id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8914 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ 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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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/emil/Downloads/J305_005_volume_map_half_A_deepEMhancer- > sharpened_zflip.mrc Opened J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc as #1, grid size 210,210,210, pixel 1.41, shown at level 0.000114, step 1, values float32 > open /Users/emil/Downloads/AF-P20851-F1-model_v4_1-2.pdb AF-P20851-F1-model_v4_1-2.pdb title: Alphafold monomer V2.0 prediction for C4B-binding protein β chain (P20851) [more info...] Chain information for AF-P20851-F1-model_v4_1-2.pdb #2 --- Chain | Description | UniProt A | C4B-binding protein β chain | C4BPB_HUMAN > open /Users/emil/Library/CloudStorage/OneDrive- > LundUniversity/Postdoc/Dahlbäck/Phenix/DockPredictedModel_56/AF-P07225-F1-model_v4_docked.pdb Summary of feedback from opening /Users/emil/Library/CloudStorage/OneDrive- LundUniversity/Postdoc/Dahlbäck/Phenix/DockPredictedModel_56/AF-P07225-F1-model_v4_docked.pdb --- warning | Ignored bad PDB record found on line 460 BREAK Chain information for AF-P07225-F1-model_v4_docked.pdb #3 --- Chain | Description A | No description available > volume #1 level 0.01236 > select add #2 882 atoms, 906 bonds, 114 residues, 1 model selected > select add #3 4046 atoms, 4128 bonds, 4 pseudobonds, 518 residues, 3 models selected > select subtract #2 3164 atoms, 3222 bonds, 4 pseudobonds, 404 residues, 2 models selected > select subtract #3 Nothing selected > select add #2 882 atoms, 906 bonds, 114 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,168.1,0,1,0,170.13,0,0,1,204.08 > view matrix models #2,1,0,0,203.23,0,1,0,163.07,0,0,1,145.98 > hide #2 models > hide #!3 models > view #3 clip false > volume #1 level 0.1073 > volume #1 level 0.05829 > volume #1 style mesh > show #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #3/A:451 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:451-474 187 atoms, 188 bonds, 1 pseudobond, 22 residues, 2 models selected > select clear > select > #3/A:255-259,262-266,273-275,282-284,312-318,324-331,336-343,349-355,358-364,369-374,384-390,394-399,402-408,420-427,448-451,479-481,484-486,491-493,507-516,521-528,535-541,548-554,557-562,573-580,584-587,615-619,637-644,665-667 1330 atoms, 1328 bonds, 166 residues, 1 model selected > select #3/A:451-474 187 atoms, 188 bonds, 1 pseudobond, 22 residues, 2 models selected > select #3/A:460 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/A:460-468 56 atoms, 54 bonds, 1 pseudobond, 7 residues, 2 models selected > select #3/A:469 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:469-471 27 atoms, 26 bonds, 3 residues, 1 model selected > select #3/A:460 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/A:460-478 138 atoms, 137 bonds, 1 pseudobond, 17 residues, 2 models selected > select #3/A:414-415 20 atoms, 20 bonds, 2 residues, 1 model selected > select #3/A:414-458 370 atoms, 379 bonds, 45 residues, 1 model selected > select #3/A:319 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:319-340 187 atoms, 191 bonds, 22 residues, 1 model selected > select #3/A:342 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:342-354 103 atoms, 105 bonds, 13 residues, 1 model selected > select #3/A:313 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:313-320 71 atoms, 72 bonds, 8 residues, 1 model selected > select > #3/A:255-259,262-266,273-275,282-284,312-318,324-331,336-343,349-355,358-364,369-374,384-390,394-399,402-408,420-427,448-451,479-481,484-486,491-493,507-516,521-528,535-541,548-554,557-562,573-580,584-587,615-619,637-644,665-667 1330 atoms, 1328 bonds, 166 residues, 1 model selected > select clear > select #3/A:313 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:313-318 54 atoms, 55 bonds, 6 residues, 1 model selected > volume #1 level 0.02155 > select #3/A:296 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:296 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:298 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:298 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:296,298 18 atoms, 16 bonds, 2 residues, 1 model selected > select #3/A:296,298,335 27 atoms, 24 bonds, 3 residues, 1 model selected > select #3/A:296,298,335 27 atoms, 24 bonds, 3 residues, 1 model selected > select #3/A:296,298,335 27 atoms, 24 bonds, 3 residues, 1 model selected > select #3/A:296,298,333,335 35 atoms, 31 bonds, 4 residues, 1 model selected > select #3/A:296,298,333,335,451 46 atoms, 41 bonds, 5 residues, 1 model selected > select #3/A:296,298,333,335,451,464 55 atoms, 49 bonds, 6 residues, 1 model selected > select #3/A:296,298,333,335,451,464-465 64 atoms, 58 bonds, 7 residues, 1 model selected > hide #!1 models > show #!1 models > open /Users/emil/Downloads/unrelaxed_model_5.pdb Chain information for unrelaxed_model_5.pdb #4 --- Chain | Description A | No description available > view #4 clip false > view #1 clip false > hide #!1 models > hide #!3 models > hide #!4 models > select add #3 3164 atoms, 3222 bonds, 4 pseudobonds, 404 residues, 2 models selected > select subtract #3 Nothing selected > show #2 models > view #1 clip false No displayed objects specified. > select add #2 882 atoms, 906 bonds, 114 residues, 1 model selected > view #1 clip false No displayed objects specified. > select clear > show #!1 models > hide #!1 models > show #!3 models > show #!1 models > hide #2 models > view #3 clip false > hide #!3 models > show #2 models > hide #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:23 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:23-26 30 atoms, 30 bonds, 4 residues, 1 model selected > select clear > select #2/A:80 10 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:80-136 441 atoms, 455 bonds, 57 residues, 1 model selected > delete atoms sel > delete bonds sel > select add #2 441 atoms, 450 bonds, 57 residues, 1 model selected > show #!1 models > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.98625,0.084404,0.14211,204.1,0.10572,-0.98304,-0.14985,189.6,0.12705,0.16281,-0.97844,114.43 > volume #1 style surface > ui mousemode right ""translate selected models"" > view matrix models > #2,0.98625,0.084404,0.14211,154.6,0.10572,-0.98304,-0.14985,179.2,0.12705,0.16281,-0.97844,117.95 > view matrix models > #2,0.98625,0.084404,0.14211,149.66,0.10572,-0.98304,-0.14985,166,0.12705,0.16281,-0.97844,107.24 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.9045,-0.13279,0.40529,157.58,-0.22996,-0.95216,0.20125,174.44,0.35918,-0.27523,-0.89176,112.27 > ui tool show ""Fit in Map"" Opened AF-P20851-F1-model_v4_1-2.pdb map 5 as #5, grid size 35,42,37, pixel 1.67, shown at level 0.0742, step 1, values float32 > fitmap #2 inMap #1 resolution 5 Fit map AF-P20851-F1-model_v4_1-2.pdb map 5 in map J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc using 1841 points correlation = 0.5553, correlation about mean = 0.143, overlap = 70.84 steps = 168, shift = 6.2, angle = 36.4 degrees Position of AF-P20851-F1-model_v4_1-2.pdb map 5 (#5) relative to J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc (#1) coordinates: Matrix rotation and translation 0.98809918 -0.11371702 -0.10357822 142.85552251 -0.03728139 -0.83035603 0.55598467 173.79678662 -0.14923172 -0.54550646 -0.82471365 121.02467929 Axis -0.99674931 0.04131226 0.06916729 Axis point 0.00000000 109.48067971 38.40353747 Rotation angle (degrees) 146.45844004 Shift along axis -126.84025462 Average map value = 0.1286 for 441 atoms, 159 outside contour > volume #1 style mesh > view > view matrix models > #2,0.5372,0.59259,0.60021,147.42,-0.43903,0.80406,-0.40091,140.64,-0.72019,-0.048141,0.69211,141.5 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.5372,0.59259,0.60021,149.55,-0.43903,0.80406,-0.40091,141.89,-0.72019,-0.048141,0.69211,143.15 > view matrix models > #2,0.5372,0.59259,0.60021,152.65,-0.43903,0.80406,-0.40091,140.08,-0.72019,-0.048141,0.69211,143.23 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.61799,0.77851,0.10958,142.05,-0.71357,0.61394,-0.33747,147.12,-0.33,0.13036,0.93494,139.25 > fitmap #2 inMap #1 resolution 5 Fit map AF-P20851-F1-model_v4_1-2.pdb map 5 in map J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc using 1841 points correlation = 0.6123, correlation about mean = 0.2914, overlap = 71.07 steps = 168, shift = 4.83, angle = 30.5 degrees Position of AF-P20851-F1-model_v4_1-2.pdb map 5 (#5) relative to J305_005_volume_map_half_A_deepEMhancer-sharpened_zflip.mrc (#1) coordinates: Matrix rotation and translation 0.65749808 0.68154678 0.32123239 144.13222803 -0.33923215 0.64846361 -0.68148110 134.16274531 -0.67276877 0.33910016 0.65756616 139.14639038 Axis 0.58232344 0.56715736 -0.58243622 Axis point 271.35425799 -7.63192591 -0.00000000 Rotation angle (degrees) 61.19932943 Shift along axis 78.97906442 Average map value = 0.149 for 441 atoms, 139 outside contour > select clear > select #2/A:33 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:33 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:33,35 15 atoms, 13 bonds, 2 residues, 1 model selected > select #2/A:33,35,48 22 atoms, 19 bonds, 3 residues, 1 model selected > select #2/A:33,35,48,50 30 atoms, 26 bonds, 4 residues, 1 model selected > show #!3 models > select add #2 441 atoms, 450 bonds, 57 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.6575,0.68155,0.32123,146.15,-0.33923,0.64846,-0.68148,133.87,-0.67277,0.3391,0.65757,138.67 > select clear > select #2/A:33,35,48,50 30 atoms, 26 bonds, 4 residues, 1 model selected > show sel target ab > hide #!1 models > hide #2 models > hide #!3 models > show #!4 models > select add #2 441 atoms, 450 bonds, 57 residues, 1 model selected > select add #4 6301 atoms, 6431 bonds, 1 pseudobond, 811 residues, 3 models selected > view matrix models > #2,0.6575,0.68155,0.32123,273.06,-0.33923,0.64846,-0.68148,329.8,-0.67277,0.3391,0.65757,160.4,#4,1,0,0,126.9,0,1,0,195.93,0,0,1,21.73 > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A Alignment identifier is 4/A > select #4/A:1-2 13 atoms, 12 bonds, 2 residues, 1 model selected > select #4/A:1-103 812 atoms, 827 bonds, 103 residues, 1 model selected > select #4/A:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:1-152 1180 atoms, 1204 bonds, 152 residues, 1 model selected > select #4/A:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:1-204 1577 atoms, 1607 bonds, 204 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!1 models > show #2 models > show #!3 models > hide #!1 models > hide #!3 models > hide #!4 models > close #2 ===== 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 INTEL-20.2.50 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel 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: MacBookPro15,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2,7 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0) OS Loader Version: 564.40.4~66 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 6 days, 2 hours, 43 minutes 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 Support: Metal 3 Displays: HP E24q G4: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: CNK15108PQ 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-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