id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7757 Crash when asking to register chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3rc202111182158 (2021-11-18 21:58:36 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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reserved VM space 8.3G 4274 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61301e3a61217b3110231469"", ""factorPackIds"" : { ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""6216ae152a40e71046e16225"" }, ""deploymentId"" : 240000016 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000026 } ], ""experiments"" : [ { ""treatmentId"" : ""5b729754-3882-4560-826f-9c0bc27d77c6"", ""experimentId"" : ""6192fb082171a2330e561df0"", ""deploymentId"" : 400000033 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/shoichi/Library/CloudStorage/OneDrive- > YaleUniversity/Jun_Lab_documents/Project-documents/H.pylori-univ-G/Chimera- > Hp-figuire-part2/Check/build3cxs.cxs Opened C-ring.mrc as #1, grid size 250,250,250, pixel 4.3, shown at level 0.014, step 1, values float32 Opened Cage.mrc as #2, grid size 250,250,250, pixel 4.3, shown at level 0.0157, step 1, values float32 Opened Disk_bottom.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0134, step 1, values float32 Opened Disk.mrc as #5, grid size 250,250,250, pixel 4.3, shown at level 0.0154, step 1, values float32 Opened Export.mrc as #6, grid size 250,250,250, pixel 4.3, shown at level 0.0133, step 1, values float32 Opened Export2.mrc as #7, grid size 250,250,250, pixel 4.3, shown at level 0.0135, step 1, values float32 Opened Export3.mrc as #8, grid size 250,250,250, pixel 4.3, shown at level 0.0134, step 1, values float32 Opened Export4.mrc as #9, grid size 250,250,250, pixel 4.3, shown at level 0.0134, step 1, values float32 Opened MotA.mrc as #11, grid size 250,250,250, pixel 4.3, shown at level 0.0135, step 1, values float32 Opened PlfB.mrc as #14, grid size 250,250,250, pixel 4.3, shown at level 0.0134, step 1, values float32 Opened Rod-rings.mrc as #15, grid size 250,250,250, pixel 4.3, shown at level 0.0156, step 1, values float32 Opened 0838-1.mrc as #17, grid size 240,240,240, pixel 4.3, shown at level 0.0142, step 1, values float32 Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at level 0.0144, step 1, values float32 Opened 0838-top.mrc as #19, grid size 240,240,240, pixel 4.3, shown at level 0.0142, step 1, values float32 Opened 9839-out.mrc as #20, grid size 240,240,240, pixel 4.3, shown at level 0.0143, step 1, values float32 Opened OM.mrc as #22, grid size 240,240,240, pixel 4.3, shown at level 0.0381, step 1, values float32 Opened IM.mrc gaussian as #23, grid size 250,250,250, pixel 4.3, shown at level 0.0101, step 1, values float32 Opened 1xFliL.mrc as #26, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened Single-MotA-truncated.mrc as #29, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00658, step 1, values float32 Opened Single-MotA-truncated.mrc as #28, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #30, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #31, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened 1xFliL.mrc as #32, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #33, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #34, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #35, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #36, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened Single-MotA-truncated.mrc as #37, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #38, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #39, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #40, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #41, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened 1xFliL.mrc as #42, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #43, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #44, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #45, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #46, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #47, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened Single-MotA-truncated.mrc as #48, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #49, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #50, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #51, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #52, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #53, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened 1xFliL.mrc as #54, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #55, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #56, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #57, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #58, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened 1xFliL.mrc as #59, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.0066, step 1, values float32 Opened Single-MotA-truncated.mrc as #60, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #61, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened Single-MotA-truncated.mrc as #62, grid size 110,110,140, pixel 4.3,4.3,4.3, shown at level 0.00653, step 1, values float32 Opened 0838-disk.mrc as #10, grid size 240,240,240, pixel 4.3, shown at level 0.0152, step 1, values float32 Opened Cage-out-long.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level 0.0136, step 1, values float32 Opened Cage-out-other.mrc as #12, grid size 250,250,250, pixel 4.3, shown at level 0.0137, step 1, values float32 Opened Cage-out-short.mrc as #13, grid size 250,250,250, pixel 4.3, shown at level 0.0136, step 1, values float32 opened ChimeraX session ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3rc202111182158 (2021-11-18) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 8 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.3.1 (21E258) Kernel Version: Darwin 21.4.0 Time since boot: 6 days 12:42 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal ASUS MX34V: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 50.00Hz Mirror: Off Online: Yes 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: 2.0.7 ChimeraX-AddCharge: 1.2 ChimeraX-AddH: 2.1.10 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: 1.30.2 ChimeraX-AtomicLibrary: 4.1.5 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 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-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: 1.3rc202111182158 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 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-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: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.22 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: 1.11.2 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 Window Toolkit can't reproduce all ChimeraX