id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5806 Crash registering webcam command kelvin.lau@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3.dev202107280209 (2021-07-28 02:09:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x000000010e3b7600 (most recent call first): File """", line 228 in _call_with_frames_removed File """", line 1173 in create_module File """", line 565 in module_from_spec File """", line 666 in _load_unlocked File """", line 986 in _find_and_load_unlocked File """", line 1007 in _find_and_load File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/Qt/QtMultimedia.py"", line 4 in File """", line 228 in _call_with_frames_removed File """", line 850 in exec_module File """", line 680 in _load_unlocked File """", line 986 in _find_and_load_unlocked File """", line 1007 in _find_and_load File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/webcam/webcam.py"", line 424 in File """", line 228 in _call_with_frames_removed File """", line 850 in exec_module File """", line 680 in _load_unlocked File """", line 986 in _find_and_load_unlocked File """", line 1007 in _find_and_load File """", line 228 in _call_with_frames_removed File """", line 1058 in _handle_fromlist File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/webcam/__init__.py"", line 20 in register_command File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py"", line 1271 in register_command File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 312 in _register_cmd File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 302 in cb File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2105 in call File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2174 in lazy_register File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 3432 in find_aliases File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 3442 in find_aliases File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 3448 in list_aliases File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py"", line 392 in take_snapshot File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py"", line 281 in process File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py"", line 260 in discovery File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py"", line 608 in save File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py"", line 878 in save File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py"", line 82 in save File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/cmd.py"", line 88 in provider_save File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2856 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/cmd.py"", line 75 in cmd_save File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2856 in run File 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kelvinlau/Google Drive/Shared drives/Omi-Titan-Dec21-figures- > andmaps/ChimeraXsession/sugar-sup-6XLU.cxs"" format session Opened emd_22251.map as #3, grid size 440,440,440, pixel 0.85, shown at level 0.0207, step 1, values float32 opened ChimeraX session > select :643,655 132 atoms, 132 bonds, 12 residues, 2 models selected > hide #!3 models > show (#!1 & sel) target ab > show #!3 models > volume #3 level 0.02139 > close session > open > /Users/kelvinlau/Downloads/C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc Opened C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc as #1, grid size 300,300,300, pixel 1.86, shown at level 0.0753, step 2, values float32 > volume #1 step 1 > volume #1 level 0.1063 > surface dust #1 size 18.6 > fetch pdb 7P40 Unknown command: fetch pdb 7P40 > getcrd pdb 7P40 Missing or invalid ""atoms"" argument: invalid atom specifier > pdbimages 7P40 pdbimages is provided by the uninstalled bundle PDBImages versions 1.0 – 1.1 > open /Users/kelvinlau/Downloads/7p40.pdb 7p40.pdb title: P5C3 is A potent fab neutralizer [more info...] Chain information for 7p40.pdb #2 --- Chain | Description A E G | spike glycoprotein B D H | No description available C F I | No description available > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 279 tiltedSlabSpacing 1.86 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1 style surface > hide atoms > show atoms > style stick Changed 26466 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > show cartoons > hide atoms > ui tool show ""Fit in Map"" Fit molecule 7p40.pdb (#2) to map C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc (#1) using 26466 atoms average map value = 0.1532, steps = 196 shifted from previous position = 48 rotated from previous position = 23.2 degrees atoms outside contour = 12616, contour level = 0.10628 Position of 7p40.pdb (#2) relative to C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.93208336 0.33733377 -0.13200961 -8.53314766 -0.35432432 0.92479612 -0.13858720 171.72117040 0.07533183 0.17594904 0.98151263 -30.91167809 Axis 0.39936018 -0.26325715 -0.87818399 Axis point 449.51022512 90.38144541 0.00000000 Rotation angle (degrees) 23.19116726 Shift along axis -21.46848397 > transparency 50 > select #1 3 models selected > ui mousemode right ""translate selected models"" > select #2 26466 atoms, 27105 bonds, 21 pseudobonds, 3687 residues, 2 models selected > select #1 3 models selected > select #2 26466 atoms, 27105 bonds, 21 pseudobonds, 3687 residues, 2 models selected > view matrix models > #2,0.93208,0.33733,-0.13201,0.85102,-0.35432,0.9248,-0.13859,143.8,0.075332,0.17595,0.98151,22.512 > ui mousemode right select > select clear Fit molecule 7p40.pdb (#2) to map C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc (#1) using 26466 atoms average map value = 0.2745, steps = 228 shifted from previous position = 44.3 rotated from previous position = 51.3 degrees atoms outside contour = 5450, contour level = 0.10628 Position of 7p40.pdb (#2) relative to C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.86046014 -0.50832398 0.03485810 184.75618913 0.50661829 0.84627081 -0.16481391 -19.25284509 0.05427947 0.15947555 0.98570852 -7.30543102 Axis 0.30430623 -0.01822459 0.95239991 Axis point 126.92205188 298.91793788 -0.00000000 Rotation angle (degrees) 32.19714321 Shift along axis 49.61564242 Drag select of 1 C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc , 8 residues Drag select of 1 C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc , 1 residues > hide #!2 models > show #!2 models > hide #!1 models > select /A 7064 atoms, 7235 bonds, 7 pseudobonds, 998 residues, 2 models selected > select /A,E 14128 atoms, 14470 bonds, 14 pseudobonds, 1996 residues, 2 models selected > hide sel cartoons > select /F,B,C,D 3516 atoms, 3600 bonds, 462 residues, 1 model selected > hide sel cartoons > show #!1 models > hide #!1 models > select :315-551 4329 atoms, 4443 bonds, 711 residues, 1 model selected > color sel red > show #!1 models > select clear Drag select of 1 C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc , 33 residues > select clear > hide #!1 models > select : 339,371,373,375,417,440,477,478,493,498,484,496,501,505 207 atoms, 168 bonds, 42 residues, 1 model selected > select :315-551 4329 atoms, 4443 bonds, 711 residues, 1 model selected > color sel blue > select : 339,371,373,375,417,440,477,478,493,498,484,496,501,505 207 atoms, 168 bonds, 42 residues, 1 model selected > color sel red > style sel sphere Changed 207 atom styles > show sel atoms > select clear Drag select of 136 atoms, 111 residues, 2 pseudobonds > hide sel atoms Drag select of 2 atoms > hide sel atoms Drag select of 2 residues > show #!1 models Drag select of 1 C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc , 13 residues > select clear > volume #1 change image level -0.04141,0 level 0.2509,0.8 level 0.7108,1 > volume #1 level 0.1264 > select clear > save /Users/kelvinlau/Desktop/image1.png supersample 3 > turn y 180 > save /Users/kelvinlau/Desktop/image2.png supersample 3 > select clear > save /Users/kelvinlau/Desktop/image3.png supersample 3 > select : 501,484,417 45 atoms, 36 bonds, 9 residues, 1 model selected > color sel yellow > select clear Drag select of 1 C1_2Fab_Om_cryosparc_P24_J64_005_volume_map.mrc , 7 residues > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.0624 > save /Users/kelvinlau/P5C3-Fab-WT-dockedinto-double.cxs ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3.dev202107280209 (2021-07-28) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/kelvinlau/Downloads/cryosparc_P11_J81_005_volume_map.mrc Opened cryosparc_P11_J81_005_volume_map.mrc as #1, grid size 400,400,400, pixel 1.2, shown at level 0.071, step 2, values float32 OpenGL version: 4.1 INTEL-18.2.10 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0) OS Loader Version: 540.40.4~45 Software: System Software Overview: System Version: macOS 12.0.1 (21A559) Kernel Version: Darwin 21.1.0 Time since boot: 9 days 1:05 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 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 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: 1.5.0 chardet: 4.0.0 charset-normalizer: 2.0.3 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.27.1 ChimeraX-AtomicLibrary: 4.0 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.3 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.3.2 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202107280209 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.4 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 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 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: 1.2.1 ChimeraX-MDcrds: 2.4 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.2 ChimeraX-ModelPanel: 1.1 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: 1.6.2 ChimeraX-PDB: 2.5.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 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 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.1 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 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: 1.10.1 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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 comtypes: 1.1.10 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.23 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.3.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.20 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 2.11.3 jupyter-client: 6.1.12 jupyter-core: 4.7.1 kiwisolver: 1.3.1 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 1.1.1 matplotlib: 3.4.2 matplotlib-inline: 0.1.2 msgpack: 1.0.2 netCDF4: 1.5.6 networkx: 2.5.1 numexpr: 2.7.3 numpy: 1.21.0 numpydoc: 1.1.0 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.2.0 pip: 21.1.1 pkginfo: 1.7.0 prompt-toolkit: 3.0.19 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.9.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.1.0 qtconsole: 5.1.0 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.25.1 scipy: 1.6.3 setuptools: 57.0.0 sfftk-rw: 0.7.0.post1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.0.1 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: 5.0.5 urllib3: 1.26.6 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.2 wheel-filename: 1.3.0 }}} " defect closed normal Command Line can't reproduce Tom Goddard all ChimeraX