id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17715 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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\n__AUTH_CONST 33.1M 659 \n__CTF 824 1 \n__DATA 23.9M 806 \n__DATA_CONST 43.3M 813 \n__DATA_DIRTY 2056K 242 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 920.8M 155 \n__OBJC_RO 71.2M 1 \n__OBJC_RW 2171K 1 \n__TEXT 964.6M 831 \ndyld private memory 544K 4 \nmapped file 262.4M 66 \nshared memory 3232K 29 \n=========== ======= ======= \nTOTAL 9.2G 4934 \nTOTAL, minus reserved VM space 9.0G 4934 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""0bee85ae612b12b02b019f13f2e900090c2d0326"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/J203_005_volume_map_apix1.4053.mrc Opened J203_005_volume_map_apix1.4053.mrc as #1, grid size 400,400,400, pixel 1.41, shown at level 0.21, step 2, values float32 > open > /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb Chain information for 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb #2 --- Chain | Description A C | No description available B D | No description available E | No description available F G I M | No description available H J K L | No description available > style stick Changed 42808 atom styles The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > transparency 50 > set bgColor white The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 step 1 > combine #2 > split #3 Split copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb (#3) into 13 models Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb A #3.1 --- Chain | Description A | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb B #3.2 --- Chain | Description B | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb C #3.3 --- Chain | Description C | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb D #3.4 --- Chain | Description D | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb E #3.5 --- Chain | Description E | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb F #3.6 --- Chain | Description F | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb G #3.7 --- Chain | Description G | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb H #3.8 --- Chain | Description H | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb I #3.9 --- Chain | Description I | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb J #3.10 --- Chain | Description J | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb K #3.11 --- Chain | Description K | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb L #3.12 --- Chain | Description L | No description available Chain information for copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb M #3.13 --- Chain | Description M | No description available > fitmap #3/E inMap #1 Fit molecule copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb E (#3.5) to map J203_005_volume_map_apix1.4053.mrc (#1) using 2132 atoms average map value = 0.2901, steps = 60 shifted from previous position = 0.00344 rotated from previous position = 0.00696 degrees atoms outside contour = 655, contour level = 0.20953 Position of copy of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb E (#3.5) relative to J203_005_volume_map_apix1.4053.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00008055 -0.00004656 -0.02231135 -0.00008055 0.99999999 0.00007821 0.00081140 0.00004657 -0.00007821 1.00000000 0.01806129 Axis -0.64346642 -0.38308710 -0.66271807 Axis point 19.92730800 260.39244332 0.00000000 Rotation angle (degrees) 0.00696413 Shift along axis 0.00207622 Drag select of 1 J203_005_volume_map_apix1.4053.mrc , 1246 atoms, 1272 bonds > select clear Drag select of 1 J203_005_volume_map_apix1.4053.mrc , 2 atoms, 4 bonds > select clear > ui mousemode right zoom > volume #1 level 0.08111 > surface dust #1 size 14.1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Map Coordinates"" > open > /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203_005_volume_map_deepem_highRes.mrc Opened J203_005_volume_map_deepem_highRes.mrc as #4, grid size 400,400,400, pixel 1.43, shown at level 0.128, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > fitmap #4 inMap #1 Fit map J203_005_volume_map_deepem_highRes.mrc in map J203_005_volume_map_apix1.4053.mrc using 639777 points correlation = 0.9107, correlation about mean = 0.6523, overlap = 7.268e+04 steps = 44, shift = 0.022, angle = 0.00245 degrees Position of J203_005_volume_map_deepem_highRes.mrc (#4) relative to J203_005_volume_map_apix1.4053.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00003258 0.00001198 0.00273694 -0.00003258 1.00000000 0.00002501 0.00764531 -0.00001198 -0.00002501 1.00000000 0.02454574 Axis -0.58453587 0.27994224 -0.76154459 Axis point 390.64156626 241.69018473 0.00000000 Rotation angle (degrees) 0.00245111 Shift along axis -0.01815227 > color #4 darkgray > transparency 50 > volume #4 level 0.0797 > fitmap #2 inMap #4 Fit molecule 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb (#2) to map J203_005_volume_map_deepem_highRes.mrc (#4) using 42808 atoms average map value = 0.3434, steps = 40 shifted from previous position = 0.0492 rotated from previous position = 0.0148 degrees atoms outside contour = 6987, contour level = 0.079697 Position of 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb (#2) relative to J203_005_volume_map_deepem_highRes.mrc (#4) coordinates: Matrix rotation and translation 0.99999999 0.00004656 -0.00016220 0.02803223 -0.00004659 0.99999997 -0.00022013 0.07544607 0.00016219 0.00022013 0.99999996 -0.09485844 Axis 0.79363906 -0.58475785 -0.16791456 Axis point 0.00000000 435.50241357 326.90624144 Rotation angle (degrees) 0.01589195 Shift along axis -0.00594210 > volume #4 level 0.04216 Drag select of 484 atoms, 488 bonds, 4 J203_005_volume_map_deepem_highRes.mrc Drag select of 4 J203_005_volume_map_deepem_highRes.mrc > select clear > volume #4 level 0.07594 > volume #4 level 0.01588 > close #2 > close #3 > open > /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/20250517_TOG5_MT_forPDB- > coot-0.pdb Summary of feedback from opening /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/20250517_TOG5_MT_forPDB- coot-0.pdb --- warnings | Start residue of secondary structure not found: HELIX 113 113 GLY F 10 HIS F 28 1 19 Start residue of secondary structure not found: HELIX 114 114 SER F 48 THR F 51 1 4 Start residue of secondary structure not found: HELIX 115 115 THR F 73 THR F 80 1 8 Start residue of secondary structure not found: HELIX 116 116 PRO F 89 GLN F 91 1 3 Start residue of secondary structure not found: HELIX 117 117 TYR F 103 THR F 109 1 7 299 messages similar to the above omitted Cannot find LINK/SSBOND residue MG (502 ) Cannot find LINK/SSBOND residue MG (502 ) Cannot find LINK/SSBOND residue MG (502 ) Cannot find LINK/SSBOND residue MG (502 ) Cannot find LINK/SSBOND residue MG (502 ) 11 messages similar to the above omitted Chain information for 20250517_TOG5_MT_forPDB-coot-0.pdb #2 --- Chain | Description A C | No description available B D | No description available E | No description available > show cartoons > hide atoms > show atoms > style stick Changed 15708 atom styles > color byhetero Drag select of 4 J203_005_volume_map_deepem_highRes.mrc , 670 atoms, 178 residues, 567 bonds > select #4 2 models selected > select clear > hide atoms > select #2/E 2132 atoms, 2169 bonds, 1 pseudobond, 264 residues, 2 models selected > ui tool show Contacts The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > contacts sel restrict cross distanceOnly 5.0 interModel false intraMol false > ignoreHiddenModels true select true makePseudobonds false reveal true 463 distances > select clear Drag select of 4 J203_005_volume_map_deepem_highRes.mrc , 5 atoms, 9 residues, 3 bonds > select #4 2 models selected > select clear > select #2/E 2132 atoms, 2169 bonds, 1 pseudobond, 264 residues, 2 models selected > ui tool show H-Bonds The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hbonds sel radius 0.1 interModel false distSlop 1.5 intraMol false intraRes > false reveal true 16 hydrogen bonds found > select clear Drag select of 4 J203_005_volume_map_deepem_highRes.mrc , 29 residues > select #4 2 models selected > select clear > ui tool show ""Side View"" > ui mousemode right ""map eraser"" > volume erase #4 center 263.72,398.15,270.64 radius 82.666 outside true Opened J203_005_volume_map_deepem_highRes.mrc copy as #5, grid size 400,400,400, pixel 1.41, shown at step 1, values float32 > ui mousemode right zoom > ui tool show ""Side View"" > open > /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb Chain information for 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9.pdb #3 --- Chain | Description A C | No description available B D | No description available E | No description available F G I M | No description available H J K L | No description available > style stick Changed 58516 atom styles > show cartoons > hide #!3 models > show #!3 models > hide #!3 models > close #4 > open > /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/J203_005_volume_map_sharp_apix1.4053.mrc Opened J203_005_volume_map_sharp_apix1.4053.mrc as #4, grid size 400,400,400, pixel 1.41, shown at level 0.299, step 2, values float32 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > color #4 darkgray > transparency 50 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/TOG5_MT_Phenix/RealSpaceRefine_99/20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9_real_space_refined_099.pdb Chain information for 20250507_6dpu_TOG5AF2_multimer_docked_J203_apix1p4053-coot-9_real_space_refined_099.pdb #1 --- Chain | Description A C | No description available B D | No description available E | No description available F G I M | No description available H J K L | No description available > open > /Users/collinmcmanus/Desktop/Petry_Lab/CryoEM/TOG5_MT/202504_Model_Building/J203/J203_005_volume_map_apix1.4053.mrc Opened J203_005_volume_map_apix1.4053.mrc as #2, grid size 400,400,400, pixel 1.41, shown at level 0.21, step 2, values float32 > style stick Changed 42808 atom styles > transparency 50 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #2 step 1 > color byhetero > select /A:414@CD 1 atom, 1 residue, 1 model selected > select /A:414@CD 1 atom, 1 residue, 1 model selected OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,7 Model Number: Z1AJ0018XLL/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 24 days, 2 hours, 20 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL SE2719H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Television: Yes Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-maskChains: 1.4 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX