id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5921 Crash after running MatchMaker chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19043 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x000022a4 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x0000287c (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000039b8 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Current thread 0x00005564 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/camrh/OneDrive/Documents/488-Computational Protein > Design/pila.fasta.fasta"" Summary of feedback from opening C:/Users/camrh/OneDrive/Documents/488-Computational Protein Design/pila.fasta.fasta --- note | Alignment identifier is pila.fasta.fasta Opened 1 sequences from pila.fasta.fasta > open ""C:\Users\camrh\OneDrive\Documents\488-Computational Protein > Design\pila.fasta.fasta"" format fasta Summary of feedback from opening C:\Users\camrh\OneDrive\Documents\488-Computational Protein Design\pila.fasta.fasta --- notes | Destroying pre-existing alignment with identifier pila.fasta.fasta Alignment identifier is pila.fasta.fasta Opened 1 sequences from pila.fasta.fasta > open ""C:\Users\camrh\OneDrive\Documents\488-Computational Protein > Design\pila.fasta.fasta"" format fasta Summary of feedback from opening C:\Users\camrh\OneDrive\Documents\488-Computational Protein Design\pila.fasta.fasta --- notes | Destroying pre-existing alignment with identifier pila.fasta.fasta Alignment identifier is pila.fasta.fasta Opened 1 sequences from pila.fasta.fasta > open ""C:\Users\camrh\OneDrive\Documents\488-Computational Protein > Design\pila.fasta.fasta"" format fasta Summary of feedback from opening C:\Users\camrh\OneDrive\Documents\488-Computational Protein Design\pila.fasta.fasta --- notes | Destroying pre-existing alignment with identifier pila.fasta.fasta Alignment identifier is pila.fasta.fasta Opened 1 sequences from pila.fasta.fasta > open C:/Users/camrh/Downloads/1oqw_swiss.pdb 1oqw_swiss.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) 488 Lab 1-Vaccine Design [more info...] Chain information for 1oqw_swiss.pdb #1 --- Chain | Description A | No description available Associated 1oqw_swiss.pdb chain A to AAG07913.1 type 4 fimbrial precursor PilA [Pseudomonas aeruginosa PAO1] with 0 mismatches > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > open C:/Users/camrh/Downloads/1dzo.pdb 1dzo.pdb title: Truncated pak pilin from pseudomonas aeruginosa [more info...] Chain information for 1dzo.pdb #2 --- Chain | Description | UniProt A | type IV pilin | FMPA_PSEAE > rainbow > ui tool show Matchmaker > matchmaker #2 to #1 showAlignment true 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 1oqw_swiss.pdb, chain A (#1) with 1dzo.pdb, chain A (#2), sequence alignment score = 349.1 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 1oqw_swiss.pdb #1/A, 1dzo.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs: 2.078) > matchmaker #2 to #1 showAlignment true 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 1oqw_swiss.pdb, chain A (#1) with 1dzo.pdb, chain A (#2), sequence alignment score = 349.1 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: 1oqw_swiss.pdb #1/A, 1dzo.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs: 2.078) > color byattribute seq_conservation key true noValueColor gray > key blue-white-red :-1.12 :-0.12 :0.88 showTool true > ui mousemode right ""color key"" 2020 atoms, 394 residues, atom seq_conservation range -1.12 to 0.884 > color byattribute seq_conservation key true noValueColor gray palette > rainbow > key rainbow :-1.12 :-0.62 :-0.12 :0.38 :0.88 showTool true 2020 atoms, 394 residues, atom seq_conservation range -1.12 to 0.884 > ui mousemode right translate > color byattribute seq_conservation palette rainbow key true noValueColor > gray > key rainbow :-1.12 :-0.62 :-0.12 :0.38 :0.88 showTool true > ui mousemode right ""color key"" 2020 atoms, 394 residues, atom seq_conservation range -1.12 to 0.884 > ui mousemode right translate > color byattribute seq_rmsd palette rainbow key true noValueColor gray > key rainbow :0.03 :1.45 :2.88 :4.31 :5.74 showTool true > ui mousemode right ""color key"" 2020 atoms, 394 residues, atom seq_rmsd range 0.0254 to 5.74 > color byattribute seq_rmsd key true noValueColor gray > key blue-white-red :0.03 :2.88 :5.74 showTool true 2020 atoms, 394 residues, atom seq_rmsd range 0.0254 to 5.74 > color byattribute seq_rmsd palette rainbow key true noValueColor gray > key rainbow :0.03 :1.45 :2.88 :4.31 :5.74 showTool true 2020 atoms, 394 residues, atom seq_rmsd range 0.0254 to 5.74 > save ""C:/Chimera/1dzo homology modeling with correct seq.cxs"" > ui mousemode right translate > move #1 x 5 Missing or invalid ""axis"" argument: Axis argument requires 2 atoms, got 1043 atoms > move x 5 #1 Expected an integer >= 1 or a keyword > move x 5 #2 Expected an integer >= 1 or a keyword > help move QMainWindowLayout::tabPosition called with out-of-bounds value '0' > move x 5 models #1 > open C:/Users/camrh/Downloads/1x6r_swiss.pdb > C:/Users/camrh/Downloads/5kua_swiss.pdb 1x6r_swiss.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) 488 Lab 1-Vaccine Design [more info...] Chain information for 1x6r_swiss.pdb #4 --- Chain | Description A | No description available 5kua_swiss.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) 488 Lab 1-Vaccine Design [more info...] Chain information for 5kua_swiss.pdb #5 --- Chain | Description A | No description available Associated 1x6r_swiss.pdb chain A to AAG07913.1 type 4 fimbrial precursor PilA [Pseudomonas aeruginosa PAO1] with 0 mismatches Associated 5kua_swiss.pdb chain A to AAG07913.1 type 4 fimbrial precursor PilA [Pseudomonas aeruginosa PAO1] with 0 mismatches Associated 1x6r_swiss.pdb chain A to 1oqw_swiss.pdb, chain A with 0 mismatches Associated 5kua_swiss.pdb chain A to 1oqw_swiss.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 1: 1oqw_swiss.pdb #1/A, 1dzo.pdb #2/A, 1x6r_swiss.pdb #4/A, 5kua_swiss.pdb #5/A > move y 5 models #4 > move y 30 models #4 > move y 10 models #4 > move x 50 models #3 > move x -50 models #3 > move x 60 models #5 > move x -10 models #5 > rainbow > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > hide #4 models > hide #5 models > ui tool show Matchmaker > matchmaker #1 to #2 showAlignment true 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence alignment score = 349.1 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: 1oqw_swiss.pdb #1/A, 1dzo.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs: 2.078) > matchmaker #1 to #2 showAlignment true 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence alignment score = 349.1 Alignment identifier is 3 Showing conservation header (""seq_conservation"" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: 1oqw_swiss.pdb #1/A, 1dzo.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3 RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs: 2.078) > color byattribute seq_conservation palette rainbow key true noValueColor > gray > key rainbow :-1.12 :-0.62 :-0.12 :0.38 :0.88 showTool true > ui mousemode right ""color key"" 3241 atoms, 562 residues, atom seq_conservation range -1.12 to 0.884 > ui mousemode right translate > color byattribute seq_conservation key true noValueColor gray > key blue-white-red :-1.12 :-0.12 :0.88 showTool true > ui mousemode right ""color key"" 3241 atoms, 562 residues, atom seq_conservation range -1.12 to 0.884 > ui mousemode right translate > move x 30 models #1 > move x 10 models #1 > move y 30 models #3 > move y 3 models #3 > color byattribute seq_rmsd palette rainbow key true noValueColor gray > key rainbow :18.3 :29.9 :41.5 :53.1 :64.7 showTool true > ui mousemode right ""color key"" 3241 atoms, 562 residues, atom seq_rmsd range 18.3 to 64.7 > ui mousemode right translate > ui tool show Matchmaker > matchmaker #1 to #2 showAlignment true 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence alignment score = 349.1 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 1oqw_swiss.pdb #1/A, 1dzo.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs: 2.078) > matchmaker #1 to #2 showAlignment true 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence alignment score = 349.1 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: 1oqw_swiss.pdb #1/A, 1dzo.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs: 2.078) ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/camrh/Downloads/1oqw_swiss.pdb 1oqw_swiss.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) 488 Lab 1-Vaccine Design [more info...] Chain information for 1oqw_swiss.pdb #1 --- Chain | Description A | No description available > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > open C:/Users/camrh/Downloads/1dzo.pdb 1dzo.pdb title: Truncated pak pilin from pseudomonas aeruginosa [more info...] Chain information for 1dzo.pdb #2 --- Chain | Description | UniProt A | type IV pilin | FMPA_PSEAE > color gray > ui tool show Matchmaker > matchmaker #1 to #2 showAlignment true 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 1dzo.pdb, chain A (#2) with 1oqw_swiss.pdb, chain A (#1), sequence alignment score = 349.1 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 1oqw_swiss.pdb #1/A, 1dzo.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 96 pruned atom pairs is 0.442 angstroms; (across all 118 pairs: 2.078) OpenGL version: 3.3.13521 Core Profile Forward-Compatible Context 24.20.11001.8003 OpenGL renderer: Radeon RX Vega M GL Graphics OpenGL vendor: ATI Technologies Inc. Manufacturer: Dell Inc. Model: XPS 15 9575 OS: Microsoft Windows 10 Home (Build 19043) Memory: 16,982,163,456 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-8705G CPU @ 3.10GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 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: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal UI can't reproduce Tom Goddard all ChimeraX