id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8890 Crash after saving movie chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6rc202304202331 (2023-04-20 23:31:10 UTC) Description Last time you used ChimeraX it crashed. 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""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold predict > RHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRSAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIV Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction > open 1ujc 1ujc title: Structure of the protein histidine phosphatase SixA complexed with tungstate [more info...] Chain information for 1ujc #1 --- Chain | Description | UniProt A | Phosphohistidine phosphatase sixA | SIXA_ECOLI Non-standard residues in 1ujc #1 --- CA — calcium ion WO4 — tungstate(VI)ion > open 2hur 2hur title: Escherichia coli nucleoside diphosphate kinase [more info...] Chain information for 2hur #2 --- Chain | Description | UniProt A B C D E F | NUCLEOSIDE DIPHOSPHATE KINASE | NDK_ECOLI Non-standard residues in 2hur #2 --- SO4 — sulfate ion 2hur mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| software_defined_assembly 4| software_defined_assembly 5| software_defined_assembly > style stick Changed 8644 atom styles > style stick Changed 8644 atom styles > rainbow > hide #!1 models > show #!1 models > show cartoons > hide atoms > color #2 #ff2907ff > color #2 #9f9cffff > color #1 #2ddb5bff > color #1 #28db42ff > mmaker > matchmaker Missing or invalid ""matchAtoms"" argument: empty atom specifier > mmaker 1ujc 2hur > matchmaker 1ujc 2hur Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > mmaker 1ujc > matchmaker 1ujc Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > ui tool show Matchmaker > matchmaker #2 to #1 Parameters --- Chain pairing | bb 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 1ujc, chain A (#1) with 2hur, chain D (#2), sequence alignment score = 42.4 RMSD between 6 pruned atom pairs is 1.289 angstroms; (across all 69 pairs: 15.519) > select #2/A:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > select #2/B:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > select #2/C:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > select #2/D:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > select add #2 7239 atoms, 6642 bonds, 1575 residues, 1 model selected > select subtract #2 Nothing selected > select add #2 7239 atoms, 6642 bonds, 1575 residues, 1 model selected > select subtract #2 Nothing selected AlphaFold prediction finished Results in /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_3 > open /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb Chain information for best_model.pdb #3 --- Chain | Description A | No description available > hide #3 models > select #2/A:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > hide sel atoms > select #2/A:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > select #2/A:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > hide sel cartoons > select #2/B:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > hide sel cartoons > select #2/C:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > hide sel cartoons > select #2/D:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > select #2/E:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > hide sel cartoons > select #2/F:2-143 1082 atoms, 1103 bonds, 142 residues, 1 model selected > hide sel cartoons > hide #2 models > show #2 models > hide #2 models > show #3 models > ui tool show Matchmaker > matchmaker #3 to #1 Parameters --- Chain pairing | bb 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 1ujc, chain A (#1) with best_model.pdb, chain A (#3), sequence alignment score = 146.8 RMSD between 61 pruned atom pairs is 0.852 angstroms; (across all 127 pairs: 12.283) > show #2 models > lighting simple > graphics silhouettes true > graphics silhouettes false > lighting shadows true > ui tool show ""Side View"" > view orient > hide #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 #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 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 > open 3mxo Summary of feedback from opening 3mxo fetched from pdb --- notes | Fetching compressed mmCIF 3mxo from http://files.rcsb.org/download/3mxo.cif Fetching CCD EDO from http://ligand-expo.rcsb.org/reports/E/EDO/EDO.cif Fetching CCD PG4 from http://ligand-expo.rcsb.org/reports/P/PG4/PG4.cif Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif Fetching CCD PEG from http://ligand-expo.rcsb.org/reports/P/PEG/PEG.cif 3mxo title: Crystal structure oh human phosphoglycerate mutase family member 5 (PGAM5) [more info...] Chain information for 3mxo #4 --- Chain | Description | UniProt A B | Serine/threonine-protein phosphatase PGAM5, mitochondrial | PGAM5_HUMAN Non-standard residues in 3mxo #4 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) PEG — di(hydroxyethyl)ether PG4 — tetraethylene glycol PGE — triethylene glycol 3mxo mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly > hide #!1,4 atoms > ui tool show Matchmaker > matchmaker #!4 to #1 Parameters --- Chain pairing | bb 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 1ujc, chain A (#1) with 3mxo, chain B (#4), sequence alignment score = 214.1 RMSD between 94 pruned atom pairs is 0.950 angstroms; (across all 152 pairs: 7.474) > select #4/A:88-289 1500 atoms, 1530 bonds, 1 pseudobond, 188 residues, 2 models selected > hide sel cartoons > show #3 models > color #4 #eeaf73ff > color #4 #ee9045ff > color #4 #ee614dff > color #4 #ee4fe0ff > color #4 #ecee30ff > color #4 #ee9e1aff > hide #!4 models > show #2 models > hide #2 models > show #!4 models Populating font family aliases took 467 ms. Replace uses of missing font family ""Consolas"" with one that exists to avoid this cost. > alphafold predict > MAFRQALQLAACGLAGGSAAVLFSAVAVGKPRAGGDAEPRPAEPPAWAGGARPGPGVWDPNWDRREPLSLINVRKRLDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS Running AlphaFold prediction > hide #!1 models > hide #3 models > show #3 models > hide #!4 models > hide #3 models > show #!4 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models AlphaFold prediction finished Results in /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_4 > open /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_4/best_model.pdb Chain information for best_model.pdb #5 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #5 to #1 Parameters --- Chain pairing | bb 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 1ujc, chain A (#1) with best_model.pdb, chain A (#5), sequence alignment score = 194.4 RMSD between 94 pruned atom pairs is 0.918 angstroms; (across all 153 pairs: 8.270) > show #!1 models > hide #!4 models > hide #5 models > select his 8 Expected an objects specifier or a keyword > select 1ujc, his8 Expected an objects specifier or a keyword > select ::name=""HIS"" 630 atoms, 630 bonds, 63 residues, 5 models selected > show sel & #!1 atoms > rainbow sel & #!1 > show #!4 models > hide #!1 models > show sel & #!4 atoms > show #!1 models > show #5 models > hide #!1 models > hide #!4 models > nucleotides sel & #5 atoms > style nucleic & sel & #5 stick Changed 0 atom styles > show sel & #5 atoms > rainbow sel & #5 > show #!4 models > show #!1 models > hide #!4 models > hide #!1 models > show #!1 models > hide #5 models > show #5 models > show #!4 models > hide #!1 models > hide #!4 models > show #!1 models > hide #!1 models > show #!4 models > hide #!4 models > show #!4 models > color sel & #5#!4 bychain > select > ::name=""CA""::name=""CL""::name=""EDO""::name=""HOH""::name=""PEG""::name=""PG4""::name=""PGE""::name=""SO4""::name=""WO4"" 1386 atoms, 100 bonds, 5 pseudobonds, 1286 residues, 4 models selected > select #1/A 1405 atoms, 1190 bonds, 7 pseudobonds, 392 residues, 2 models selected > show #3 models > hide #3,5#!4 atoms > color #3,5#!4 byhetero > show #3,5#!4 surfaces > show #!3-5 surfaces > alphafold predict > VESGEEELASKLDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGLRLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRADARQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNNGSITHLVIRPNGRVALRTLGDTGFMPPDKITRS Running AlphaFold prediction > hide #!3-5 surfaces > hide #!4 models > hide #!3 models AlphaFold prediction finished Results in /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_5 > open /Users/akash/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb Chain information for best_model.pdb #6 --- Chain | Description A | No description available > select subtract #1 Nothing selected > hide #!5 models > show #!5 models > ui tool show Matchmaker > matchmaker #6 to #1 Parameters --- Chain pairing | bb 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 1ujc, chain A (#1) with best_model.pdb, chain A (#6), sequence alignment score = 194.4 RMSD between 94 pruned atom pairs is 0.915 angstroms; (across all 153 pairs: 8.313) > show #!4 models > hide #!5 models > show #!5 models > hide #6 models > show #6 models > hide #!5 models > show #!1 models > show #!5 models > hide #6 models > hide #!4 models > show #!1,5 surfaces > hide #!1,5 surfaces > hide #!1 models > show #!5 surfaces > show #!4 models > hide #!4-5 surfaces > hide #!4 models > hide #!5 models > show #2 models > show #!1 models > hide #2 models > show #!5 models > turn y 1 360 > set bgColor white > movie record > turn y 1 360 > wait > movie encode Movie saved to /Users/akash/Desktop/movie.mp4 > hide #!5 models > show #!4 models > hide #!1 models > rainbow #!4 > show #!4 cartoons > select #4/B:88-289 1514 atoms, 1544 bonds, 1 pseudobond, 191 residues, 2 models selected > show #!1 models > select #4/B:88-289 1514 atoms, 1544 bonds, 1 pseudobond, 191 residues, 2 models selected > select #4/B:88-289 1514 atoms, 1544 bonds, 1 pseudobond, 191 residues, 2 models selected > select #4/B:88-289 1514 atoms, 1544 bonds, 1 pseudobond, 191 residues, 2 models selected > select #4/A:88-289 1500 atoms, 1530 bonds, 1 pseudobond, 188 residues, 2 models selected > hide sel cartoons > hide #!4 models > show #!4 models > hide #!1 models > color (#!4 & sel) byhetero > color (#!4 & sel) #cdffd6ff > color (#!4 & sel) #cffff0ff > color (#!4 & sel) #b6daffff > color (#!4 & sel) #7990ffff > color (#!4 & sel) #667bffff > color (#!4 & sel) #6174ffff > color (#!4 & sel) #5e73ffff > color (#!4 & sel) #516affff > color (#!4 & sel) #4a63ffff > color (#!4 & sel) #4963ffff > color (#!4 & sel) #4962ffff > color (#!4 & sel) #4a62ffff > color (#!4 & sel) #5060ffff > color (#!4 & sel) #585bffff > color (#!4 & sel) #5d5bffff > color (#!4 & sel) #5e5cffff > select add #4 3413 atoms, 3146 bonds, 2 pseudobonds, 706 residues, 3 models selected > color (#!4 & sel) byhetero > color (#!4 & sel) blue > color (#!4 & sel) light sea green > color (#!4 & sel) cornflower blue > select subtract #4 2 models selected > show #!1 models > movie record > turn y 1 360 > wait > movie encode Movie saved to /Users/akash/Desktop/movie.mp4 > hide #!1 models > show #!3 models > hide #!3 models > show #!5 models > hide #!4 models > show #6 models > hide #!5 models > show #!1 models > movie record > turn y 1 360 > wait > movie encode Movie saved to /Users/akash/Desktop/movie.mp4 > show #!5 models > hide #6 models > movie record > turn y 1 360 > wait > movie encode Movie saved to /Users/akash/Desktop/movie.mp4 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.6rc202304202331 (2023-04-20) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.2.44 OpenGL renderer: Intel(R) UHD Graphics 617 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir8,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0) OS Loader Version: 564.40.4~27 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 22 minutes, 33 seconds Graphics/Displays: Intel UHD Graphics 617: Chipset Model: Intel UHD Graphics 617 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x87c0 Revision ID: 0x0002 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9 ChimeraX-AddH: 2.2.4 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6rc202304202331 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 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: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 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-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 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: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 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: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.2.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Input/Output can't reproduce all ChimeraX