id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8172 Read MOLE format: KeyError: 'Channels' chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold match > MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV No AlphaFold model with similar sequence for 1 sequences Opened 0 AlphaFold model > alphafold search > MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Webservices job id: XN6ICFTRP8ITV6W2 > alphafold fetch A0A1B6FCL0 version 4 Fetching compressed AlphaFold A0A1B6FCL0 from https://alphafold.ebi.ac.uk/files/AF-A0A1B6FCL0-F1-model_v4.cif Chain information for AlphaFold A0A1B6FCL0 #1 --- Chain | Description | UniProt A | Neur_chan_LBD domain-containing protein | A0A1B6FCL0_9HEMI Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % A0A1B6FCL0 | MGHNI...IMLIV | 22.1 | 58.8 > alphafold fetch A0A1B6LFJ7 version 4 Fetching compressed AlphaFold A0A1B6LFJ7 from https://alphafold.ebi.ac.uk/files/AF-A0A1B6LFJ7-F1-model_v4.cif | Chain information for AlphaFold A0A1B6LFJ7 #2 --- Chain | Description | UniProt A | Neur_chan_LBD domain-containing protein | A0A1B6LFJ7_9HEMI Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % A0A1B6LFJ7 | MGHNI...IMLIV | 25.6 | 67.0 > alphafold fetch A0A023EY00 version 4 Fetching compressed AlphaFold A0A023EY00 from https://alphafold.ebi.ac.uk/files/AF-A0A023EY00-F1-model_v4.cif | Chain information for AlphaFold A0A023EY00 #3 --- Chain | Description | UniProt A | Putative nicotinic acetylcholine receptor alpha9 subunit | A0A023EY00_TRIIF Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % A0A023EY00 | MGHNI...IMLIV | 21.2 | 50.6 > hide #3 models > hide #2 models > hide #1 models > show #2 models > hide #2 models > show #3 models > hide #3 models > show #2 models > show #1 models > hide #2 models > alphafold predict > MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction > alphafold predict > MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV Running AlphaFold prediction [Repeated 4 time(s)]AlphaFold prediction finished Results in C:\Users\ferna/Downloads/ChimeraX/AlphaFold/prediction_2 > open C:\Users\ferna/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb | Chain information for best_model.pdb #4 --- Chain | Description A | No description available > open ""C:/Users/ferna/OneDrive/Área de > Trabalho/Euschistus/nAchR_euschistus_prediction_1/best_model_nAchR_euschistus_1.pdb"" Chain information for best_model_nAchR_euschistus_1.pdb #5 --- Chain | Description A | No description available > hide #5 models > show #5 models > hide #4 models > show #4 models > hide #5 models > show #5 models > hide #4 models > hide #1 models > show #1 models > show #2 models > hide #1 models > hide #5 models > hide #2 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #5 models > hide #5 target m > show #4 models > hide #4 models > alphafold predict > MGHNILLLLSLGILVKHCLGGCNVERSSLSKLKDDIFCGYDPYLRPVRHQNNKTLVTLTLYPRHIDFEEDRNSLYVDTWIYMSWIDTNLVWNPKDYDDINYLHVPAHMLWFPDLTVYNKLDLDLDTESNSAVVSSNGRVYVVVMTDFTAYCSMDLRHWPNDEHSCTAMLGSRSYTGALLDFMFNEQMAVGMKNYFANRMWKLQSANATRKVTELGKKNGTVYLVTVQYHFVVKRHATFIIATVFVPVLLLTLMVLLPLLLPFSSERCYNTLALAAVGHVAYLQYLGLILPHNADNTILMVAYIRDSLVMTVFALIVCIWIDKITSTTDLPIWLSNIIKNLQTTKYTRLLLVSQIDSKQKSEEDVNLVNPDVVCTSKDWSILLILIQRSIFIIYLVIYTIMLIV Running AlphaFold prediction > show #5 models > select add #5 3253 atoms, 3329 bonds, 403 residues, 1 model selected > select subtract #5 Nothing selected > hide #5 models > show #4 models > select add #4 3253 atoms, 3329 bonds, 403 residues, 1 model selected > alphafold fetch A0A1B6FCL0 version 4 Chain information for AlphaFold A0A1B6FCL0 #6 --- Chain | Description | UniProt A | Neur_chan_LBD domain-containing protein | A0A1B6FCL0_9HEMI Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % A0A1B6FCL0 | MGHNI...IMLIV | 22.1 | 58.8 > select subtract #4 Nothing selected > matchmaker #1 to #4 | Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker best_model.pdb, chain A (#4) with AlphaFold A0A1B6FCL0, chain A (#1), sequence alignment score = 928 RMSD between 217 pruned atom pairs is 1.140 angstroms; (across all 403 pairs: 9.785) > matchmaker #1 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker best_model.pdb, chain A (#4) with AlphaFold A0A1B6FCL0, chain A (#1), sequence alignment score = 928 RMSD between 217 pruned atom pairs is 1.140 angstroms; (across all 403 pairs: 9.785) > hide #6 models > hide #4 models > show #1 models > hide #1 atoms > style #1 stick Changed 3571 atom styles > style #1 stick Changed 3571 atom styles > ui tool show ""Color Actions"" > color cyan > show #4 models > hide #1 models > color bfactor #4 palette alphafold 3253 atoms, 403 residues, atom bfactor range 29.5 to 98.1 > show #1 models > show #1,4 atoms > hide #1,4 atoms > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > hide #4 models > hide #1 models AlphaFold prediction finished Results in C:\Users\ferna/Downloads/ChimeraX/AlphaFold/prediction_2 > open C:\Users\ferna/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb Chain information for best_model.pdb #7 --- Chain | Description A | No description available > show #4 models > open C:/Users/ferna/Downloads/thiamethoxam_Conformer3D_CID_5821911.json Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""C:\Program Files\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:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 457, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mole\\__init__.py"", line 27, in open return mole.read_mole_json(session, data, file_name, **kw) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py"", line 40, in read_mole_json models = channel_models(session, j['Channels'], transparency/100.0) KeyError: 'Channels' KeyError: 'Channels' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py"", line 40, in read_mole_json models = channel_models(session, j['Channels'], transparency/100.0) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 27.20.100.9664 OpenGL renderer: Intel(R) HD Graphics 530 OpenGL vendor: Intel Python: 3.9.11 Locale: pt_BR.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Dell Inc. Model: OptiPlex 7040 OS: Microsoft Windows 10 Pro (Build 19044) Memory: 17,061,920,768 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz OSLanguage: pt-BR Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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-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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.11.0 }}} " defect closed normal Input/Output fixed all ChimeraX