id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15466 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.6.7-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff8447197c0 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, 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""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000004 } ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/chrst874/Postdoc/Cryo-EM/Masks/Mask selection.cxs"" format > session opened ChimeraX session > show LSU_RNA > select ~sel & ##selected 139150 atoms, 142690 bonds, 5748 pseudobonds, 17243 residues, 4 models selected > hide LSU_RNA > select SSU_RNA & ~#1/A:921-1396 22424 atoms, 25113 bonds, 1086 pseudobonds, 1043 residues, 3 models selected > show sel > open /Users/chrst874/Downloads/cryosparc_P2_J81_007_volume_map_sharp.mrc Opened cryosparc_P2_J81_007_volume_map_sharp.mrc as #2, grid size 576,576,576, pixel 0.758, shown at level 0.164, step 4, values float32 > hide #!1 models > volume #2 level 0.2123 > volume #2 step 1 > volume #2 level 0.2709 > lighting full > vop gaussian #2 sdev 2.27 Opened cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian as #3, grid size 576,576,576, pixel 0.758, shown at step 1, values float32 > show #!1 models > show #1 > fitmap #1 inMap #3 Fit molecule 7k00.cif (#1) to map cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian (#3) using 149338 atoms average map value = 0.02772, steps = 524 shifted from previous position = 72.5 rotated from previous position = 26.6 degrees atoms outside contour = 126217, contour level = 0.070321 Position of 7k00.cif (#1) relative to cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian (#3) coordinates: Matrix rotation and translation 0.96652782 0.13367976 0.21898334 -5.62474097 -0.04141802 0.92363397 -0.38103128 123.30558046 -0.25319662 0.35920748 0.89825468 37.88899460 Axis 0.82680296 0.52739712 -0.19557388 Axis point 0.00000000 -60.01737860 262.32086602 Rotation angle (degrees) 26.59309001 Shift along axis 52.97035764 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.96653,0.13368,0.21898,-42.658,-0.041418,0.92363,-0.38103,139.39,-0.2532,0.35921,0.89825,105.41 > view matrix models > #1,0.96653,0.13368,0.21898,-56.905,-0.041418,0.92363,-0.38103,146.87,-0.2532,0.35921,0.89825,134.28 > view matrix models > #1,0.96653,0.13368,0.21898,-149.73,-0.041418,0.92363,-0.38103,177.56,-0.2532,0.35921,0.89825,282.01 > lighting simple > lighting soft > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.59195,0.77019,-0.2375,-110.12,-0.74556,0.6352,0.20164,247.35,0.30616,0.057707,0.95023,224.9 > view matrix models > #1,0.9174,-0.060934,0.39327,-138.59,0.21432,0.90831,-0.35921,129.48,-0.33533,0.41383,0.84635,296.97 > lighting simple > view matrix models > #1,-0.41909,-0.078334,0.90456,10.906,0.7296,0.56392,0.38687,-44.496,-0.5404,0.8221,-0.17918,456.07 > view matrix models > #1,-0.011702,0.025494,0.99961,-100.61,0.73861,0.67408,-0.0085453,9.3838,-0.67403,0.73822,-0.026718,466.62 > view matrix models > #1,0.089014,-0.69599,0.71252,67.487,0.75876,0.51081,0.40417,-43.442,-0.64526,0.50466,0.57356,389.18 > view matrix models > #1,-0.033013,0.18127,0.98288,-121.94,0.74034,0.66508,-0.097793,27.776,-0.67142,0.72444,-0.15616,493.41 > view matrix models > #1,0.098538,-0.51917,0.84897,7.4022,-0.94397,-0.3188,-0.085393,512.48,0.31499,-0.79299,-0.52149,659.89 > view matrix models > #1,0.98983,-0.092286,0.10823,-91.591,-0.1182,-0.95696,0.26505,411.04,0.079114,-0.27515,-0.95814,692.02 > view matrix models > #1,0.95173,-0.23289,0.19994,-76.522,-0.29832,-0.85518,0.42389,395,0.072261,-0.46307,-0.88337,713.25 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.95173,-0.23289,0.19994,56.25,-0.29832,-0.85518,0.42389,336.7,0.072261,-0.46307,-0.88337,447.64 > fitmap #1 inMap #3 Fit molecule 7k00.cif (#1) to map cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian (#3) using 149338 atoms average map value = 0.03607, steps = 1120 shifted from previous position = 6.19 rotated from previous position = 64.2 degrees atoms outside contour = 120975, contour level = 0.070321 Position of 7k00.cif (#1) relative to cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian (#3) coordinates: Matrix rotation and translation 0.54184864 -0.59482204 0.59379018 123.25184509 -0.69207264 0.08511079 0.71679257 193.25558810 -0.47690197 -0.79933902 -0.36554289 507.86969820 Axis -0.81572665 0.57606617 -0.05232389 Axis point 0.00000000 351.07738561 165.80502873 Rotation angle (degrees) 111.67194321 Shift along axis -15.78552864 > lighting soft > hide #!1 models > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > volume #3 level 0.04296 > show #!1 models > show #!2 models > hide #!1 models > hide #!3 models > show #!1 models > volume #2 level 0.2226 > hide #!2 models > show #!3 models > view matrix models > #1,0.54185,-0.59482,0.59379,113.36,-0.69207,0.085111,0.71679,231.98,-0.4769,-0.79934,-0.36554,365.48 > view matrix models > #1,0.54185,-0.59482,0.59379,103.83,-0.69207,0.085111,0.71679,261.15,-0.4769,-0.79934,-0.36554,230.59 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.95157,0.0031194,0.3074,-25.3,-0.29016,0.33943,0.89476,107.33,-0.10155,-0.94062,0.3239,55.96 > view matrix models > #1,0.2926,0.95553,-0.036771,-12.842,-0.67008,0.23232,0.70499,232.54,0.68218,-0.18164,0.70826,-299.12 > lighting simple > view matrix models > #1,0.056532,0.30319,0.95125,-39.686,0.054394,-0.9523,0.30029,393.68,0.99692,0.034767,-0.070327,-247.18 > view matrix models > #1,-0.43936,0.42169,0.79319,59.497,0.81662,-0.18042,0.54825,66.266,0.3743,0.88861,-0.26509,-251.96 > view matrix models > #1,0.49289,-0.3818,0.78185,37.951,0.84915,0.40704,-0.33655,122.38,-0.18975,0.82979,0.52483,-289.27 > view matrix models > #1,0.73673,-0.32114,-0.59506,245.66,-0.34279,-0.93594,0.080702,505.23,-0.58286,0.14453,-0.79962,160.79 > view matrix models > #1,0.63011,-0.48985,-0.6025,297.33,-0.30167,-0.86939,0.39135,426.18,-0.71551,-0.064843,-0.69559,203.31 > view matrix models > #1,0.9303,-0.21619,-0.29633,134.04,-0.078953,-0.90694,0.4138,388.06,-0.35821,-0.36156,-0.86079,223.77 > vop zflip #3 > volume zflip #3 Expected a density maps specifier or a keyword > volume flip #3 axis z Opened cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian z flip as #4, grid size 576,576,576, pixel 0.758, shown at step 1, values float32 > view matrix models > #1,0.52982,-0.46652,0.70828,60.729,0.84766,0.26401,-0.46018,172.38,0.027688,0.84419,0.53533,-333.62 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.52982,-0.46652,0.70828,19.028,0.84766,0.26401,-0.46018,99.814,0.027688,0.84419,0.53533,-41.615 > view matrix models > #1,0.52982,-0.46652,0.70828,74.97,0.84766,0.26401,-0.46018,102.98,0.027688,0.84419,0.53533,-32.703 > volume flip #2 axis z Opened cryosparc_P2_J81_007_volume_map_sharp.mrc z flip as #5, grid size 576,576,576, pixel 0.758, shown at step 1, values float32 > hide #!4 models > hide #!5 models > show #!4 models > fitmap #1 inMap #4 Fit molecule 7k00.cif (#1) to map cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian z flip (#4) using 149338 atoms average map value = 0.06778, steps = 244 shifted from previous position = 7.24 rotated from previous position = 13.1 degrees atoms outside contour = 25314, contour level = 0.04296 Position of 7k00.cif (#1) relative to cryosparc_P2_J81_007_volume_map_sharp.mrc gaussian z flip (#4) coordinates: Matrix rotation and translation 0.39703798 -0.59829171 0.69599417 130.96109092 0.89520295 0.08520064 -0.43743864 122.79336205 0.20241675 0.79673577 0.56942039 -60.22550979 Axis 0.61729315 0.24687107 0.74699655 Axis point 17.24203322 133.24637388 0.00000000 Rotation angle (degrees) 88.51991375 Shift along axis 66.16726562 > ui mousemode right translate > ui mousemode right zoom > ui mousemode right translate > ui mousemode right rotate > lighting full > hide #!4 models > show #!5 models > close #2-4 > volume #5 level 0.2519 > hide #!1 models > show #!1 models > volume style surface > lighting soft > hide #!5 models > show #!5 models > hide #!5 models > hide ~sel > show #!5 models > hide #!5 models > select #1/A:921-1396 10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected > hide > select #1/A:921-1396 10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected > show sel > show #!5 models > hide #!5 models > select sel : select sel : show sel > select up 43999 atoms, 48246 bonds, 450 pseudobonds, 2806 residues, 3 models selected > show sel > select #1/A:921-1396 10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected > select #1/A & ~sel 24642 atoms, 25176 bonds, 1443 pseudobonds, 3202 residues, 4 models selected > hide sel > select #1/A:921-1396 10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected > select protein 43768 atoms, 44383 bonds, 1 pseudobond, 5587 residues, 2 models selected > hide sel > hide > select #1/A:921-1396 10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected > show sel > select zone sel 5 protein residues true Selected 2975 atoms > show sel > select SSU_protein 19000 atoms, 19278 bonds, 2410 residues, 1 model selected > show sel > select #1/A:921-1396 10188 atoms, 11400 bonds, 487 pseudobonds, 476 residues, 2 models selected > select zone sel 5 protein residues true Selected 2975 atoms > select up 6281 atoms, 6352 bonds, 780 residues, 1 model selected > select up 10600 atoms, 10756 bonds, 1345 residues, 1 model selected > select protein & ~sel 33168 atoms, 33627 bonds, 4242 residues, 1 model selected > hide sel > hide protein > select #1/B,C 3424 atoms, 3435 bonds, 477 residues, 1 model selected > select #1/B,C,G,I,J,M,N,S 8913 atoms, 8886 bonds, 1268 residues, 1 model selected > show sel > select #1/A:921 20 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:921,1396 42 atoms, 45 bonds, 2 pseudobonds, 2 residues, 2 models selected Drag select of 19101 atoms, 487 pseudobonds > select clear Drag select of 19101 atoms, 487 pseudobonds > name frozen SSU_head sel > hide sel > show SSU_head > save ""/Users/chrst874/Postdoc/Cryo-EM/Masks/Mask selection.cxs"" > close session > open /Users/chrst874/Downloads/cryosparc_P2_J82_class_00_00035_volume.mrc Opened cryosparc_P2_J82_class_00_00035_volume.mrc as #1, grid size 160,160,160, pixel 2.73, shown at level 0.44, step 1, values float32 > open /Users/chrst874/Downloads/cryosparc_P2_J82_class_01_00035_volume.mrc Opened cryosparc_P2_J82_class_01_00035_volume.mrc as #2, grid size 160,160,160, pixel 2.73, shown at level 0.479, step 1, values float32 > open /Users/chrst874/Downloads/cryosparc_P2_J82_class_02_00035_volume.mrc Opened cryosparc_P2_J82_class_02_00035_volume.mrc as #3, grid size 160,160,160, pixel 2.73, shown at level 0.442, step 1, values float32 > hide #!3 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > show #!1 models > lighting soft > lighting full > hide #!3 models > hide #!2 models > show #!3 models > hide #!1 models > show #!2 models > show #!1 models > hide #!2 models > hide #!3 models > show #!2 models > show #!3 models > ui tool show ""Show Volume Menu"" > ui tool show ""Volume Viewer"" ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/chrst874/Downloads/cryosparc_P2_J81_007_volume_map_sharp.mrc Opened cryosparc_P2_J81_007_volume_map_sharp.mrc as #1, grid size 576,576,576, pixel 0.758, shown at level 0.164, step 4, values float32 OpenGL version: 4.1 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 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: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 577.140.2~22 Software: System Software Overview: System Version: macOS 13.6.7 (22G720) Kernel Version: Darwin 22.6.0 Time since boot: 1 day, 2 hours, 38 minutes 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: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-019 Option ROM Version: 113-D32207P1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP Z27n G2: 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: 6CM00316BF Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort HP Z27n G2: 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: 6CM0101JDD Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 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: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 Send2Trash: 1.8.2 SEQCROW: 1.8.8 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX