id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9218 ISOLDE: OpenMMException: Error compiling kernel gregp@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description isolde start sel #1.2 press ""start simulation"" button Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Updating list of available bundles failed: Internal Server Error > open ""C:/Users/greg/My Drive/_data/2023 CLC/CLC2-CTDasym.mrc"" > ""C:/Users/greg/My Drive/_data/2023 CLC/CLC2-CTDasym.pdb"" Summary of feedback from opening C:/Users/greg/My Drive/_data/2023 CLC/CLC2-CTDasym.pdb --- warnings | Start residue of secondary structure not found: SHEET 1 1 3 LEU B 15 THR B 20 0 Start residue of secondary structure not found: SHEET 2 2 4 TYR B 23 GLN B 28 0 Opened CLC2-CTDasym.mrc as #1, grid size 256,256,256, pixel 0.946, shown at level 0.388, step 1, values float32 Chain information for CLC2-CTDasym.pdb #2 --- Chain | Description A | No description available B | No description available > camera mono > volume #1 level 1.168 > lighting soft > clipper associate #1 toModel #2 Opened CLC2-CTDasym.mrc as #1.1.1.1, grid size 256,256,256, pixel 0.946, shown at level 1.15, step 1, values float32 Chain information for CLC2-CTDasym.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available > select H Nothing selected > addh Summary of feedback from adding hydrogens to CLC2-CTDasym.pdb #1.2 --- notes | No usable SEQRES records for CLC2-CTDasym.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for CLC2-CTDasym.pdb (#1.2) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A ALA 14, /B GLY 88 Chain-initial residues that are not actual N termini: /A GLY 88, /A GLU 231, /A THR 301, /A SER 419, /A TRP 774, /B GLU 231, /B THR 301, /B LYS 362, /B SER 419, /B ARG 577, /B TRP 774 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 841, /A GLN 28, /A LEU 225, /A ARG 297, /A ARG 408, /A ARG 644, /B ILE 839, /B LEU 225, /B ARG 297, /B GLN 352, /B ARG 408, /B LEU 568, /B ARG 644 997 hydrogen bonds Adding 'H' to /A GLY 88 Adding 'H' to /A GLU 231 Adding 'H' to /A THR 301 Adding 'H' to /A SER 419 Adding 'H' to /A TRP 774 6 messages similar to the above omitted /A GLY 841 is not terminus, removing H atom from 'C' /B ILE 839 is not terminus, removing H atom from 'C' 9729 hydrogens added > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 70 residues in model #1.2 to IUPAC-IUB standards. Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield > isolde sim start /A-B Sim termination reason: None ISOLDE: stopped sim Fetching CCD N7P from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/N7P/N7P.cif > open ""C:/Users/greg/My Drive/_data/2023 CLC/CLC2-CTDasym.pdb"" Summary of feedback from opening C:/Users/greg/My Drive/_data/2023 CLC/CLC2-CTDasym.pdb --- warnings | Start residue of secondary structure not found: SHEET 1 1 3 LEU B 15 THR B 20 0 Start residue of secondary structure not found: SHEET 2 2 4 TYR B 23 GLN B 28 0 Chain information for CLC2-CTDasym.pdb #2 --- Chain | Description A | No description available B | No description available > hide #1.3 models > hide #!1.2 models > hide #!1.1 models > select clear [Repeated 5 time(s)] > hide #!1 models > select clear [Repeated 2 time(s)] > hide #!2 models > show #1.3 models > show #!1.2 models > show #!1.1 models > addbond Unknown command: addbond > addh bond Expected a keyword > select H 9728 atoms, 1210 residues, 1 model selected > delete sel > select clear > addh bond sel Expected a keyword > close session > open ""C:/Users/greg/My Drive/_data/2023 CLC/CLC2-CTDasym.mrc"" Opened CLC2-CTDasym.mrc as #1, grid size 256,256,256, pixel 0.946, shown at level 0.388, step 1, values float32 > open ""C:/Users/greg/My Drive/_data/2023 CLC/CLC2-CTDasym_f.pdb"" Summary of feedback from opening C:/Users/greg/My Drive/_data/2023 CLC/CLC2-CTDasym_f.pdb --- warnings | Start residue of secondary structure not found: SHEET 1 1 3 LEU B 15 THR B 20 0 Start residue of secondary structure not found: SHEET 2 2 4 TYR B 23 GLN B 28 0 Chain information for CLC2-CTDasym_f.pdb #2 --- Chain | Description A | No description available B | No description available > volume #1 level 1.805 > camera stereo > addh Summary of feedback from adding hydrogens to CLC2-CTDasym_f.pdb #2 --- notes | No usable SEQRES records for CLC2-CTDasym_f.pdb (#2) chain A; guessing termini instead No usable SEQRES records for CLC2-CTDasym_f.pdb (#2) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A ALA 14, /B GLY 88 Chain-initial residues that are not actual N termini: /A GLY 88, /A GLU 231, /A THR 301, /A SER 419, /A TRP 774, /B GLU 231, /B THR 301, /B LYS 362, /B SER 419, /B ARG 577, /B TRP 774 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLY 841, /A GLN 28, /A LEU 225, /A ARG 297, /A ARG 408, /A ARG 644, /B ILE 839, /B LEU 225, /B ARG 297, /B GLN 352, /B ARG 408, /B LEU 568, /B ARG 644 997 hydrogen bonds Adding 'H' to /A GLY 88 Adding 'H' to /A GLU 231 Adding 'H' to /A THR 301 Adding 'H' to /A SER 419 Adding 'H' to /A TRP 774 6 messages similar to the above omitted /A GLY 841 is not terminus, removing H atom from 'C' /B ILE 839 is not terminus, removing H atom from 'C' 9726 hydrogens added > clipper associate #1 toModel #2 Opened CLC2-CTDasym.mrc as #1.1.1.1, grid size 256,256,256, pixel 0.946, shown at level 1.15, step 1, values float32 Chain information for CLC2-CTDasym_f.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available > isolde start > camera stereo > select #1.2 19113 atoms, 19326 bonds, 11 pseudobonds, 1210 residues, 2 models selected ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 70 residues in model #1.2 to IUPAC-IUB standards. > isolde sim start /A-B Traceback (most recent call last): File ""C:\Users\greg\\_mol\ChimeraX\bin\lib\site- packages\chimerax\toolbar\tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""C:\Users\greg\\_mol\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""C:\Users\greg\\_mol\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""C:\Users\greg\AppData\Local\UCSF\ChimeraX\1.6\site- packages\chimerax\isolde\\__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""C:\Users\greg\AppData\Local\UCSF\ChimeraX\1.6\site- packages\chimerax\isolde\toolbar.py"", line 21, in toolbar_command run(session, f'isolde sim start {_current_residue_sel_string(session)}') File ""C:\Users\greg\\_mol\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Users\greg\\_mol\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Users\greg\AppData\Local\UCSF\ChimeraX\1.6\site- packages\chimerax\isolde\cmd\cmd.py"", line 122, in isolde_sim isolde.start_sim() File ""C:\Users\greg\AppData\Local\UCSF\ChimeraX\1.6\site- packages\chimerax\isolde\isolde.py"", line 896, in start_sim sm.start_sim() File ""C:\Users\greg\AppData\Local\UCSF\ChimeraX\1.6\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 401, in start_sim sh.start_sim() File ""C:\Users\greg\AppData\Local\UCSF\ChimeraX\1.6\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1432, in start_sim self._prepare_sim() File ""C:\Users\greg\AppData\Local\UCSF\ChimeraX\1.6\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1377, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Users\greg\\_mol\ChimeraX\bin\lib\site- packages\openmm\app\simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Users\greg\\_mol\ChimeraX\bin\lib\site-packages\openmm\openmm.py"", line 4584, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: openmm.OpenMMException: Error compiling kernel: File ""C:\Users\greg\\_mol\ChimeraX\bin\lib\site-packages\openmm\openmm.py"", line 4584, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 392.58 OpenGL renderer: Quadro K5000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_CA.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: System manufacturer Model: System Product Name OS: Microsoft Windows 10 Pro Education (Build 19045) Memory: 17,117,229,056 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-4960X CPU @ 3.60GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 comtypes: 1.1.14 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pywin32: 305 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 WMI: 1.5.1 zipp: 3.15.0 }}} " defect assigned normal Third Party Tom Goddard all ChimeraX