id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20591 Multiple consecutive Find Cavities: object of type ShortASLWidget has been deleted chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.13.dev202607020135 (2026-07-02 01:35:19 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.13.dev202607020135 (2026-07-02) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/challeppa/Ifeoluwapo/h-ENT1 dock analysis ChimeraX.pdb"" Summary of feedback from opening C:/Users/challeppa/Ifeoluwapo/h-ENT1 dock analysis ChimeraX.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK BIOVIA PDB file Ignored bad PDB record found on line 2 REMARK Created: 2026-07-07T11:07:35Z Start residue of secondary structure not found: HELIX 1 1 ARG A 10 LYS A 12 1 3 Start residue of secondary structure not found: HELIX 2 2 ALA A 13 LEU A 27 1 15 Start residue of secondary structure not found: HELIX 3 3 PRO A 28 THR A 34 1 7 Start residue of secondary structure not found: HELIX 4 4 THR A 36 ASP A 44 1 9 Start residue of secondary structure not found: HELIX 5 5 PHE A 80 LEU A 102 1 23 1955 messages similar to the above omitted Chain information for h-ENT1 dock analysis ChimeraX.pdb --- Chain | Description 1.1/A | No description available 1.1/B | No description available > select #1.1/A:7-450 5536 atoms, 5612 bonds, 3 pseudobonds, 365 residues, 2 models selected > sequence chain #1.1/A Alignment identifier is 1.1/A > close > open C:/Users/challeppa/Ifeoluwapo/h-ENT1.dsv Unrecognized file suffix '.dsv' > open C:/Users/challeppa/Ifeoluwapo/h-ENT1.dsv Unrecognized file suffix '.dsv' > open C:/Users/challeppa/Ifeoluwapo/h-ENT1.pdb format zdock Summary of feedback from opening C:/Users/challeppa/Ifeoluwapo/h-ENT1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK BIOVIA PDB file Ignored bad PDB record found on line 2 Ignored bad PDB record found on line 3 REMARK Created: 2026-07-07T11:07:35Z Ignored bad PDB record found on line 4 Ignored bad PDB record found on line 5543 96 messages similar to the above omitted Chain information for h-ENT1.pdb #1 --- Chain | Description A | No description available B | No description available Computing secondary structure > ui tool show ""Find Cavities"" > kvfinder 35 cavities found for h-ENT1.pdb #1 h-ENT1.pdb Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1463.4 | 993.94 | 6775 | 18 | 6.87 1.2.5 | | 1457.14 | 1006.04 | 6746 | 17.53 | 6.95 1.2.15 | | 1370.3 | 875.78 | 6344 | 12.06 | 2.71 1.2.26 | | 97.63 | 170.44 | 452 | 0 | 0 1.2.27 | | 69.34 | 75.44 | 321 | 3.7 | 1.18 1.2.32 | | 62.21 | 68.39 | 288 | 1.7 | 0.45 1.2.7 | | 57.24 | 55.29 | 265 | 2.16 | 0.64 1.2.20 | | 45.58 | 71.39 | 211 | 3.55 | 1.48 1.2.3 | | 41.9 | 60.51 | 194 | 1.8 | 0.5 1.2.1 | | 38.66 | 59.31 | 179 | 0 | 0 1.2.34 | | 33.05 | 53.02 | 153 | 0 | 0 1.2.6 | | 28.94 | 32.16 | 134 | 1.9 | 0.49 1.2.28 | | 28.73 | 45.58 | 133 | 3.6 | 1.67 1.2.19 | | 27.43 | 45.23 | 127 | 0 | 0 1.2.4 | | 27.22 | 36.03 | 126 | 1.7 | 0.45 1.2.22 | | 27.22 | 46.67 | 126 | 0 | 0 1.2.35 | | 26.14 | 30.78 | 121 | 1.8 | 0.65 1.2.17 | | 24.62 | 45.55 | 114 | 3.55 | 1.72 1.2.12 | | 23.54 | 37.11 | 109 | 0.85 | 0.27 1.2.13 | | 22.03 | 40.03 | 102 | 0 | 0 1.2.21 | | 21.82 | 40.63 | 101 | 0 | 0 1.2.30 | | 21.82 | 40.63 | 101 | 0 | 0 1.2.8 | | 21.38 | 37.45 | 99 | 0 | 0 1.2.23 | | 21.17 | 39.07 | 98 | 0 | 0 1.2.16 | | 19.87 | 36.19 | 92 | 0 | 0 1.2.29 | | 17.93 | 29.92 | 83 | 2.16 | 0.85 1.2.14 | | 16.85 | 32.3 | 78 | 0 | 0 1.2.31 | | 15.77 | 28.41 | 73 | 1.34 | 0.38 1.2.24 | | 14.9 | 26.03 | 69 | 1.7 | 0.53 1.2.9 | | 14.47 | 22.59 | 67 | 1.34 | 0.4 1.2.10 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.18 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.25 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.33 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.11 | | 11.23 | 25.38 | 52 | 1.9 | 0.9 > kvfinder 35 cavities found for h-ENT1.pdb #1 h-ENT1.pdb Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1463.4 | 993.94 | 6775 | 18 | 6.87 1.2.5 | | 1457.14 | 1006.04 | 6746 | 17.53 | 6.95 1.2.15 | | 1370.3 | 875.78 | 6344 | 12.06 | 2.71 1.2.26 | | 97.63 | 170.44 | 452 | 0 | 0 1.2.27 | | 69.34 | 75.44 | 321 | 3.7 | 1.18 1.2.32 | | 62.21 | 68.39 | 288 | 1.7 | 0.45 1.2.7 | | 57.24 | 55.29 | 265 | 2.16 | 0.64 1.2.20 | | 45.58 | 71.39 | 211 | 3.55 | 1.48 1.2.3 | | 41.9 | 60.51 | 194 | 1.8 | 0.5 1.2.1 | | 38.66 | 59.31 | 179 | 0 | 0 1.2.34 | | 33.05 | 53.02 | 153 | 0 | 0 1.2.6 | | 28.94 | 32.16 | 134 | 1.9 | 0.49 1.2.28 | | 28.73 | 45.58 | 133 | 3.6 | 1.67 1.2.19 | | 27.43 | 45.23 | 127 | 0 | 0 1.2.4 | | 27.22 | 36.03 | 126 | 1.7 | 0.45 1.2.22 | | 27.22 | 46.67 | 126 | 0 | 0 1.2.35 | | 26.14 | 30.78 | 121 | 1.8 | 0.65 1.2.17 | | 24.62 | 45.55 | 114 | 3.55 | 1.72 1.2.12 | | 23.54 | 37.11 | 109 | 0.85 | 0.27 1.2.13 | | 22.03 | 40.03 | 102 | 0 | 0 1.2.21 | | 21.82 | 40.63 | 101 | 0 | 0 1.2.30 | | 21.82 | 40.63 | 101 | 0 | 0 1.2.8 | | 21.38 | 37.45 | 99 | 0 | 0 1.2.23 | | 21.17 | 39.07 | 98 | 0 | 0 1.2.16 | | 19.87 | 36.19 | 92 | 0 | 0 1.2.29 | | 17.93 | 29.92 | 83 | 2.16 | 0.85 1.2.14 | | 16.85 | 32.3 | 78 | 0 | 0 1.2.31 | | 15.77 | 28.41 | 73 | 1.34 | 0.38 1.2.24 | | 14.9 | 26.03 | 69 | 1.7 | 0.53 1.2.9 | | 14.47 | 22.59 | 67 | 1.34 | 0.4 1.2.10 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.18 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.25 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.33 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.11 | | 11.23 | 25.38 | 52 | 1.9 | 0.9 > kvfinder 35 cavities found for h-ENT1.pdb #1 h-ENT1.pdb Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1463.4 | 993.94 | 6775 | 18 | 6.87 1.2.5 | | 1457.14 | 1006.04 | 6746 | 17.53 | 6.95 1.2.15 | | 1370.3 | 875.78 | 6344 | 12.06 | 2.71 1.2.26 | | 97.63 | 170.44 | 452 | 0 | 0 1.2.27 | | 69.34 | 75.44 | 321 | 3.7 | 1.18 1.2.32 | | 62.21 | 68.39 | 288 | 1.7 | 0.45 1.2.7 | | 57.24 | 55.29 | 265 | 2.16 | 0.64 1.2.20 | | 45.58 | 71.39 | 211 | 3.55 | 1.48 1.2.3 | | 41.9 | 60.51 | 194 | 1.8 | 0.5 1.2.1 | | 38.66 | 59.31 | 179 | 0 | 0 1.2.34 | | 33.05 | 53.02 | 153 | 0 | 0 1.2.6 | | 28.94 | 32.16 | 134 | 1.9 | 0.49 1.2.28 | | 28.73 | 45.58 | 133 | 3.6 | 1.67 1.2.19 | | 27.43 | 45.23 | 127 | 0 | 0 1.2.4 | | 27.22 | 36.03 | 126 | 1.7 | 0.45 1.2.22 | | 27.22 | 46.67 | 126 | 0 | 0 1.2.35 | | 26.14 | 30.78 | 121 | 1.8 | 0.65 1.2.17 | | 24.62 | 45.55 | 114 | 3.55 | 1.72 1.2.12 | | 23.54 | 37.11 | 109 | 0.85 | 0.27 1.2.13 | | 22.03 | 40.03 | 102 | 0 | 0 1.2.21 | | 21.82 | 40.63 | 101 | 0 | 0 1.2.30 | | 21.82 | 40.63 | 101 | 0 | 0 1.2.8 | | 21.38 | 37.45 | 99 | 0 | 0 1.2.23 | | 21.17 | 39.07 | 98 | 0 | 0 1.2.16 | | 19.87 | 36.19 | 92 | 0 | 0 1.2.29 | | 17.93 | 29.92 | 83 | 2.16 | 0.85 1.2.14 | | 16.85 | 32.3 | 78 | 0 | 0 1.2.31 | | 15.77 | 28.41 | 73 | 1.34 | 0.38 1.2.24 | | 14.9 | 26.03 | 69 | 1.7 | 0.53 1.2.9 | | 14.47 | 22.59 | 67 | 1.34 | 0.4 1.2.10 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.18 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.25 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.33 | | 12.31 | 29.54 | 57 | 0 | 0 1.2.11 | | 11.23 | 25.38 | 52 | 1.9 | 0.9 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.13.dev202607020135\bin\Lib\site- packages\chimerax\kvfinder\tool.py"", line 147, in find_cavities structures = self.structures_list.value ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.13.dev202607020135\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 149, in value return self.get_value() ^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.13.dev202607020135\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 152, in get_value self._sleep_check() File ""C:\Program Files\ChimeraX 1.13.dev202607020135\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 105, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): ^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: wrapped C/C++ object of type ShortASLWidget has been deleted RuntimeError: wrapped C/C++ object of type ShortASLWidget has been deleted File ""C:\Program Files\ChimeraX 1.13.dev202607020135\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 105, in _sleep_check if not self._handlers and not hasattr(self, '_recursion'): ^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 595.79 OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.9 Locale: en_US.cp1252 Qt version: PyQt6 6.11.0, Qt 6.11.0 Qt runtime version: 6.11.1 Qt platform: windows Manufacturer: HP Model: HP Z8 G4 Workstation OS: Microsoft Windows 11 Pro for Workstations (Build 22631.6199) Memory: 137,127,550,976 MaxProcessMemory: 137,438,953,344 CPU: 24 Intel(R) Xeon(R) Gold 6136 CPU @ 3.00GHz OSLanguage: en-US Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.7.1 aiohttp: 3.13.4 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.14.1 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.7.0 build: 1.5.0 certifi: 2026.6.17 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.3.1 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2.2 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: 1.70 ChimeraX-AtomicLibrary: 14.4.1 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: 2.4 ChimeraX-Cluster: 1.0 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: 1.13.dev202607020135 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.6 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.2 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: 2.5.4 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: 1.8.3 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.2.1 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.4.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.17 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.24 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-NMRSTAR: 1.0.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.16.2 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.10.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 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: 2.19.1 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: 1.20 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.53 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.4 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.4.2 colorama: 0.4.6 comm: 0.2.3 comtypes: 1.4.11 contourpy: 1.3.3 coverage: 7.14.3 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.21 decorator: 5.3.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.18 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.3.0 ipython: 9.14.1 ipython_pygments_lexers: 1.1.1 jedi: 0.20.0 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.9.1 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 markdown-it-py: 4.2.0 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.2 mcp: 1.18.0 mdurl: 0.1.2 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.23.0 ndindex: 1.10.1 nest-asyncio2: 1.7.2 netCDF4: 1.7.4 networkx: 3.3 numexpr: 2.14.1 numpy: 2.4.6 numpy: 1.26.4 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.4.0 OpenMM-CUDA-12: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 11.3.0 pip: 26.1.2 pkginfo: 1.12.1.2 platformdirs: 4.10.0 plotly: 6.8.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.4 pydantic-settings: 2.14.2 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.19.0 Pygments: 2.18.0 pyKVFinder: 0.9.3 pynmrstar: 3.5.1 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6: 6.11.0 PyQt6-Qt6: 6.11.1 PyQt6-WebEngine: 6.11.0 PyQt6-WebEngine-Qt6: 6.11.1 PyQt6_sip: 13.11.1 pytest: 9.1.1 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.32 pywin32: 311 pyzmq: 27.1.0 qtconsole: 5.7.2 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 rich: 15.0.0 roman-numerals: 4.1.0 rpds-py: 2026.6.3 scipy: 1.14.0 setuptools: 82.0.1 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.1 sortedcontainers: 2.4.0 soupsieve: 2.8.4 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: 3.4.5 stack-data: 0.6.3 starlette: 1.3.1 superqt: 0.7.6 tables: 3.11.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tomlkit: 0.15.0 tornado: 6.5.7 traitlets: 5.15.1 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.7.0 uvicorn: 0.49.0 wcwidth: 0.8.2 webcolors: 24.11.1 wheel: 0.47.0 wheel-filename: 1.4.2 WMI: 1.5.1 yarl: 1.24.2 }}} " defect closed normal Surface/Binding Analysis can't reproduce all ChimeraX