id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14988 Cannot write into Modeller temporary folder robertperezmd@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.7.4-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Unable to model TAPV sequence usong alignment with pdb file 5F1B Chain A. Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5F1B format mmcif fromDatabase pdb 5f1b title: Structural basis of Ebola virus entry: viral glycoprotein bound to its endosomal receptor Niemann-Pick C1 [more info...] Chain information for 5f1b #1 --- Chain | Description | UniProt A | GP1 | VGP_EBOZ5 32-188 B | GP2 | VGP_EBOZ5 509-632 C | Niemann-Pick C1 protein | NPC1_HUMAN 2-248 Non-standard residues in 5f1b #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open ""/Users/rickricketson/Desktop/TAPV-5F1B Chain A MSA.fasta"" Summary of feedback from opening /Users/rickricketson/Desktop/TAPV-5F1B Chain A MSA.fasta --- notes | Alignment identifier is TAPV-5F1B Chain A MSA.fasta Associated 5f1b chain A to 5F1B_1|Chain/1-132 A|GP1|Zaire ebolavirus (128951) with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment TAPV-5F1B Chain A MSA.fasta Opened 2 sequences from TAPV-5F1B Chain A MSA.fasta > ui tool show ""Modeller Comparative"" > modeller comparative ""TAPV-5F1B Chain A MSA.fasta:2"" numModels 5 fast false > multichain true hetPreserve false hydrogens false waterPreserve false Webservices job id: 4BI53R9CPI9THYUT Modeller job (ID 4BI53R9CPI9THYUT) finished Parameters --- Chain pairing | ss 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 5f1b, chain A (#1) with 5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence alignment score = 636.1 RMSD between 117 pruned atom pairs is 0.589 angstroms; (across all 132 pairs: 1.041) Parameters --- Chain pairing | ss 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 5f1b, chain A (#1) with 5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence alignment score = 636.1 RMSD between 128 pruned atom pairs is 0.730 angstroms; (across all 132 pairs: 0.904) Parameters --- Chain pairing | ss 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 5f1b, chain A (#1) with 5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence alignment score = 636.1 RMSD between 127 pruned atom pairs is 0.928 angstroms; (across all 132 pairs: 1.033) Parameters --- Chain pairing | ss 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 5f1b, chain A (#1) with 5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence alignment score = 628.9 RMSD between 121 pruned atom pairs is 0.556 angstroms; (across all 132 pairs: 0.957) Parameters --- Chain pairing | ss 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 5f1b, chain A (#1) with 5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence alignment score = 636.1 RMSD between 131 pruned atom pairs is 0.368 angstroms; (across all 132 pairs: 0.417) Associated 5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951) chain A to 5F1B_1|Chain/1-132 A|GP1|Zaire ebolavirus (128951) with 0 mismatches [Repeated 4 time(s)] Chain information for 5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951) --- Chain | Description 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A | No description available > ui tool show ""Show Sequence Viewer"" > ui tool show ""Modeller Comparative"" > modeller comparative ""TAPV-5F1B Chain A MSA.fasta:1"" numModels 5 fast false > multichain true hetPreserve false hydrogens false waterPreserve false Traceback (most recent call last): File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/modeller/tool.py"", line 311, in launch_modeller run( File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/modeller/cmd.py"", line 48, in sequence_model comparative.model(session, targets, block=block, multichain=multichain, File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/modeller/comparative.py"", line 303, in model save_pdb(session, pdb_file_name, models=[structure], polymeric_res_names=ATOM_res_names) File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/pdb/pdb.py"", line 224, in save_pdb _pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only, OSError: Unable to open file '/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmp42hlpdsl/template_struc/5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)_2.4.pdb' for writing OSError: Unable to open file '/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmp42hlpdsl/template_struc/5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)_2.4.pdb' for writing File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/pdb/pdb.py"", line 224, in save_pdb _pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only, See log for complete Python traceback. > modeller comparative ""TAPV-5F1B Chain A MSA.fasta:1"" numModels 5 fast false > multichain true hetPreserve false hydrogens false waterPreserve false Traceback (most recent call last): File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/modeller/tool.py"", line 311, in launch_modeller run( File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/modeller/cmd.py"", line 48, in sequence_model comparative.model(session, targets, block=block, multichain=multichain, File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/modeller/comparative.py"", line 303, in model save_pdb(session, pdb_file_name, models=[structure], polymeric_res_names=ATOM_res_names) File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/pdb/pdb.py"", line 224, in save_pdb _pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only, OSError: Unable to open file '/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmpfsciswuo/template_struc/5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)_2.4.pdb' for writing OSError: Unable to open file '/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmpfsciswuo/template_struc/5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)_2.4.pdb' for writing File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/pdb/pdb.py"", line 224, in save_pdb _pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only, See log for complete Python traceback. OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac17,1 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 32 GB System Firmware Version: 526.0.0.0.0 OS Loader Version: 540.120.3~37 SMC Version (system): 2.33f12 Software: System Software Overview: System Version: macOS 12.7.4 (21H1123) Kernel Version: Darwin 21.6.0 Time since boot: 18 minutes Graphics/Displays: AMD Radeon R9 M380: Chipset Model: AMD Radeon R9 M380 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 2 GB Vendor: AMD (0x1002) Device ID: 0x6640 Revision ID: 0x0080 ROM Revision: 113-C6005R-800 VBIOS Version: 113-C6005T-009 EFI Driver Version: 01.00.800 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 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: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 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: 1.1.3 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 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: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 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: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 File attachment: TAPV-5F1B Chain A MSA.fasta }}} [attachment:""TAPV-5F1B Chain A MSA.fasta""] " defect closed normal Sequence nonchimerax all ChimeraX