id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6674 Graphics crash, macOS 12.3.1, Intel HD Graphics 6000 biou@… 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. Hello I updated my Mac book air to MacOS 12.3 (previously it was 10.5). Chimera X crashed when displaying a cryoem map with a protein model. it became very slow when I clipped using Side View. then it stopped displaying the ligand bonds and it crashed. Best regards, Valerie Fatal Python error: Aborted Current thread 0x0000000117600600 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 1626 in set_multishadow_view File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 227 in _draw_scene File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 165 in draw File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in 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University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/biou/cahier_de_manips/ExBB- > EXBD/Microscopie_Electronique/Cryo_EM/ExbB_ESRF_mars19/map_comparision_review/ExbB_6PGT- > coot-0.pdb ExbB_6PGT-coot-0.pdb title: Structure of EXBB pentamer from serratia marcescens by single particle cryo electron microscopy [more info...] Chain information for ExbB_6PGT-coot-0.pdb #1 --- Chain | Description A B C D E | TOL-PAL system-associated ACYL-COA thioesterase Non-standard residues in ExbB_6PGT-coot-0.pdb #1 --- PGT — (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethylstearate (phosphatidylglycerol;1-palmitoyl-2-oleoyl-Sn-glycero-3-[phospho- rac-(1-glycerol)](sodium salt)) > open /Users/biou/cahier_de_manips/ExBB- > EXBD/Microscopie_Electronique/Cryo_EM/ExbB_ESRF_mars19/Refine3D/job083_C1/postprocJ83Zflip_onJ111.mrc Opened postprocJ83Zflip_onJ111.mrc as #2, grid size 364,364,364, pixel 0.827, shown at level 0.00215, step 2, values float32 > volume #2 level 0.013 > volume #2 step 1 > toolshed show > show cartoons > hide atoms > hide #!2 models > show #!2 models > volume #2 level 0.013 > color #2 #b2b2b280 models > volume #2 level 0.02046 > ui tool show ""Side View"" > open /Users/biou/cahier_de_manips/ExBB- > EXBD/Microscopie_Electronique/Cryo_EM/ExbB_ESRF_mars19/map_comparision_review/ExbB_6PGT- > coot-0.pdb ExbB_6PGT-coot-0.pdb title: Structure of EXBB pentamer from serratia marcescens by single particle cryo electron microscopy [more info...] Chain information for ExbB_6PGT-coot-0.pdb #3 --- Chain | Description A B C D E | TOL-PAL system-associated ACYL-COA thioesterase Non-standard residues in ExbB_6PGT-coot-0.pdb #3 --- PGT — (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethylstearate (phosphatidylglycerol;1-palmitoyl-2-oleoyl-Sn-glycero-3-[phospho- rac-(1-glycerol)](sodium salt)) > hide #1 models > show #1 models > close #1 > hide atoms > show cartoons > select ::name=""PGT"" 349 atoms, 343 bonds, 6 residues, 1 model selected > show sel atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 129 atoms, 128 bonds, 1 residue, 1 model selected > color sel byhetero > volume #2 level 0.01388 > select /E:401@C15 1 atom, 1 residue, 1 model selected > select /E:401@C15 1 atom, 1 residue, 1 model selected > select /E:401@C15 1 atom, 1 residue, 1 model selected > select /E:401@C15 1 atom, 1 residue, 1 model selected > volume #2 style mesh > volume #2 style image > volume #2 style surface > select /E:401@C20 1 atom, 1 residue, 1 model selected > select /E:401@C21 1 atom, 1 residue, 1 model selected > select /E:401@C22 1 atom, 1 residue, 1 model selected > surface cap false > surface cap true > surface cap false > select ::name=""PGT"" 349 atoms, 343 bonds, 6 residues, 1 model selected > style sel stick Changed 349 atom styles > show sel atoms > style sel sphere Changed 349 atom styles > style sel stick Changed 349 atom styles > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel ball Changed 349 atom styles ===== Log before crash end ===== Log: 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-18.5.8 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir7,2 Processor Name: Dual-Core Intel Core i7 Processor Speed: 2.2 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: 8 GB System Firmware Version: 428.60.3.0.0 OS Loader Version: 540.100.7~23 SMC Version (system): 2.27f2 Software: System Software Overview: System Version: macOS 12.3.1 (21E258) Kernel Version: Darwin 21.4.0 Time since boot: 1 day 7:16 Graphics/Displays: Intel HD Graphics 6000: Chipset Model: Intel HD Graphics 6000 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1626 Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: LCD Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus) UI Looks like: 1440 x 900 Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Cinema Display: Display Type: LCD Resolution: 1680 x 1050 (Widescreen Super eXtended Graphics Array Plus) UI Looks like: 1680 x 1050 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported 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 File attachment: chimeraX_crash.txt }}} [attachment:""chimeraX_crash.txt""] " defect closed normal Graphics nonchimerax all ChimeraX