id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9231 XMAS: crash in ~QGridLayout() chimerax-bug-report@… "{{{ 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. 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: ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""6112e14f37f5d11121dcd519"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""634710168e8be655c1316aaa"" }, ""deploymentId"" : 240000231 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000013 } ] } } ===== 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/laura/Documents/RSC/Cartes > cryo/Cartes1/cryosparc_P197_J770_map_sharp.mrc"" Opened cryosparc_P197_J770_map_sharp.mrc as #1, grid size 300,300,300, pixel 0.84, shown at level 0.00718, step 2, values float32 > surface dust #1 size 8.4 > volume #1 step 1 > volume #1 level 0.008817 > open ""/Users/laura/Documents/RSC/Cartes > cryo/Cartes2/cryosparc_P197_J776_005_volume_map_sharp.mrc"" Opened cryosparc_P197_J776_005_volume_map_sharp.mrc as #2, grid size 450,450,450, pixel 0.84, shown at level 0.134, step 2, values float32 > open ""/Users/laura/Documents/RSC/Cartes > cryo/Cartes2/cryosparc_P197_J781_006_volume_map_sharp.mrc"" Opened cryosparc_P197_J781_006_volume_map_sharp.mrc as #3, grid size 450,450,450, pixel 0.84, shown at level 0.098, step 2, values float32 > open ""/Users/laura/Documents/RSC/Cartes > cryo/Cartes3/cryosparc_P197_J792_007_volume_map_sharp.mrc"" Opened cryosparc_P197_J792_007_volume_map_sharp.mrc as #4, grid size 450,450,450, pixel 0.84, shown at level 0.0932, step 2, values float32 > volume #2 step 1 > volume #3 step 1 > volume #4 step 1 > volume #2 level 0.1866 > volume #3 level 0.1506 > volume #4 level 0.1787 > hide #!3 models > hide #!4 models > hide #!2 models > show #!2 models > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,0.87773,-0.33325,-0.34429,93.421,0.060432,0.78979,-0.6104,88.9,0.47533,0.51496,0.71336,-81.963 > view matrix models > #1,0.95788,-0.21121,-0.19457,52.225,0.081622,0.84984,-0.52068,68.906,0.27533,0.48287,0.83129,-68.407 > view matrix models > #1,0.95788,-0.21121,-0.19457,105.92,0.081622,0.84984,-0.52068,130.52,0.27533,0.48287,0.83129,-1.563 > fitmap #1 inMap #2 Fit map cryosparc_P197_J770_map_sharp.mrc in map cryosparc_P197_J776_005_volume_map_sharp.mrc using 189333 points correlation = 0.6319, correlation about mean = 0.1245, overlap = 917.7 steps = 440, shift = 14.3, angle = 34.9 degrees Position of cryosparc_P197_J770_map_sharp.mrc (#1) relative to cryosparc_P197_J776_005_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99999906 -0.00135361 0.00019561 63.10057465 0.00135375 0.99999882 -0.00072958 62.82585820 -0.00019462 0.00072984 0.99999971 62.78499078 Axis 0.47073172 0.12586611 0.87325218 Axis point -37801.53402626 14496.30393359 0.00000000 Rotation angle (degrees) 0.08881763 Shift along axis 92.43821875 > show #!3 models > show #!4 models > surface dust #1 size 8.4 > select subtract #1 Nothing selected > hide #!3 models > hide #!4 models > hide #!2 models > show #!2 models > hide #!1 models > surface dust #2 size 8.4 > hide #!2 models > show #!3 models > surface dust #3 size 8.4 > show #!4 models > hide #!3 models > surface dust #4 size 8.4 > show #!1 models > show #!2 models > show #!3 models > volume #2 level 0.2925 > volume #3 level 0.2119 > open /Users/laura/Downloads/HBlobe_166-ajust(2).pdb Chain information for HBlobe_166-ajust(2).pdb #5 --- Chain | Description A | No description available B | No description available D | No description available F | No description available G | No description available H | No description available K | No description available > open /Users/laura/Downloads/HBlobe_166-ajust(1).pdb Chain information for HBlobe_166-ajust(1).pdb #6 --- Chain | Description A | No description available B | No description available D | No description available F | No description available G | No description available H | No description available K | No description available > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > close #6 > open /Users/laura/Downloads/DBLOBE_2805_renumbered(2).pdb Chain information for DBLOBE_2805_renumbered(2).pdb #6 --- Chain | Description A | No description available E | No description available F | No description available G | No description available H | No description available K | No description available N | No description available > show #!5 models > open /Volumes/ibs-equipe- > petosa/CaRSC_Structure/NB_Lobe/NB_AF_comp_RB_job50v1.pdb Chain information for NB_AF_comp_RB_job50v1.pdb #7 --- Chain | Description F | No description available G | No description available I | No description available M | No description available > hide atoms > show cartoons > hide cartoons > show surfaces > hide surfaces > show atoms > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > style stick Changed 20974 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides fill > style nucleic stick Changed 0 atom styles > nucleotides tube/slab shape box > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > ui tool show XMAS Peptide pair mapping of Xi evidence file: /Users/laura/Downloads/RSC_BS3_msconvert_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5(2).csv Unique peptide pairs: 1198 out of 1211 Unique peptide pairs with pseudobonds: 104 Pseudobonds are stored in /Users/laura/Downloads/RSC_BS3_msconvert_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5(2)_5,6,7.pb Mapping information is stored in /Users/laura/Downloads/RSC_BS3_msconvert_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5(2)_5,6,7.tsv Venn diagrams can only be plotted for two or three groups /Users/laura/Library/Application Support/ChimeraX/1.5/site- packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette using color= is deprecated and will be removed in version 0.13. Set `palette='dark:gray'` for same effect. warnings.warn(msg, FutureWarning) ===== 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 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies 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 Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2,3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6.2 (21G320) Kernel Version: Darwin 21.6.0 Time since boot: 5 days 17:16 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal PHL 258B6QU: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 59.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: UHB1949004141 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort 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: 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-XMAS: 1.1.2 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 et-xmlfile: 1.1.0 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 openpyxl: 3.1.0 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.3 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 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 seaborn: 0.12.2 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 Third Party duplicate all ChimeraX