grouped 149 regions Opened cryosparc_P232_J277_004_volume_map_imasked as #3, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > hide #3.1 models > show #3.1 models > hide #3.1 models > hide #!3 models > show #!3 models > show #3.1 models > hide #2.2 models > hide #3.1 models > show #3.1 models > hide #!3 models > show #!3 models > hide #!3 models > hide #3.1 models Opened cryosparc_P232_J277_004_volume_map_imasked as #4, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > show #!3 models > select #4 2 models selected > color #3 silver models transparency 0 > color #3 darkgrey models transparency 0 > select #3 2 models selected > ~select #4 2 models selected > ~select #3 Nothing selected > show #2.2 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > show #!4 models > show #!3 models > close #3 > close #4 > show #!2 models > hide #2.1 models > show #2.1 models > hide #2.2 models > show #2.2 models > select #2.2 1 model selected Opened cryosparc_P232_J277_004_volume_map_imasked as #3, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > ~select #2.2 1 model selected > select #2.1 1 model selected > ~select #2.1 Nothing selected > select #2.1 1 model selected Opened cryosparc_P232_J277_004_volume_map_imasked as #4, grid size 412,412,412, pixel 0.833, shown at step 1, values float32 > hide #!2 models > hide #!4 models > show #!4 models > close #3 > close #4 > close #2 > show #!1 models Segmenting cryosparc_P232_J277_004_volume_map.mrc, density threshold 0.032100 Only showing 150 of 187 regions. Showing 150 of 187 region surfaces 6422 watershed regions, grouped to 187 regions Showing cryosparc_P232_J277_004_volume_map.seg - 187 regions, 150 surfaces > hide #!1 models > hide #!2 models ===== Log before crash end ===== Log: > set bgColor white > cd Current working directory is: /Users/elizabethmcfadden > cd Desktop Current working directory is: /Users/elizabethmcfadden/Desktop UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.7.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0) OS Loader Version: 540.120.3~6 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 23:28 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 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: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 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: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 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: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 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: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX