id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9844 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.5-arm64-arm-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. 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\nKernel Alloc Once 32K 1 \nMALLOC 24.8G 614 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 776.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 96K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 560K 35 \nStack 176.8M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 249.7M 452 \nVM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)\n__AUTH 2624K 311 \n__AUTH_CONST 20.6M 510 \n__CTF 756 1 \n__DATA 24.2M 670 \n__DATA_CONST 27.9M 676 \n__DATA_DIRTY 1804K 216 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 611.9M 166 \n__OBJC_CONST 3665K 282 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 734.1M 695 \n__UNICODE 592K 1 \ndyld private memory 1216K 3 \nmapped file 719.4M 70 \nshared memory 3424K 32 \n=========== ======= ======= \nTOTAL 28.5G 4968 \nTOTAL, minus reserved VM space 27.5G 4968 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 } ], ""experiments"" : [ { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] } } ===== 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/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/.shortcut-targets-by- > id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/TVMT_maps/48nm_to_be_improved/cryosparc_P9_J475_map_sharp.mrc > format mrc Opened cryosparc_P9_J475_map_sharp.mrc as #1, grid size 640,640,640, pixel 1.1, shown at level 0.106, step 4, values float32 > volume #1 level 0.08861 > volume #1 level 0.04711 > volume #1 step 1 > ui tool show ""Hide Dust"" > surface dust #1 size 6.6 > lighting full > close session > open ""/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1. > Research/Project #4 - TVMT/TVMT Modeling (my > reference)/B_tubule_ID_08182023.cxs"" format session Opened cryosparc_P9_J475_map_sharp.mrc as #1, grid size 640,640,640, pixel 1.1, shown at level 0.0456, step 4, values float32 opened ChimeraX session > lighting soft > lighting simple > lighting full > select /HZ:45@OE2 1 atom, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /HD Alignment identifier is 2/HD > select /HD 1563 atoms, 1603 bonds, 2 pseudobonds, 198 residues, 2 models selected > select /HD:195-232 300 atoms, 300 bonds, 38 residues, 1 model selected > select /HD 1563 atoms, 1603 bonds, 2 pseudobonds, 198 residues, 2 models selected > select /HD 1563 atoms, 1603 bonds, 2 pseudobonds, 198 residues, 2 models selected > select /HD 1563 atoms, 1603 bonds, 2 pseudobonds, 198 residues, 2 models selected > close session > open ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/My Drive/3. Extracurricular/1. Research/Project #4 - > TVMT/TVMT Modeling (my reference)/FAP52_fit_09052023.cxs"" format session Opened cryosparc_P9_J475_map_sharp.mrc as #1.1.1.1, grid size 640,640,640, pixel 1.1, shown at level 0.0801, step 1, values float32 Opened cryosparc_P9_J475_map_sharp.mrc as #2, grid size 640,640,640, pixel 1.1, shown at level 0.0829, step 1, values float32 opened ChimeraX session > hide #!1 models > volume #2 level 0.06766 > volume #2 level 0.05895 > ui mousemode right ""crop volume"" > volume #2 region 337,187,403,427,276,549 > volume #2 region 337,187,403,435,276,549 > volume #2 level 0.05024 > volume #2 level 0.04661 > volume #2 level 0.0408 > close session > open ""/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1. > Research/Project #4 - TVMT/TVMT Modeling (my > reference)/B_tubule_ID_08182023.cxs"" format session Opened cryosparc_P9_J475_map_sharp.mrc as #1, grid size 640,640,640, pixel 1.1, shown at level 0.0456, step 4, values float32 opened ChimeraX session > volume #1 level 0.03378 > volume #1 step 1 > volume #1 step 2 > volume #1 level 0.02892 > hide #!2 models > volume #1 step 1 > volume #1 step 2 > show #!2 models > close session > open ""/Users/ethancrofut/Library/CloudStorage/GoogleDrive- > ecrofut@g.ucla.edu/My Drive/3. Extracurricular/1. Research/Project #4 - > TVMT/TVMT Modeling (my reference)/FAP52_fit_09052023.cxs"" format session Opened cryosparc_P9_J475_map_sharp.mrc as #1.1.1.1, grid size 640,640,640, pixel 1.1, shown at level 0.0801, step 1, values float32 Opened cryosparc_P9_J475_map_sharp.mrc as #2, grid size 640,640,640, pixel 1.1, shown at level 0.0829, step 1, values float32 opened ChimeraX session > volume #2 level 0.07275 > volume #2 level 0.06912 > volume #2 level 0.07638 > volume #2 level 0.08219 > volume #2 level 0.06185 > volume #2 level 0.06694 > select clear > volume #2 level 0.06403 > close session > open ""/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1. > Research/Project #4 - TVMT/TVMT Modeling (my > reference)/B_tubule_ID_08182023.cxs"" format session Opened cryosparc_P9_J475_map_sharp.mrc as #1, grid size 640,640,640, pixel 1.1, shown at level 0.0456, step 4, values float32 opened ChimeraX session > view orient > select /Go:247@CB 1 atom, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > close session ===== 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 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple 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: MacBookAir10,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 7459.141.1 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.5 (21G72) Kernel Version: Darwin 21.6.0 Time since boot: 16 days 20:26 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 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 DELL P2714H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 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-Clipper: 0.19.0 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-ISOLDE: 1.5 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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 normal Core duplicate all ChimeraX