id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20310 Crash deleting a QDockWidget involving QWindowContainer::parentWasChanged chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.4.1-arm64-arm-64bit ChimeraX Version: 1.12.dev202603022002 (2026-03-02 20:02:06 UTC) Description Last time you used ChimeraX it crashed. 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""65a8173205d942272410674b"", ""factorPackIds"" : [ ""65d39fa4cb0e2417d11ce5f6"" ], ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""67d07cd6a7affa169ae21f45"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } Log: UCSF ChimeraX version: 1.12.dev202603022002 (2026-03-02) © 2016-2026 Regents of the University of California. All rights reserved. > open ""/Users/tj4488/Library/Mobile > Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA > project/4_NC_reviewer comments/3_experiments/3.4_Chimera X analysis/2_iadDE > compare to 7YLS.cxs"" Log from Tue Mar 3 19:47:08 2026UCSF ChimeraX version: 1.12.dev202603022002 (2026-03-02) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/tj4488/Library/Mobile > Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA > project/2_items/2_Protein and crystal > structure/2_iadDE/1.3_structure/1.2_model1c_refine_001.pdb"" Summary of feedback from opening /Users/tj4488/Library/Mobile Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA project/2_items/2_Protein and crystal structure/2_iadDE/1.3_structure/1.2_model1c_refine_001.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2022-10-18 Time 14:28:29 EDT -0400 (1666117709.28 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : jc12-4-fast_dp-truncated-unique.mtz 36 messages similar to the above omitted Chain information for 1.2_model1c_refine_001.pdb #1 --- Chain | Description A | No description available B | No description available Computing secondary structure > open ""/Users/tj4488/Library/Mobile > Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA > project/2_items/2_Protein and crystal > structure/2_iadDE/1.3_structure/2.1_model1h_refmac1_expanded.pdb"" 2.1_model1h_refmac1_expanded.pdb title: \--- [more info...] Chain information for 2.1_model1h_refmac1_expanded.pdb #2 --- Chain | Description A C E | No description available B D F | No description available Non-standard residues in 2.1_model1h_refmac1_expanded.pdb #2 --- EDO — (EDO) FES — (FES) ZN — (ZN) 315 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open ""/Users/tj4488/Library/Mobile > Documents/com~apple~CloudDocs/5_work_princeton/1_projects/1_IAA > project/2_items/2_Protein and crystal > structure/2_iadDE/1.3_structure/2.2_model1h_refmac1.pdb"" 2.2_model1h_refmac1.pdb title: \--- [more info...] Chain information for 2.2_model1h_refmac1.pdb #3 --- Chain | Description A | No description available B | No description available Non-standard residues in 2.2_model1h_refmac1.pdb #3 --- EDO — (EDO) FES — (FES) ZN — (ZN) 105 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > hide #!1 models > hide #!3 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > close #1 > close #2 > open 7YLS.pdb No such file/path: 7YLS.pdb > open /Users/tj4488/Desktop/7YLS.cif Summary of feedback from opening /Users/tj4488/Desktop/7YLS.cif --- notes | Fetching CCD ACT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif Fetching CCD FE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif Fetching CCD FES from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/FES/FES.cif Fetching CCD GOL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif 7YLS.cif title: Structure of a bacteria protein complex [more info...] Chain information for 7YLS.cif #1 --- Chain | Description | UniProt A | Aromatic-ring-hydroxylating dioxygenase beta subunit | C5CSP7_VARPS 1-162 B | Rieske (2Fe-2S) domain protein | C5CSP6_VARPS 1-437 Non-standard residues in 7YLS.cif #1 --- ACT — acetate ion FE — Fe (III) ion FES — FE2/S2 (inorganic) cluster GOL — glycerol (glycerin; propane-1,2,3-triol) 4807 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > 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 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3), sequence alignment score = 2230.9 RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs: 0.924) > cartoon > color cyan #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color orange #3 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 40 #3 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > cartoon > color cyan #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > cartoon > color cyan #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color orange #3 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 40 #3 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > cartoon [Repeated 1 time(s)] > color cyan cartoons #1 Expected ',' or a keyword > color orange cartoons #3 Expected ',' or a keyword > cartoon > hide atoms > color cyan #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color orange #3 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 40 #3 target c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > rmsd #3 to #1 perResidue true Expected a keyword > 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 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3), sequence alignment score = 2230.9 RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs: 0.924) > rmsd #3 to #1 Number of atoms from first atom spec (5625) differs from number in second (9866) > select add #1 9866 atoms, 9516 bonds, 9 pseudobonds, 1072 residues, 2 models selected > select add #3 15491 atoms, 14432 bonds, 18 pseudobonds, 2502 residues, 4 models selected > select subtract #3 9866 atoms, 9516 bonds, 9 pseudobonds, 1072 residues, 2 models selected > select subtract #1 Nothing selected > color cyan #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > cartoon > color cyan models #1 Expected ',' or a keyword > toolshed show > show target ab > color #1 #00c8b3ff > color #3 #f2a350ff > transparency 50 > 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 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3), sequence alignment score = 2230.9 RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs: 0.924) > morph #1 #2 Require at least 2 structures for morph > morph #1 #3 Computed 51 frame morph #2 > coordset #2 1,51 > distance #1@ca #3@ca Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 1188 atoms and 0 measurable objects > transparency 50 #3 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > movie record > movie encode /Users/tj4488/Desktop/movie1.mp4 framerate 25.0 Movie saved to /Users/tj4488/Desktop/movie1.mp4 > show #2 target ab > select add #2 844 atoms, 838 bonds, 4 pseudobonds, 135 residues, 2 models selected > close #2 No visible models! > show #!1 models > show #!3 models > transparency cartoons 50 #3 Missing or invalid ""percent"" argument: Expected a number > transparency #3 50 target c > 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 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3), sequence alignment score = 2230.9 RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs: 0.924) > show #!1 target m > view #1 clip false > select add #1 9866 atoms, 9516 bonds, 9 pseudobonds, 1072 residues, 2 models selected > select add #3 15491 atoms, 14432 bonds, 18 pseudobonds, 2502 residues, 4 models selected > transparency (#!1,3 & sel) 70 > select subtract #3 9866 atoms, 9516 bonds, 9 pseudobonds, 1072 residues, 2 models selected > select subtract #1 Nothing selected > rmsd #1 to #3 perResidue true Expected a keyword > rmsd #1 to #3 perResidue Expected a keyword > align #1 toAtoms #3 Unequal number of atoms to pair, 9866 and 5625 > matchmaker #1 to #3 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 2.2_model1h_refmac1.pdb, chain A (#3) with 7YLS.cif, chain B (#1), sequence alignment score = 2230.9 RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs: 0.924) > help matchmaker > mmaker #3/A to #1/B 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 7YLS.cif, chain B (#1) with 2.2_model1h_refmac1.pdb, chain A (#3), sequence alignment score = 2230.9 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: 7YLS.cif #1/B, 2.2_model1h_refmac1.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 418 pruned atom pairs is 0.419 angstroms; (across all 435 pairs: 0.924) > select #1/B:234 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:234-240 104 atoms, 105 bonds, 7 residues, 1 model selected > select #1/B:234 #3/A:234 20 atoms, 18 bonds, 2 residues, 2 models selected > select #1/B:226 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/B:226-300 1155 atoms, 1175 bonds, 75 residues, 1 model selected > hide atoms > show cartoons > select #3/A:234 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:234-240 57 atoms, 58 bonds, 7 residues, 1 model selected > select #1/B:245 #3/A:245 23 atoms, 21 bonds, 2 residues, 2 models selected > mmaker #3/B to #1/A 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 7YLS.cif, chain A (#1) with 2.2_model1h_refmac1.pdb, chain B (#3), sequence alignment score = 839.4 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: 7YLS.cif #1/A, 2.2_model1h_refmac1.pdb #3/B Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 158 pruned atom pairs is 0.190 angstroms; (across all 158 pairs: 0.190) > select #1/B:280 #3/A:280 22 atoms, 21 bonds, 2 residues, 2 models selected > select #1/B:280 17 atoms, 17 bonds, 1 residue, 1 model selected > select #1/B:280-292 186 atoms, 189 bonds, 13 residues, 1 model selected > save ""/Users/tj4488/Desktop/iadDE compare to 7YLS.cxs"" ——— End of log from Tue Mar 3 19:47:08 2026 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PySide6 6.10.1, Qt 6.10.1 Qt runtime version: 6.10.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,9 Model Number: Z1AF001AGLL/A Chip: Apple M3 Max Total Number of Cores: 16 (12 Performance and 4 Efficiency) Memory: 64 GB System Firmware Version: 18000.101.7 OS Loader Version: 18000.101.7 Software: System Software Overview: System Version: macOS 26.4.1 (25E253) Kernel Version: Darwin 25.4.0 Time since boot: 2 hours, 49 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 40 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: DELL U2412M: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.1.1 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.64.1 ChimeraX-AtomicLibrary: 14.2.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12.dev202603022002 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.3 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.18 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.5 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 ChimeraX-MutationScores: 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.5.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.5 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.3 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.1 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.4 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.6 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.9.2 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.13.1 pydantic_core: 2.41.5 pydata-sphinx-theme: 0.16.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.0 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PySide6: 6.10.1 PySide6_Addons: 6.10.1 PySide6_Essentials: 6.10.1 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.22 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.1 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 shiboken6: 6.10.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.3.2 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.41.0 wcwidth: 0.6.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.23.0 }}} " defect closed normal Window Toolkit duplicate chimera-programmers all ChimeraX