id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7375 "Unknown crash after ""volume level"" command" chimerax-bug-report@… Eric Pettersen "{{{ 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. 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24 \n__LINKEDIT 192.9M 7 \n__OBJC_RO 82.7M 1 \n__OBJC_RW 3200K 2 \n__TEXT 13.0M 50 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 6.6G 948 \nshared memory 5352K 35 \nunshared pmap 11.8M 8 \n=========== ======= ======= \nTOTAL 9.9G 2257 \nTOTAL, minus reserved VM space 8.6G 2257 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/rflores/Downloads/cryosparc_P117_J24_005_volume_map (2).mrc"" Opened cryosparc_P117_J24_005_volume_map (2).mrc as #1, grid size 300,300,300, pixel 0.834, shown at level 0.208, step 2, values float32 > volume flip #1 Opened cryosparc_P117_J24_005_volume_map (2).mrc z flip as #2, grid size 300,300,300, pixel 0.834, shown at step 1, values float32 > volume #2 level 0.1736 > ui windowfill toggle > open emdb:8697 Opened emdb 8697 as #3, grid size 256,256,256, pixel 1, shown at level 0.0268, step 1, values float32 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > show #!2 models > select subtract #2 Nothing selected > select add #3 2 models selected > view matrix models #3,1,0,0,21.603,0,1,0,48.691,0,0,1,105.16 > view matrix models #3,1,0,0,-4.3285,0,1,0,49.812,0,0,1,113.67 > view matrix models > #3,0.1257,0.98776,0.092389,-31.532,-0.53668,-0.010622,0.84372,138.13,0.83437,-0.15564,0.52877,88.516 > view matrix models > #3,-0.37709,0.31653,0.87041,17.642,0.80801,-0.34691,0.47621,58.047,0.45269,0.88287,-0.12494,88.491 > view matrix models > #3,-0.45989,0.39804,0.79377,27.594,0.76999,-0.26648,0.57975,39.272,0.44229,0.87781,-0.18393,98.048 > view matrix models > #3,-0.45989,0.39804,0.79377,23.772,0.76999,-0.26648,0.57975,-15.957,0.44229,0.87781,-0.18393,-18.31 > view matrix models > #3,-0.45989,0.39804,0.79377,22.477,0.76999,-0.26648,0.57975,-14.194,0.44229,0.87781,-0.18393,-20.769 > view matrix models > #3,-0.45989,0.39804,0.79377,23.498,0.76999,-0.26648,0.57975,-20.231,0.44229,0.87781,-0.18393,-23.506 > view matrix models > #3,-0.45989,0.39804,0.79377,22.566,0.76999,-0.26648,0.57975,-19.027,0.44229,0.87781,-0.18393,-25.861 > view matrix models > #3,-0.45989,0.39804,0.79377,22.666,0.76999,-0.26648,0.57975,-18,0.44229,0.87781,-0.18393,-22.129 > view matrix models > #3,-0.24606,0.48988,0.83634,-21.615,0.89397,-0.21871,0.39112,-15.517,0.37452,0.84391,-0.38412,16.549 > view matrix models > #3,-0.25638,0.098565,0.96154,13.509,0.8776,-0.39316,0.2743,23.853,0.40508,0.91417,0.014299,-47.573 > view matrix models > #3,-0.63331,-0.20262,0.7469,127.3,0.6836,-0.59888,0.41717,56.281,0.36278,0.77478,0.51779,-89.241 > view matrix models > #3,-0.39672,0.48729,0.77792,5.3177,0.75594,-0.30732,0.57802,-10.788,0.52073,0.81738,-0.24644,-16.306 > fitmap #3 inMap #2 Fit map emdb 8697 in map cryosparc_P117_J24_005_volume_map (2).mrc z flip using 167649 points correlation = 0.6051, correlation about mean = 0.01272, overlap = 765.3 steps = 112, shift = 8.04, angle = 10.3 degrees Position of emdb 8697 (#3) relative to cryosparc_P117_J24_005_volume_map (2).mrc z flip (#2) coordinates: Matrix rotation and translation -0.50973133 0.37292178 0.77530853 42.03747489 0.69424845 -0.35395134 0.62668775 -3.64502823 0.50812701 0.85769913 -0.07848028 -40.66860054 Axis 0.48379686 0.55954638 0.67294016 Axis point 35.50899958 19.26350229 0.00000000 Rotation angle (degrees) 166.18732265 Shift along axis -9.06949861 > select subtract #3 Nothing selected > volume #2 level 0.344 > volume #2 level 0.2188 > ui windowfill toggle > transparency #2.1#3.1 50 > transparency #2.1#3.1 0 > open ""/Users/rflores/Downloads/cryosparc_P117_J23_004_volume_map (1).mrc"" Opened cryosparc_P117_J23_004_volume_map (1).mrc as #4, grid size 300,300,300, pixel 0.834, shown at level 0.203, step 2, values float32 > volume #4 level 0.1725 > volume #4 level 0.1198 > open ""/Users/rflores/Downloads/cryosparc_P117_J25_004_volume_map (1).mrc"" Opened cryosparc_P117_J25_004_volume_map (1).mrc as #5, grid size 300,300,300, pixel 0.834, shown at level 0.211, step 2, values float32 > volume #5 level 0.1709 > volume flip #5 Opened cryosparc_P117_J25_004_volume_map (1).mrc z flip as #6, grid size 300,300,300, pixel 0.834, shown at step 1, values float32 > volume #6 level 0.1247 > volume #2 level 0.1572 > volume #3 level 0.01093 ===== 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 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 16 MB Memory: 32 GB Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 32 days 4:04 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG UltraFine: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Automatically Adjust Brightness: 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: 2.0.9 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-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-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 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX