id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16222 Similar Structures: key error from clicking Traces Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.7-arm64-arm-64bit ChimeraX Version: 1.9.dev202410300405 (2024-10-30 04:05:08 UTC) Description using Similar Structures tool Not sure of the series of events that causes this but I opened a previously saved mmseqs2 search from a .sms file. Then I clicked Ligands, which fetched structures and showed ligands successfully. Then I clicked Traces, which again started to fetch structures but then ran into this error. Another possibly unintended observation is that when I open an sms file it makes another identical sms file. I'll attach one of them Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > alias start tool show $1 > alias whereprefs info path user unversioned config > alias captut open help:user/tutorials/binding-sites.html#cap-example > alias previewts toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu;toolshed reload available > alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload > available > alias btut open > https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding- > sites.html; ui dockable false ""Help Viewer"" > alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/conservation-coloring.html; ui dockable false ""Help Viewer"" > alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop- > modeling.html; ui dockable false ""Help Viewer"" > alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole- > channel.html; ui dockable false ""Help Viewer""; windowsize 600 800 executed startup.cxc UCSF ChimeraX version: 1.9.dev202410300405 (2024-10-30) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/meng/Desktop/startup.cxc format cmd > alias reset view orient; view initial > alias start tool show $1 > alias whereprefs info path user unversioned config > alias captut open help:user/tutorials/binding-sites.html#cap-example > alias previewts toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu;toolshed reload available > alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload > available > alias btut open > https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding- > sites.html; ui dockable false ""Help Viewer"" > alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/conservation-coloring.html; ui dockable false ""Help Viewer"" > alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop- > modeling.html; ui dockable false ""Help Viewer"" > alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole- > channel.html; ui dockable false ""Help Viewer""; windowsize 600 800 executed startup.cxc > open /Users/meng/Downloads/ChimeraX/Foldseek/1hxz_foldseek_pdb_1_2.sms > format sms No such file/path: /Users/meng/Downloads/ChimeraX/Foldseek/1hxz_foldseek_pdb_1_2.sms > open /Users/meng/Downloads/ChimeraX/MMseqs2/1hxz_mmseqs2_pdb.sms format sms Summary of feedback from opening /Users/meng/Downloads/ChimeraX/MMseqs2/1hxz_mmseqs2_pdb.sms --- notes | > open /Users/meng/Downloads/ChimeraX/PDB/1hxz.cif1hxz.cif title: Miniprotein MP-2 complex with streptavidin [more info...] | Chain information for 1hxz.cif #1 --- Chain | Description | UniProt A B | STREPTAVIDIN | SAV_STRAV 11-139 C D | MP-2 | 1hxz.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly Found 9 similar structures to 1hxz.cif #1/D in pdb database using mmseqs2, name mm1 Read 9 similar structures to 1hxz.cif #1/D in pdb database using mmseqs2, name mm1 > close session > open /Users/meng/Downloads/ChimeraX/Foldseek/2gbp_foldseek_pdb.sms format > sms Summary of feedback from opening /Users/meng/Downloads/ChimeraX/Foldseek/2gbp_foldseek_pdb.sms --- notes | > open /Users/meng/Downloads/ChimeraX/PDB/2gbp.cif2gbp.cif title: Sugar and signal-transducer binding sites of the escherichia coli galactose chemoreceptor protein [more info...] | Chain information for 2gbp.cif #1 --- Chain | Description | UniProt A | D-GALACTOSE/D-GLUCOSE BINDING PROTEIN | DGAL_ECOLI 1-309 Non-standard residues in 2gbp.cif #1 --- BGC — β-D-glucose CA — calcium ion Found 727 similar structures to 2gbp.cif #1/A in pdb database using foldseek, name fs1 Read 727 similar structures to 2gbp.cif #1/A in pdb database using foldseek, name fs1 > sequence search /A Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm1 > similarstructures fetchcoords Fetching compressed mmCIF 1glg from http://files.rcsb.org/download/1glg.cif Fetching compressed mmCIF 2fvy from http://files.rcsb.org/download/2fvy.cif Fetching CCD CO2 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/CO2/CO2.cif Fetching compressed mmCIF 2hph from http://files.rcsb.org/download/2hph.cif Fetching compressed mmCIF 2qw1 from http://files.rcsb.org/download/2qw1.cif Fetching CCD 3MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/3MG/3MG.cif Fetching compressed mmCIF 2ipn from http://files.rcsb.org/download/2ipn.cif Fetching compressed mmCIF 2ipm from http://files.rcsb.org/download/2ipm.cif Fetching compressed mmCIF 2ipl from http://files.rcsb.org/download/2ipl.cif Fetching compressed mmCIF 8fxt from http://files.rcsb.org/download/8fxt.cif Fetching CCD YDM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/YDM/YDM.cif Fetching compressed mmCIF 1gca from http://files.rcsb.org/download/1gca.cif Fetching compressed mmCIF 3ga5 from http://files.rcsb.org/download/3ga5.cif Fetching CCD RGG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/RGG/RGG.cif Fetching CCD SCN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/SCN/SCN.cif Fetching compressed mmCIF 5kws from http://files.rcsb.org/download/5kws.cif Fetching compressed mmCIF 4z0n from http://files.rcsb.org/download/4z0n.cif Fetching compressed mmCIF 8fxu from http://files.rcsb.org/download/8fxu.cif Fetching CCD YDQ from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/YDQ/YDQ.cif Fetching compressed mmCIF 4yo7 from http://files.rcsb.org/download/4yo7.cif Fetching CCD INS from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/INS/INS.cif Fetching compressed mmCIF 5jx2 from http://files.rcsb.org/download/5jx2.cif Fetching CCD ALY from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ALY/ALY.cif Fetching CCD BTB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/BTB/BTB.cif Fetching compressed mmCIF 6bgc from http://files.rcsb.org/download/6bgc.cif Fetching compressed mmCIF 6bgd from http://files.rcsb.org/download/6bgd.cif Fetching compressed mmCIF 4rsm from http://files.rcsb.org/download/4rsm.cif Fetching CCD 3VB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/3VB/3VB.cif Fetching compressed mmCIF 4rs3 from http://files.rcsb.org/download/4rs3.cif Fetching CCD XYL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/XYL/XYL.cif Fetching compressed mmCIF 5hko from http://files.rcsb.org/download/5hko.cif Fetching CCD 62W from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/62W/62W.cif Fetching compressed mmCIF 2ioy from http://files.rcsb.org/download/2ioy.cif Fetching CCD RIP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/RIP/RIP.cif Fetching compressed mmCIF 7e7m from http://files.rcsb.org/download/7e7m.cif Fetching compressed mmCIF 2gx6 from http://files.rcsb.org/download/2gx6.cif Fetching compressed mmCIF 3urm from http://files.rcsb.org/download/3urm.cif Fetching compressed mmCIF 3uug from http://files.rcsb.org/download/3uug.cif Fetching CCD BDP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/BDP/BDP.cif Fetching compressed mmCIF 1urp from http://files.rcsb.org/download/1urp.cif Fetching compressed mmCIF 2dri from http://files.rcsb.org/download/2dri.cif Fetching compressed mmCIF 4yv7 from http://files.rcsb.org/download/4yv7.cif Fetching compressed mmCIF 1drj from http://files.rcsb.org/download/1drj.cif Fetching compressed mmCIF 1drk from http://files.rcsb.org/download/1drk.cif Fetching compressed mmCIF 4zjp from http://files.rcsb.org/download/4zjp.cif Fetching compressed mmCIF 1dbp from http://files.rcsb.org/download/1dbp.cif Fetching compressed mmCIF 4ry0 from http://files.rcsb.org/download/4ry0.cif Fetching compressed mmCIF 5ibq from http://files.rcsb.org/download/5ibq.cif Fetching CCD XXM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/XXM/XXM.cif Fetching compressed mmCIF 1ba2 from http://files.rcsb.org/download/1ba2.cif Fetching compressed mmCIF 4ry9 from http://files.rcsb.org/download/4ry9.cif Fetching CCD TLZ from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/TLZ/TLZ.cif Fetching compressed mmCIF 4ys6 from http://files.rcsb.org/download/4ys6.cif Fetching compressed mmCIF 4irx from http://files.rcsb.org/download/4irx.cif Fetching compressed mmCIF 4ywh from http://files.rcsb.org/download/4ywh.cif Fetching CCD XYP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/XYP/XYP.cif Fetching compressed mmCIF 4wwh from http://files.rcsb.org/download/4wwh.cif Fetching compressed mmCIF 5dte from http://files.rcsb.org/download/5dte.cif Fetching CCD ALL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/ALL/ALL.cif Fetching compressed mmCIF 6hb0 from http://files.rcsb.org/download/6hb0.cif Fetching compressed mmCIF 6hbd from http://files.rcsb.org/download/6hbd.cif Fetching compressed mmCIF 6hbm from http://files.rcsb.org/download/6hbm.cif Fetching CCD AHR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/AHR/AHR.cif Fetching compressed mmCIF 6hyh from http://files.rcsb.org/download/6hyh.cif Fetching CCD GYE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/GYE/GYE.cif Fetching compressed mmCIF 4rxm from http://files.rcsb.org/download/4rxm.cif Fetching compressed mmCIF 3m9w from http://files.rcsb.org/download/3m9w.cif Fetching compressed mmCIF 3m9x from http://files.rcsb.org/download/3m9x.cif Fetching compressed mmCIF 3ma0 from http://files.rcsb.org/download/3ma0.cif Fetching compressed mmCIF 1gub from http://files.rcsb.org/download/1gub.cif Fetching compressed mmCIF 1gud from http://files.rcsb.org/download/1gud.cif Fetching compressed mmCIF 1rpj from http://files.rcsb.org/download/1rpj.cif Fetching compressed mmCIF 2rjo from http://files.rcsb.org/download/2rjo.cif Fetching compressed mmCIF 5ocp from http://files.rcsb.org/download/5ocp.cif Fetching CCD FUB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/FUB/FUB.cif Fetching compressed mmCIF 4yle from http://files.rcsb.org/download/4yle.cif Fetching compressed mmCIF 8wl5 from http://files.rcsb.org/download/8wl5.cif Fetching compressed mmCIF 8wl7 from http://files.rcsb.org/download/8wl7.cif Fetching compressed mmCIF 8wl9 from http://files.rcsb.org/download/8wl9.cif Fetching compressed mmCIF 8wlb from http://files.rcsb.org/download/8wlb.cif Fetching CCD WEB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/WEB/WEB.cif Fetching compressed mmCIF 3l6u from http://files.rcsb.org/download/3l6u.cif Fetching compressed mmCIF 3rot from http://files.rcsb.org/download/3rot.cif Fetched coordinates for 99 hits, time 0:35 Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm1 > sequence search /A Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm2 > similarstructures traces > foldseek /A Found 727 similar structures to 2gbp.cif #1/A in pdb database using foldseek, name fs1 > open /Users/meng/Downloads/ChimeraX/mmseqs2/2gbp*sms Summary of feedback from opening /Users/meng/Downloads/ChimeraX/mmseqs2/2gbp_mmseqs2_pdb.sms --- note | Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm1 Summary of feedback from opening /Users/meng/Downloads/ChimeraX/mmseqs2/2gbp_mmseqs2_pdb_1.sms --- note | Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm2 Read 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm1 Read 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm2 > similarstructures ligands Found 8973 ligands in 99 hits: 3MG, 62W, ACT, AHR, ALL, ASP, BGC, BTB, CA, CIT, CL, CO2, EDO, FUB, GAL, GLC, GOL, GYE, GZL, HOH, INS, MG, MLA, NA, PO4, RGG, RIP, SO4, TRS, UNL, WEB, XYL, XYP, YDM, YDQ, ZN > similarstructures traces Fetched coordinates for 99 hits, time 0:02 Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm2 Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/similarstructures/gui.py"", line 333, in _show_backbone_traces run(self.session, cmd) File ""/Users/meng/Desktop/ChimeraX_Daily.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 ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/similarstructures/traces.py"", line 80, in similar_structures_traces hresname = [hitseq[i] for i in hi] ^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/similarstructures/traces.py"", line 80, in hresname = [hitseq[i] for i in hi] ~~~~~~^^^ KeyError: 0 KeyError: 0 File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/similarstructures/traces.py"", line 80, in hresname = [hitseq[i] for i in hi] ~~~~~~^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Model Number: MK1F3LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.1.1 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7 (23H124) Kernel Version: Darwin 23.6.0 Time since boot: 5 hours, 34 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 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: 2023.11.17 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: 14.1.10 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: 1.9.dev202410300405 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-PhenixUI: 1.3 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-ScholAR: 0.4.2 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.2.2 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 contourpy: 1.3.0 coverage: 7.6.4 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 iniconfig: 2.0.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 joblib: 1.4.2 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 llvmlite: 0.43.0 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 numba: 0.60.0 numexpr: 2.10.1 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 plotly: 5.24.1 pluggy: 1.5.0 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.7.0 pynmrstar: 3.3.4 pynndescent: 0.5.13 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 pytest: 8.3.3 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.1 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scikit-learn: 1.5.2 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 threadpoolctl: 3.5.0 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tornado: 6.4.1 tqdm: 4.66.5 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 umap-learn: 0.5.6 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 File attachment: 2gbp_mmseqs2_pdb.sms }}} [attachment:""2gbp_mmseqs2_pdb.sms""] " defect closed normal Structure Comparison fixed all ChimeraX