id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8574 Graphics crash, macOS 12.5.1, Intel HD Graphics 6000 chimerax-bug-report@… Tom Goddard "The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x000070000dc3c000 (most recent call first): File ""/private/var/folders/0h/b7_nc8zd1tgd5mhwjmcmmhww0000gn/T/AppTranslocation/97E18513-99A2-4475-B793-03B14368191D/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/private/var/folders/0h/b7_nc8zd1tgd5mhwjmcmmhww0000gn/T/AppTranslocation/97E18513-99A2-4475-B793-03B14368191D/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/private/var/folders/0h/b7_nc8zd1tgd5mhwjmcmmhww0000gn/T/AppTranslocation/97E18513-99A2-4475-B793-03B14368191D/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File 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240000251 }, { ""rolloutId"" : ""6112e14f37f5d11121dcd519"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""634710168e8be655c1316aaa"" }, ""deploymentId"" : 240000229 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open /Users/hoanglan/Downloads/5u74.pdb 5u74.pdb title: Structure of human niemann-pick C1 protein [more info...] Chain information for 5u74.pdb #1 --- Chain | Description | UniProt A | niemann-pick C1 protein | NPC1_HUMAN Non-standard residues in 5u74.pdb #1 --- MAN — α-D-mannopyranose MES — 2-(N-morpholino)-ethanesulfonic acid NAG — 2-acetamido-2-deoxy-β-D-glucopyranose select helix 4494 atoms, 4573 bonds, 565 residues, 1 model selected color sel cyan undo select /A 7185 atoms, 7379 bonds, 2 pseudobonds, 909 residues, 2 models selected undo show cartoons undo style ball Changed 7291 atom styles select add #1 7291 atoms, 7493 bonds, 2 pseudobonds, 917 residues, 2 models selected select subtract #1 Nothing selected select helix 4494 atoms, 4573 bonds, 565 residues, 1 model selected log metadata #1 Metadata for 5u74.pdb #1 --- Title | Structure of human niemann-pick C1 protein Citation | 3.3 angstrom structure of niemann-pick C1 protein revealsinsights INTO the function of the C-terminal luminal domainin cholesterol transport. PMID: 28784760 Non-standard residues | MAN — α-D-mannopyranose MES — 2-(N-morpholino)-ethanesulfonic acid NAG — 2-acetamido-2-deoxy-β-D-glucopyranose Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 3.34Å sequence chain #1/A Alignment identifier is 1/A select /A:404-411,418-420,429-431,547-548,560-567,600-604,888-893,958-960,966-967,976-978,1025-1027,1031-1033,1036-1041,1080-1081 481 atoms, 484 bonds, 57 residues, 1 model selected select helix 4494 atoms, 4573 bonds, 565 residues, 1 model selected show sel atoms hide sel atoms show sel atoms hide sel atoms show sel cartoons hide sel cartoons show sel cartoons select /A:396 8 atoms, 7 bonds, 1 residue, 1 model selected select /A:386-396 97 atoms, 98 bonds, 11 residues, 1 model selected undo select /A:396-397 17 atoms, 16 bonds, 2 residues, 1 model selected select /A:394-397 40 atoms, 41 bonds, 4 residues, 1 model selected undo select /A:396 8 atoms, 7 bonds, 1 residue, 1 model selected select /A:386-396 97 atoms, 98 bonds, 11 residues, 1 model selected select helix 4494 atoms, 4573 bonds, 565 residues, 1 model selected select /A:386 6 atoms, 5 bonds, 1 residue, 1 model selected select /A:386-396 97 atoms, 98 bonds, 11 residues, 1 model selected color sel yellow color sel orange red color sel forest green color sel cyan select /A:491 6 atoms, 5 bonds, 1 residue, 1 model selected select /A:491-495 37 atoms, 37 bonds, 5 residues, 1 model selected color sel cyan select /A:496-497 18 atoms, 18 bonds, 2 residues, 1 model selected select /A:496-497 18 atoms, 18 bonds, 2 residues, 1 model selected undo select /A:491 6 atoms, 5 bonds, 1 residue, 1 model selected select /A:491-496 45 atoms, 45 bonds, 6 residues, 1 model selected select helix 4494 atoms, 4573 bonds, 565 residues, 1 model selected select /A:491 6 atoms, 5 bonds, 1 residue, 1 model selected select /A:491-496 45 atoms, 45 bonds, 6 residues, 1 model selected color sel cyan select /A:508 8 atoms, 7 bonds, 1 residue, 1 model selected select /A:508-517 91 atoms, 95 bonds, 10 residues, 1 model selected color sel cyan select /A:334-369,377-382,386-396,432-451,463-468,483-489,491-496,508-517,542-545,554-558,574-593,608-617,620-638,653-679,683-712,719-750,754-792,817-831,834-852,871-883,901-907,918-929,942-955,993-1005,1019-1023,1047-1069,1084-1117,1120-1145,1150-1177,1182-1199,1202-1216,1218-1252 4494 atoms, 4573 bonds, 565 residues, 1 model selected color sel yellow undo select /A:386 6 atoms, 5 bonds, 1 residue, 1 model selected select /A:386-396 97 atoms, 98 bonds, 11 residues, 1 model selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.8.4 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir7,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 4 GB System Firmware Version: 430.140.3.0.0 OS Loader Version: 540.120.3~19 SMC Version (system): 2.27f2 Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 14:54 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) 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 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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: 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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: 2.7.2 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 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: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 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 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0" defect closed moderate Graphics nonchimerax all ChimeraX