id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6587 PDB format cristina.viola@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Hello, When I save my model as a PDB file, colouring of the model is not preserved. If I reopen the newly created PDB in ChimeraX all the colour changes are lost. Am I saving incorrectly? Many thanks for any advice, Cristina Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs > format session Log from Mon Apr 11 22:00:23 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs > format session Log from Mon Feb 7 14:45:13 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs Log from Mon Feb 7 14:28:24 2022UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/ysblnfs/people/cv558/moro/DATA/EM/dmIRholo1_Diamond2020/SPA4/Marek_IRviews_super_220203/IRaligned_fn1.cxs > To Restore session: > > * update Atomic bundle to version 1.31 or newer (have 1.13.2) > Unable to restore session: need to update bundle > open > /Volumes/ysblnfs/people/cv558/moro/DATA/EM/dmIRholo1_Diamond2020/SPA4/Marek_IRviews_super_220203/2_6SOFcolor.pdb.pdb > /Volumes/ysblnfs/people/cv558/moro/DATA/EM/dmIRholo1_Diamond2020/SPA4/Marek_IRviews_super_220203/2_7pg0.pdb.pdb > /Volumes/ysblnfs/people/cv558/moro/DATA/EM/dmIRholo1_Diamond2020/SPA4/Marek_IRviews_super_220203/2_dIR_01_real_space_refined_008.pdb.pdb 2_6SOFcolor.pdb.pdb title: Human insulin receptor ectodomain bound by 4 insulin [more info...] Chain information for 2_6SOFcolor.pdb.pdb #1 --- Chain | Description A C | IR B D | IR E G I K | insulin F H J L | insulin 2_7pg0.pdb.pdb title: Low resolution cryo-em structure of full-length insulin receptor bound to 3 insulin with visible DDM micelle, conf 1 [more info...] Chain information for 2_7pg0.pdb.pdb #2 --- Chain | Description A B | IR C E I | insulin D F J | insulin Chain information for 2_dIR_01_real_space_refined_008.pdb.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs ——— End of log from Mon Feb 7 14:28:24 2022 ——— opened ChimeraX session > show atoms > hide atoms > show cartoons > ui tool show Matchmaker > ui tool show ""Model Panel"" > select #3/A800-920 Nothing selected > select #3/A:800-920 928 atoms, 946 bonds, 121 residues, 1 model selected > matchmaker #!2 to #1 & sel No 'to' model specified > matchmaker #!2 to #3/A & sel pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2_dIR_01_real_space_refined_008.pdb.pdb, chain A (#3) with 2_7pg0.pdb.pdb, chain A (#2), sequence alignment score = 157.6 RMSD between 63 pruned atom pairs is 0.946 angstroms; (across all 107 pairs: 7.304) > 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 > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > hide #!2 models > show #!2 models > show #3 models > hide #3 models > show #3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 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 > 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 > 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 #!2 models > show #!2 models > show #3 models > hide #3 models > show #3 models > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs > matchmaker #1 to #3/A & sel pairing bs Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2_dIR_01_real_space_refined_008.pdb.pdb, chain A (#3) with 2_6SOFcolor.pdb.pdb, chain C (#1), sequence alignment score = 136 RMSD between 64 pruned atom pairs is 0.899 angstroms; (across all 106 pairs: 6.486) > hide #!2 models > show #!2 models > hide #3 models > show #3 models > hide #!2 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > show #!2 models > hide #3 models > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs ——— End of log from Mon Feb 7 14:45:13 2022 ——— opened ChimeraX session > hide #!2 models > show #!2 models > hide #1 models > hide #!2 models > show #!2 models > show #3 models > hide #3 models > hide #!2 models > show #3 models > show #!2 models > hide #3 models > show #3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #3 models > show #3 models > show #1 models > hide #!2 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #1 models > show #1 models > hide #3 models > show #!2 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 > show #!2 models > hide #!2 models > show #3 models > hide #3 models > show #!2 models > hide #!2 models > show #3 models > hide #3 models > show #3 models > show #!2 models > hide #!2 models > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs > includeMaps true > select up 1098 atoms, 1120 bonds, 143 residues, 1 model selected > select down 928 atoms, 946 bonds, 121 residues, 1 model selected > select up 1098 atoms, 1120 bonds, 143 residues, 1 model selected > select up 6841 atoms, 6994 bonds, 863 residues, 1 model selected > select #1/C:429-600 2713 atoms, 2754 bonds, 172 residues, 1 model selected > select down 3811 atoms, 3874 bonds, 315 residues, 2 models selected > select up 3845 atoms, 3910 bonds, 317 residues, 2 models selected > select down 3811 atoms, 3874 bonds, 315 residues, 2 models selected > select #1/C:429-600 2713 atoms, 2754 bonds, 172 residues, 1 model selected > select #3/A:920-1200 1338 atoms, 1367 bonds, 161 residues, 1 model selected > select #1/C:429-600 2713 atoms, 2754 bonds, 172 residues, 1 model selected > select up 2747 atoms, 2790 bonds, 174 residues, 1 model selected > select up 11118 atoms, 11280 bonds, 719 residues, 1 model selected > select up 30333 atoms, 30770 bonds, 1966 residues, 1 model selected > select up 59218 atoms, 60367 bonds, 5607 residues, 3 models selected > select up 59218 atoms, 60367 bonds, 5607 residues, 3 models selected > select down 30333 atoms, 30770 bonds, 1966 residues, 1 model selected > select down 11118 atoms, 11280 bonds, 719 residues, 1 model selected > select down 2747 atoms, 2790 bonds, 174 residues, 1 model selected > select down 2713 atoms, 2754 bonds, 172 residues, 1 model selected > select #1/D:600-810 859 atoms, 868 bonds, 55 residues, 1 model selected > select #1/D:600-810 859 atoms, 868 bonds, 55 residues, 1 model selected > select #2/A:700-900 1137 atoms, 1163 bonds, 1 pseudobond, 142 residues, 2 models selected > show #!2 models > select #2/A:700-900 1137 atoms, 1163 bonds, 1 pseudobond, 142 residues, 2 models selected > ui tool show Matchmaker > select #3/A800-920 Nothing selected > select #3/A:800-920 928 atoms, 946 bonds, 121 residues, 1 model selected > select up 1098 atoms, 1120 bonds, 143 residues, 1 model selected > select up 6841 atoms, 6994 bonds, 863 residues, 1 model selected > hide #3 models > hide #!2 models > hide #1 models > show #1 models > hide #1 models > show #3 models > show #1 models > hide #3 models > select #2/A:800-920 872 atoms, 895 bonds, 108 residues, 1 model selected > select #1/A:800-920 Nothing selected > select #1/D:600-810 859 atoms, 868 bonds, 55 residues, 1 model selected > select up 893 atoms, 902 bonds, 58 residues, 1 model selected > select up 2508 atoms, 2541 bonds, 162 residues, 1 model selected > select up 30333 atoms, 30770 bonds, 1966 residues, 1 model selected > select down 2508 atoms, 2541 bonds, 162 residues, 1 model selected > select #1/A 11127 atoms, 11290 bonds, 719 residues, 1 model selected > select #1/B 2532 atoms, 2565 bonds, 162 residues, 1 model selected > select #1/C 11118 atoms, 11280 bonds, 719 residues, 1 model selected > select #1/D 2508 atoms, 2541 bonds, 162 residues, 1 model selected > show #3 models > hide #3 models > ui tool show ""Color Actions"" > color sel slate blue > select #1/C 11118 atoms, 11280 bonds, 719 residues, 1 model selected > color sel slate blue > select #1/A 11127 atoms, 11290 bonds, 719 residues, 1 model selected > color sel light salmon > color sel salmon > color sel dark salmon > color sel salmon > select #1/B 2532 atoms, 2565 bonds, 162 residues, 1 model selected > color sel salmon > show #!2 models > show #3 models > select clear > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #!2 models > hide #1 models > hide #3 models > show #!2 models > show #1 models > hide #!2 models > show #!2 models > show #3 models > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs > includeMaps true > hide #!2 models > hide #1 models No model chosen to save relative to > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/NAME_.pdb > relModel #3 > open > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/NAME_.pdb Summary of feedback from opening /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/NAME_.pdb --- warnings | Start residue of secondary structure not found: HELIX 9 9 ASP A 689 PHE A 714 1 26 Start residue of secondary structure not found: HELIX 11 11 ASN C 16 GLU C 24 1 9 Start residue of secondary structure not found: HELIX 12 12 ARG C 42 LEU C 49 1 8 Start residue of secondary structure not found: HELIX 13 13 ASN C 148 GLU C 153 1 6 Start residue of secondary structure not found: HELIX 14 14 PRO C 193 LYS C 197 1 5 157 messages similar to the above omitted NAME_.pdb title: Human insulin receptor ectodomain bound by 4 insulin [more info...] Chain information for NAME_.pdb --- Chain | Description 4.1/A 4.1/C | IR 4.2/A | IR 4.3/A | IR 4.1/B 4.1/D | IR 4.2/B | IR 4.3/B | IR 4.2/C | IR 4.3/C | IR 4.2/D | IR 4.3/D | IR 4.1/E 4.2/E 4.1/G 4.1/I 4.2/I 4.1/K | insulin 4.3/E | insulin 4.1/F 4.1/H 4.1/J 4.1/L | insulin 4.2/F 4.2/J | insulin 4.3/F | insulin 4.3/G | insulin 4.3/H | insulin 4.3/I | insulin 4.3/J | insulin > hide #4.1 models > show #4.1 models > hide #!4.2 models > show #!4.2 models > hide #4.3 models > show #4.3 models > close #4 > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/[NAME]_.pdb > relModel #3 > open > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/2_6SOFcolor.pdb.pdb_.pdb 2_6SOFcolor.pdb.pdb_.pdb title: Human insulin receptor ectodomain bound by 4 insulin [more info...] Chain information for 2_6SOFcolor.pdb.pdb_.pdb #4 --- Chain | Description A C | IR B D | IR E G I K | insulin F H J L | insulin > open > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/2_7pg0.pdb.pdb_.pdb 2_7pg0.pdb.pdb_.pdb title: Low resolution cryo-em structure of full-length insulin receptor bound to 3 insulin with visible DDM micelle, conf 1 [more info...] Chain information for 2_7pg0.pdb.pdb_.pdb #5 --- Chain | Description A B | IR C E I | insulin D F J | insulin > open > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test_saving_alignedPDBs/2_dIR_01_real_space_refined_008.pdb.pdb_.pdb Chain information for 2_dIR_01_real_space_refined_008.pdb.pdb_.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available > hide #4 models > show #4 models > hide #3 models > hide #4 models > hide #!5 models > hide #6 models > show #3 models > hide #3 models > show #4 models > show #!5 models > show #6 models > hide #6 models > hide #!5 models > hide #4 models > show #1 models > show #4 models > show #!5 models > show #6 models > hide #1 models > close #4,6#5 > show #3 models > show #1 models > save > /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/colour.cxs > includeMaps true ——— End of log from Mon Apr 11 22:00:23 2022 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-14.7.18 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0) Software: System Software Overview: System Version: macOS 10.15.7 (19H1323) Kernel Version: Darwin 19.6.0 Time since boot: 15 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Input/Output not a bug all ChimeraX