id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17481 Boltz: process_chem_name() arg is None chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.10.dev202504240337 (2025-04-24 03:37:50 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10.dev202504240337 (2025-04-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/PFT7/Dropbox/PF/Postdoc/Science/MITOMICS2/C15orf61/AlphaFold3/ATPsynthase_monomer_250417/fold_atpsynthase_nof1_c15orf61_2025_04_17_17_43/fold_atpsynthase_nof1_c15orf61_2025_04_17_17_43_model_1.cif Chain information for fold_atpsynthase_nof1_c15orf61_2025_04_17_17_43_model_1.cif #1 --- Chain | Description A | . B | . C | . D | . E | . F | . G | . H | . I | . J | . K | . L | . M | . N | . O P Q R S T U V | . W | . > select /D:1-69 559 atoms, 567 bonds, 69 residues, 1 model selected > select /J:1-68 559 atoms, 580 bonds, 68 residues, 1 model selected > select /K:1-214 1736 atoms, 1771 bonds, 214 residues, 1 model selected > select /W:1-131 1075 atoms, 1113 bonds, 131 residues, 1 model selected > select /W:1-131 1075 atoms, 1113 bonds, 131 residues, 1 model selected > select /W:1-131 1075 atoms, 1113 bonds, 131 residues, 1 model selected > sequence chain #1/W Alignment identifier is 1/W Computing secondary structure > select clear > rainbow [Repeated 1 time(s)] > undo [Repeated 1 time(s)] > show surfaces [Repeated 1 time(s)] > hide surfaces [Repeated 1 time(s)] > show surfaces [Repeated 1 time(s)] > hide surfaces > color bychain > hide surfaces > hide cartoons > hide atoms [Repeated 1 time(s)] > show atoms > style sphere Changed 19426 atom styles > show surfaces > hide atoms > hide cartoons > hide surfaces > show surfaces > hide surfaces > show atoms > nucleotides fill > style nucleic stick Changed 0 atom styles > show cartoons > hide atoms > open ""/Volumes/PFT7/Dropbox/PF/Postdoc/Science/MITOMICS2/C15orf61/ATP > synthase/8h9s-pdb-bundle/8h9s-pdb-bundle1.pdb"" Summary of feedback from opening /Volumes/PFT7/Dropbox/PF/Postdoc/Science/MITOMICS2/C15orf61/ATP synthase/8h9s-pdb-bundle/8h9s-pdb-bundle1.pdb --- warning | Ignored bad PDB record found on line 1 HEADER MEMBRANE PROTEIN 2022-10-25 XXXX Chain information for 8h9s-pdb-bundle1.pdb #2 --- Chain | Description 1 2 3 4 5 6 7 8 | No description available 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 K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available 16 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Drag select of 38914 atoms, 5 pseudobonds, 302 bonds > select clear > hide #!2 models > show #!2 models > ui tool show ""Selection Inspector"" > select add #2 38914 atoms, 39547 bonds, 5 pseudobonds, 5077 residues, 2 models selected Drag select of 2423 atoms, 2 pseudobonds, 31 bonds > select add #2 38914 atoms, 39547 bonds, 5 pseudobonds, 5077 residues, 2 models selected > select subtract #2 Nothing selected > select add #2 38914 atoms, 39547 bonds, 5 pseudobonds, 5077 residues, 2 models selected > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,-146,0,1,0,-193.81,0,0,1,48.836 > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-254.2,0,1,0,-92.756,0,0,1,-398.34 > show sel cartoons Computing secondary structure > hide sel atoms > color sel bychain > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.26365,-0.94663,0.18543,26.364,-0.41106,0.06365,0.90939,-9.6973,-0.87265,-0.31598,-0.37234,79.478 > view matrix models > #2,-0.25467,0.96576,-0.049461,-184.08,0.32991,0.038693,-0.94322,195.72,-0.90901,-0.25653,-0.32847,67.348 > view matrix models > #2,-0.069739,0.81491,-0.57537,-94.42,0.35365,-0.51912,-0.77811,263.55,-0.93278,-0.25774,-0.25199,57.981 > view matrix models > #2,-0.070997,0.8144,-0.57595,-93.979,0.35489,-0.519,-0.77762,263.2,-0.93221,-0.25961,-0.25218,58.251 > view matrix models > #2,-0.27361,0.62319,-0.73265,8.7969,0.58227,-0.49896,-0.64187,191.13,-0.76557,-0.60222,-0.22634,84.897 > ui mousemode right ""move picked models"" > view matrix models > #2,-0.27361,0.62319,-0.73265,34.574,0.58227,-0.49896,-0.64187,185.59,-0.76557,-0.60222,-0.22634,143.62 > ui mousemode right select > select clear > ui mousemode right ""rotate selected models"" > ui mousemode right ""move picked models"" > ui mousemode right select Drag select of 2514 residues > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.74979,0.010029,0.6616,12.315,0.59406,0.43013,-0.67977,-20.111,-0.29139,0.90271,0.31655,-0.55178 > view matrix models > #1,0.67882,0.029586,0.73371,14.378,0.63826,0.47027,-0.60948,-19.657,-0.36308,0.88202,0.30035,0.18847 > view matrix models > #1,0.75259,-0.093701,0.65179,11.675,0.52674,0.67966,-0.51049,-15.789,-0.39517,0.72751,0.56086,3.3484 > ui mousemode right select Drag select of 5064 residues, 5 pseudobonds > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.37394,0.43852,-0.81724,103.34,0.74872,-0.37729,-0.54504,113.57,-0.54734,-0.81569,-0.18724,134.18 > ui mousemode right select > select clear [Repeated 1 time(s)]Drag select of 26 residues > select clear Drag select of 419 residues > select clear Drag select of 128 residues > select clear Drag select of 107 residues > select clear Drag select of 104 residues Drag select of 38 residues > select clear > hide #1.23 models > show #1.23 models > hide #1.23 models > show #1.23 models > hide #!1 models > show #!1 models > hide #1.1 models > show #1.1 models > hide #1.23 models > show #1.23 models > hide #!2 models > show #!2 models > select /K:1-214 3309 atoms, 3376 bonds, 1 pseudobond, 412 residues, 3 models selected > select /M:1-76 1194 atoms, 1221 bonds, 148 residues, 2 models selected > select /N:1-190 2893 atoms, 2942 bonds, 377 residues, 2 models selected > select /G:1-58 923 atoms, 940 bonds, 115 residues, 2 models selected > select /A:1-273 4132 atoms, 4178 bonds, 1 pseudobond, 540 residues, 3 models selected > select /B:1-146 1970 atoms, 1992 bonds, 269 residues, 2 models selected > select /N:1-190 2893 atoms, 2942 bonds, 377 residues, 2 models selected > select /M:1-76 1194 atoms, 1221 bonds, 148 residues, 2 models selected > select clear > select #1/W:13 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/W:13-14 18 atoms, 18 bonds, 2 residues, 1 model selected > select #1/W:2 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/W:2-115 931 atoms, 965 bonds, 114 residues, 1 model selected > select #1/W:1 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/W:1 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/W:9 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/W:9-10 15 atoms, 14 bonds, 2 residues, 1 model selected > select #1/W:6-16,75-87,91-103 302 atoms, 307 bonds, 37 residues, 1 model selected > select #1/W:3 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/W:3 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/I:33 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select #2/Q:1-51 422 atoms, 437 bonds, 51 residues, 1 model selected > select #2/S:26-102 605 atoms, 619 bonds, 77 residues, 1 model selected > select #2/T:2-45 346 atoms, 354 bonds, 44 residues, 1 model selected > select #2/H:15-146 975 atoms, 987 bonds, 132 residues, 1 model selected > select #2/I:2-46 354 atoms, 359 bonds, 45 residues, 1 model selected > sequence chain #2/I Alignment identifier is 2/I > select #2/I:8 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/I:8-16 72 atoms, 73 bonds, 9 residues, 1 model selected > select #2/I:23 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/I:13-23 86 atoms, 86 bonds, 11 residues, 1 model selected > select #2/I:18-19 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/I:18-20 19 atoms, 18 bonds, 3 residues, 1 model selected > select #2/I:24-25 19 atoms, 18 bonds, 2 residues, 1 model selected > select #2/I:24-25 19 atoms, 18 bonds, 2 residues, 1 model selected > select #2/I:15 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/I:15 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/I:20 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/I:20-21 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/I:4-7,12-25,29-38 242 atoms, 245 bonds, 28 residues, 1 model selected > select #2/I:21 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/I:21-22 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/I:21 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/I:21 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show Boltz Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1399, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/__init__.py"", line 33, in start_tool return boltz_gui.show_boltz_panel(session) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 965, in show_boltz_panel return boltz_panel(session, create = True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 960, in boltz_panel return BoltzPredictionGUI.get_singleton(session, create=create) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 104, in get_singleton return tools.get_singleton(session, cls, 'Boltz', create=create) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/tools.py"", line 216, in get_singleton tinst = tool_class(session, tool_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 67, in __init__ sm = self._create_molecule_menu(parent) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 144, in _create_molecule_menu entries = self._update_molecule_menu() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 242, in _update_molecule_menu entries = self._menu_entries() ^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 255, in _menu_entries values.extend(_specifiers_with_descriptions(s)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 794, in _specifiers_with_descriptions values.extend(_chain_descriptions(structure)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 816, in _chain_descriptions desc = _chain_description(c) ^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 805, in _chain_description chain_desc = process_chem_name(desc) ^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/pdb/pdb.py"", line 447, in process_chem_name if name.isupper() and ("" "" in name or len(name) > 5): ^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'isupper' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 1891, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3219, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Boltz in bundle ChimeraX-Boltz: 'NoneType' object has no attribute 'isupper' chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Boltz in bundle ChimeraX-Boltz: 'NoneType' object has no attribute 'isupper' File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac mini Model Identifier: Mac16,10 Model Number: MU9D3LL/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 7 days, 21 hours, 32 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.3.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.3 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.15 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202504240337 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: 1.1.4 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: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.9 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 1.45.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.2 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.57.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.6 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.14 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.7 pluggy: 1.5.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.4.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Structure Prediction fixed all ChimeraX