id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19693 Add charges: out of memory chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\\\Users\\\dgp15\\\Desktop\\\gjcl_PLP_CYS.pdbqt Chain information for gjcl_PLP_CYS.pdb #1 --- Chain | Description A | No description available Computing secondary structure Opened gjcl_PLP_CYS.pdbqt containing 1 structures (5262 atoms, 5336 bonds) Drag select of 4 atoms, 13 residues, 4 bonds > select clear > select /A:99@CD 1 atom, 1 residue, 1 model selected > select /A:300 7 atoms, 7 bonds, 1 residue, 1 model selected > select /A:245@OG1 1 atom, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select /A:211@OH 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > select up 16 atoms, 15 bonds, 2 residues, 1 model selected > select up 18 atoms, 16 bonds, 3 residues, 1 model selected > select up 20 atoms, 18 bonds, 3 residues, 1 model selected > hide sel atoms > show sel atoms > hide sel cartoons > hide sel atoms > select /A:136@HG 1 atom, 1 residue, 1 model selected > select clear > select /?:0@@serial_number=24 1 atom, 1 residue, 1 model selected > select clear > select /A:136@HN 1 atom, 1 residue, 1 model selected > select /A:80 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 34 atoms, 33 bonds, 3 residues, 1 model selected > select up 5232 atoms, 5308 bonds, 557 residues, 1 model selected > hide sel atoms > select clear > select /?:0@@serial_number=24 1 atom, 1 residue, 1 model selected > hide sel atoms > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Traceback (most recent call last): File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-packages\chimerax\toolbar\tool.py"", line 230, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1420, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\\__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1393, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 403, in try_shortcut self.run_shortcut(keys) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 421, in run_shortcut sc.run(self.session, status = self._enabled) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 340, in run f(s) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 72, in func_plus_tip func(cmd + "" %s"")(session) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 594, in run_expanded_command run(session, cmd) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 537, in run run_command(session, command, **kw) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-packages\chimerax\coulombic\cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\coulombic\coulombic.py"", line 110, in assign_charges add_charges(session, charged_residues, method=charge_method, status=status, File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\add_charge\charge.py"", line 34, in add_charges uncharged_res_types = add_standard_charges(session, residues, status=status, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\add_charge\charge.py"", line 204, in add_standard_charges br_type = ""%s[non-%s]"" % (br_type, a.name) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ MemoryError MemoryError File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\add_charge\charge.py"", line 204, in add_standard_charges br_type = ""%s[non-%s]"" % (br_type, a.name) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ See log for complete Python traceback. > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Traceback (most recent call last): File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-packages\chimerax\toolbar\tool.py"", line 230, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1420, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\\__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 1393, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 403, in try_shortcut self.run_shortcut(keys) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 421, in run_shortcut sc.run(self.session, status = self._enabled) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 340, in run f(s) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 72, in func_plus_tip func(cmd + "" %s"")(session) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 594, in run_expanded_command run(session, cmd) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py"", line 537, in run run_command(session, command, **kw) File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site-packages\chimerax\coulombic\cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\coulombic\coulombic.py"", line 110, in assign_charges add_charges(session, charged_residues, method=charge_method, status=status, File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\add_charge\charge.py"", line 34, in add_charges uncharged_res_types = add_standard_charges(session, residues, status=status, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\add_charge\charge.py"", line 204, in add_standard_charges br_type = ""%s[non-%s]"" % (br_type, a.name) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ MemoryError MemoryError File ""D:\\u65b0\u5efa\u6587\u4ef6\u5939\ChimeraX 1.11\bin\Lib\site- packages\chimerax\add_charge\charge.py"", line 204, in add_standard_charges br_type = ""%s[non-%s]"" % (br_type, a.name) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ See log for complete Python traceback. Invalid texture upload for 0x1b8bc0d5e80 layer=0 mip=0 OpenGL version: 3.3.0 NVIDIA 546.92 OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.9 Locale: zh_CN.cp936 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: windows Manufacturer: LENOVO Model: 82TF OS: Microsoft Windows 11 \u5bb6\u5ead\u7248 (Build 22631) Memory: 16,979,447,808 MaxProcessMemory: 137,438,953,344 CPU: 16 12th Gen Intel(R) Core(TM) i5-12500H OSLanguage: zh-CN Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.11.12 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: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 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: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 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 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: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 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: 2.5.3 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: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 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: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 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: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 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: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 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-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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 comtypes: 1.4.11 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 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: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 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: 6.7.0 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 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.2.0 OpenMM-CUDA-12: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pywin32: 311 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 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 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 WMI: 1.5.1 yarl: 1.22.0 }}} " defect closed normal Structure Editing can't reproduce Tom Goddard all ChimeraX