id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15743 Index out of bounds morphing morphs gbrierley@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.8rc202405230136 (2024-05-23 01:36:41 UTC) Description Attempting to morph two previous morphs of two strucutres each. Attempting to morph the strucutres directly results in movements that are not physically possible Log: UCSF ChimeraX version: 1.8rc202405230136 (2024-05-23) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/gemmabrierley/Library/CloudStorage/OneDrive- > RoyalVeterinaryCollege/Documents/Research/INSR Structure-Function/7sti.pdb1"" 7sti.pdb1 title: Full-length insulin receptor bound with unsaturated insulin WT (1 insulin bound) asymmetric conformation [more info...] Chain information for 7sti.pdb1 #1 --- Chain | Description A B | No description available C | No description available > delete /C > select /A /B 13155 atoms, 13509 bonds, 14 pseudobonds, 1630 residues, 2 models selected > hide sel atoms > hide sel cartoons > show sel surfaces > colour sel grey > open ""/Users/gemmabrierley/Library/CloudStorage/OneDrive- > RoyalVeterinaryCollege/Documents/Research/INSR Structure-Function/7stj.pdb1"" 7stj.pdb1 title: Full-length insulin receptor bound with unsaturated insulin WT (2 insulins bound) asymmetric conformation (conformation 1) [more info...] Chain information for 7stj.pdb1 #2 --- Chain | Description A B | No description available C D | No description available > delete /c /d > select /A /B 25974 atoms, 26676 bonds, 29 pseudobonds, 3213 residues, 4 models selected > colour sel dark grey > hide sel atoms > hide sel cartoons > show sel surfaces > matchmaker #1 to #2 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 7stj.pdb1, chain B (#2) with 7sti.pdb1, chain B (#1), sequence alignment score = 6110.3 RMSD between 761 pruned atom pairs is 0.908 angstroms; (across all 792 pairs: 2.589) > morph #1,2 frames 40 Computed 41 frame morph #3 > coordset #3 1,41 > show #!3 cartoons > close session The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open ""/Users/gemmabrierley/Library/CloudStorage/OneDrive- > RoyalVeterinaryCollege/Documents/Research/INSR Structure-Function/7sti.pdb1"" 7sti.pdb1 title: Full-length insulin receptor bound with unsaturated insulin WT (1 insulin bound) asymmetric conformation [more info...] Chain information for 7sti.pdb1 #1 --- Chain | Description A B | No description available C | No description available > delete /c > open ""/Users/gemmabrierley/Library/CloudStorage/OneDrive- > RoyalVeterinaryCollege/Documents/Research/INSR Structure-Function/7stj.pdb1"" 7stj.pdb1 title: Full-length insulin receptor bound with unsaturated insulin WT (2 insulins bound) asymmetric conformation (conformation 1) [more info...] Chain information for 7stj.pdb1 #2 --- Chain | Description A B | No description available C D | No description available > delete /c /d > open ""/Users/gemmabrierley/Library/CloudStorage/OneDrive- > RoyalVeterinaryCollege/Documents/Research/INSR Structure-Function/7sth.pdb1"" 7sth.pdb1 title: Full-length insulin receptor bound with unsaturated insulin WT (2 insulin bound) symmetric conformation [more info...] Chain information for 7sth.pdb1 #3 --- Chain | Description A B | No description available C D | No description available > delete /c /d > matchmaker #1,2 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 7sth.pdb1, chain A (#3) with 7sti.pdb1, chain B (#1), sequence alignment score = 6080.3 RMSD between 316 pruned atom pairs is 1.316 angstroms; (across all 811 pairs: 8.425) Matchmaker 7sth.pdb1, chain B (#3) with 7stj.pdb1, chain B (#2), sequence alignment score = 6043.1 RMSD between 310 pruned atom pairs is 1.321 angstroms; (across all 796 pairs: 6.094) > morph #1, 2, 3 frames 100 Computed 201 frame morph #4 > coordset #4 1,201 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > delete #4 > select add #1 13155 atoms, 13509 bonds, 14 pseudobonds, 1630 residues, 2 models selected > select subtract #1 Nothing selected > show #!1 models > show #!2 models > show #!3 models > morph #1,2,3 frames 100 Computed 201 frame morph #4 > coordset #4 1,201 > delete #4 > show #!1 models > show #!2 models > show #!3 models > matchmaker #1,2 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 7sth.pdb1, chain A (#3) with 7sti.pdb1, chain B (#1), sequence alignment score = 6080.3 RMSD between 316 pruned atom pairs is 1.316 angstroms; (across all 811 pairs: 8.425) Matchmaker 7sth.pdb1, chain B (#3) with 7stj.pdb1, chain B (#2), sequence alignment score = 6043.1 RMSD between 310 pruned atom pairs is 1.321 angstroms; (across all 796 pairs: 6.094) > morph #1, 2, 3 frames 40 Computed 81 frame morph #4 > coordset #4 1,81 > delete #4 > matchmaker #1 to #2 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 7stj.pdb1, chain B (#2) with 7sti.pdb1, chain B (#1), sequence alignment score = 6110.3 RMSD between 761 pruned atom pairs is 0.908 angstroms; (across all 792 pairs: 2.589) > morph #1,2 frames 40 Computed 41 frame morph #4 > coordset #4 1,41 > matchmaker #4 to 3 Invalid ""to"" argument: invalid atoms specifier > matchmaker #4 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 7sth.pdb1, chain B (#3) with Morph - 7sti.pdb1, chain B (#4), sequence alignment score = 6032.9 RMSD between 334 pruned atom pairs is 1.309 angstroms; (across all 791 pairs: 5.324) > morph #4, 3 frames 40 /Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/geometry/align.py:72: RuntimeWarning: overflow encountered in multiply rms2 = (Si*Si).sum() + (Sj*Sj).sum() - 2 * (transpose(R)*Sij).sum() /Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/sieve_fit.py:48: RuntimeWarning: overflow encountered in multiply dsq = add.reduce(transpose(multiply(d, d))) Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/morph.py"", line 84, in morph traj = compute_morph(structures, session.logger, method=method, rate=rate, frames=frames, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 28, in compute_morph motion.interpolate(res_groups, atom_map, res_interp) File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ IndexError: index 12776 is out of bounds for axis 0 with size 12776 IndexError: index 12776 is out of bounds for axis 0 with size 12776 File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ See log for complete Python traceback. > morph #4, 3 frames 40 Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/morph.py"", line 84, in morph traj = compute_morph(structures, session.logger, method=method, rate=rate, frames=frames, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 28, in compute_morph motion.interpolate(res_groups, atom_map, res_interp) File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ IndexError: index 12776 is out of bounds for axis 0 with size 12776 IndexError: index 12776 is out of bounds for axis 0 with size 12776 File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ See log for complete Python traceback. > morph #3, 4 frames 40 Computed 41 frame morph #5 > coordset #5 1,41 > morph #3, 4 frames 40 Computed 41 frame morph #6 > coordset #6 1,41 > delete #5 > delete #6 > show #!4 models > hide #!4 models > show #!4 models > matchmaker #2 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 7sth.pdb1, chain B (#3) with 7stj.pdb1, chain B (#2), sequence alignment score = 6043.1 RMSD between 310 pruned atom pairs is 1.321 angstroms; (across all 796 pairs: 6.094) > morph #2, 3 frames 40 Computed 41 frame morph #5 > coordset #5 1,41 > matchmaker #4 to #5 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 Morph - 7stj.pdb1, chain B (#5) with Morph - 7sti.pdb1, chain B (#4), sequence alignment score = 6040.1 RMSD between 327 pruned atom pairs is 1.301 angstroms; (across all 791 pairs: 6.559) > morph #4, 5 frames 40 Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/morph.py"", line 84, in morph traj = compute_morph(structures, session.logger, method=method, rate=rate, frames=frames, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 28, in compute_morph motion.interpolate(res_groups, atom_map, res_interp) File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ IndexError: index 12776 is out of bounds for axis 0 with size 12776 IndexError: index 12776 is out of bounds for axis 0 with size 12776 File ""/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/morph/motion.py"", line 149, in interpolate coords0[maindices] = matoms.coords ~~~~~~~^^^^^^^^^^^ See log for complete Python traceback. The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,7 Model Number: MRW23B/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 17 days, 4 hours, 12 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2415: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.4 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-clix: 0.1.6 ChimeraX-ColorActions: 1.0.4 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202405230136 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 ChimeraX-ModelPanel: 1.5 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBImages: 1.2 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.2 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Structure Editing fixed all ChimeraX