id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16250 "KVFinder: error in ""pip install"" error handling" yongquan0043@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.9rc202411012347 (2024-11-01 23:47:45 UTC) Description Replace this text with list of actions that caused this problem to occur Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""S:/alphafold predict/mTORC2 电镜扫描结构/6zwo.pdb"" 6zwo.pdb title: Cryo-em structure of human mtor complex 2, focused on one half [more info...] Chain information for 6zwo.pdb #1 --- Chain | Description | UniProt B | serine/threonine-protein kinase mtor | MTOR_HUMAN 1-2549 D | target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326 F | rapamycin-insensitive companion of mtor | RICTR_HUMAN 1-1708 H | target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 2-522 Non-standard residues in 6zwo.pdb #1 --- ACE — acetyl group AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine 5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate); adenosine-5'-diphosphate monothiophosphate) IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) ZN — zinc ion > select /B:791-2549 12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected > select /B:791-2549 12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected > select /B:791-2549 12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected > select /B:791-2549 12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected > select /B:791-2549 12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected > color (#!1 & sel) yellow > color (#!1 & sel) light sea green > Incomplete command: sequence > help help:user > select sequence ""chain B"" Nothing selected > help help:user > lighting simple [Repeated 3 time(s)] > select /B:791-2549 12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected > 1026 Unknown command: sequence 1026 > 1026, chainB Unknown command: sequence 1026, chainB > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select clear [Repeated 3 time(s)] > select > /B:792-809,816-829,836-847,855-861,863-871,877-892,895-902,929-936,946-960,967-983,989-1023,1027-1039,1048-1064,1066-1084,1090-1101,1115-1123,1128-1142,1149-1165,1169-1182,1185-1189,1191-1202,1206-1218,1228-1238,1265-1270,1276-1294,1297-1308,1310-1327,1330-1348,1350-1366,1376-1389,1392-1407,1409-1423,1425-1440,1446-1453,1455-1468,1476-1499,1505-1534,1540-1554,1558-1579,1582-1608,1611-1624,1629-1641,1650-1663,1665-1678,1693-1708,1711-1729,1739-1763,1768-1784,1786-1809,1875-1896,1899-1914,1916-1930,1932-1944,1950-1968,1972-1981,1984-1999,2003-2059,2064-2091,2093-2113,2123-2127,2192-2217,2246-2257,2262-2272,2274-2293,2297-2306,2309-2335,2380-2385,2394-2423,2429-2433,2493-2508,2520-2546 9638 atoms, 9784 bonds, 1176 residues, 1 model selected > select clear > select > /B:792-809,816-829,836-847,855-861,863-871,877-892,895-902,929-936,946-960,967-983,989-1023,1027-1039,1048-1064,1066-1084,1090-1101,1115-1123,1128-1142,1149-1165,1169-1182,1185-1189,1191-1202,1206-1218,1228-1238,1265-1270,1276-1294,1297-1308,1310-1327,1330-1348,1350-1366,1376-1389,1392-1407,1409-1423,1425-1440,1446-1453,1455-1468,1476-1499,1505-1534,1540-1554,1558-1579,1582-1608,1611-1624,1629-1641,1650-1663,1665-1678,1693-1708,1711-1729,1739-1763,1768-1784,1786-1809,1875-1896,1899-1914,1916-1930,1932-1944,1950-1968,1972-1981,1984-1999,2003-2059,2064-2091,2093-2113,2123-2127,2192-2217,2246-2257,2262-2272,2274-2293,2297-2306,2309-2335,2380-2385,2394-2423,2429-2433,2493-2508,2520-2546 9638 atoms, 9784 bonds, 1176 residues, 1 model selected > select /B:1028 11 atoms, 10 bonds, 1 residue, 1 model selected > select /B:1028 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > view sel > select /F:463 9 atoms, 8 bonds, 1 residue, 1 model selected > select /F:463 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /F:464 18 atoms, 16 bonds, 2 residues, 1 model selected > select subtract /F:463 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /F:463 18 atoms, 16 bonds, 2 residues, 1 model selected > show sel target ab > undo > select subtract /F:463 9 atoms, 8 bonds, 1 residue, 1 model selected > view sel > show sel target ab > select add /B:1028@CZ 10 atoms, 8 bonds, 2 residues, 1 model selected > show sel target ab > ui tool show H-Bonds > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /F PRO 27 N; /H PRO 134 N; /H PRO 133 N; /F PRO 642 N; /F PRO 34 N 2 hydrogen bonds found > select clear > hide #!1 models > show #!1 models > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... Traceback (most recent call last): File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 37, in register_command import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 42, in register_command run(logger.session, ""pip install pyKVFinder"", log=False) File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\pip.py"", line 88, in pip run_logged_pip(pip_cmd, session.logger) File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\python_utils.py"", line 143, in run_logged_pip raise RuntimeError(s) RuntimeError During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 330, in _register_cmd api._api_caller.register_command(api, self, ci, logger) File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1403, in register_command return cls._get_func(api, ""register_command"")(ci.name, logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\kvfinder\\__init__.py"", line 44, in register_command from chimerax.core.logger import report_exception ImportError: cannot import name 'report_exception' from 'chimerax.core.logger' (S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\logger.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 2475, in lazy_register deferred.call() File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 2403, in call return self.proxy() ^^^^^^^^^^^^ File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 320, in cb s._register_cmd(ci, logger) File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 332, in _register_cmd raise ToolshedError( chimerax.core.toolshed.ToolshedError: register_command() failed for command kvfinder in bundle ChimeraX-KVFinder: cannot import name 'report_exception' from 'chimerax.core.logger' (S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\logger.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\kvfinder\tool.py"", line 67, in find_cavities run(self.session, ""kvfinder %s"" % concise_model_spec(self.session, structures, File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3139, in run self._find_command_name(final, used_aliases=_used_aliases) File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 2863, in _find_command_name what.lazy_register(cmd_name) File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 2477, in lazy_register raise RuntimeError( RuntimeError: delayed command registration for 'kvfinder' failed (register_command() failed for command kvfinder in bundle ChimeraX-KVFinder: cannot import name 'report_exception' from 'chimerax.core.logger' (S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\logger.py)) RuntimeError: delayed command registration for 'kvfinder' failed (register_command() failed for command kvfinder in bundle ChimeraX-KVFinder: cannot import name 'report_exception' from 'chimerax.core.logger' (S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\logger.py)) File ""S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 2477, in lazy_register raise RuntimeError( See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 551.86 OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: zh_CN.cp936 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: windows Manufacturer: LENOVO Model: 82B6 OS: Microsoft Windows 10 家庭版 (Build 19045) Memory: 16,505,966,592 MaxProcessMemory: 137,438,953,344 CPU: 12 AMD Ryzen 5 4600H with Radeon Graphics OSLanguage: zh-CN Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 2.4.1 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.7.1 build: 1.2.1 certifi: 2024.8.30 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 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: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.7 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.7 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 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: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 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: 1.9rc202411012347 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.5 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: 1.4.1 ChimeraX-Hbonds: 2.5 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: 1.2 ChimeraX-Label: 1.1.11 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.17 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-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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.1 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.2.4 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 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: 1.18.1 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 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: 1.41 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 comtypes: 1.4.5 contourpy: 1.3.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.7 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.54.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.12.1 html2text: 2024.2.26 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 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: 2.10.1 numpy: 2.1.3 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 plotly: 5.24.1 prompt_toolkit: 3.0.48 psutil: 6.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pywin32: 306 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.1 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tenacity: 9.0.0 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tornado: 6.4.1 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 WMI: 1.5.1 }}} " defect feedback normal Surface/Binding Analysis chimera-programmers all ChimeraX