id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6313 atom_search_lib missing Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.4.dev202203030220 (2022-03-03 02:20:09 UTC) Description AddH seems broken in the daily build. Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.4.dev202203030220 (2022-03-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > isolde demo crystal_intro > set selectionWidth 4 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 before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description | UniProt A | predicted microcompartment protein | A5N734_CLOK5 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 12 residues in model #1 to IUPAC-IUB standards. before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description | UniProt 1.2/A | predicted microcompartment protein | A5N734_CLOK5 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 WARNING: multiple experimental reflection datasets found: (dataset) FOBS, SIGFOBS, (dataset) IOBS, SIGIOBS, (dataset) DANO, SIGDANO, (dataset) F(+), SIGF(+), F(-), SIGF(-), (dataset) I(+), SIGI(+), I(-), SIGI(-) Automatically choosing ""(dataset) FOBS, SIGFOBS"". Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at level 0.303, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at level -0.0575,0.0575, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723, shown at level 0.603, step 1, values float32 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723, shown at level 0.366, step 1, values float32 Loaded crystallographic demo: PDB ID 3io0 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: started sim > select clear > graphics rate true > ui tool show Shell > graphics rate false QCoreApplication::exec: The event loop is already running ISOLDE: paused sim Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim > select clear > graphics rate true > graphics rate false QCoreApplication::exec: The event loop is already running [Repeated 1 time(s)]Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1 3348 atoms, 3371 bonds, 229 residues, 30 models selected ISOLDE: started sim > select clear > st [Repeated 52 time(s)]Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > close #1 Deleting Crystallographic maps (3io0-sf.mtz) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_sharp_29 Deleting (LIVE) MDFF potential > open 2rf4 structureFactors true overSampling 2 Summary of feedback from opening 2rf4 fetched from pdb --- warnings | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma, pdbx_anom_difference, pdbx_anom_difference_sigma Automatically choosing ""F_meas_au, F_meas_sigma_au"". No free flags detected in this dataset! Automatically generated a new random set with 874 free from 18174 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 3.099903641564608 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 34,34,34, pixel 0.766,0.761,0.727, shown at level 0.191, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 34,34,34, pixel 0.766,0.761,0.727, shown at level -0.0889,0.0889, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_32 as #1.1.1.4, grid size 34,34,34, pixel 0.766,0.761,0.727, shown at level 0.412, step 1, values float32 2rf4 title: Crystal structure of the RNA Polymerase I subcomplex A14/43 [more info...] Chain information for 2rf4 --- Chain | Description | UniProt 1.2/A 1.2/C 1.2/E | DNA-directed RNA polymerase I subunit RPA4 | RPA43_YEAST 1.2/B 1.2/D 1.2/F | DNA-directed RNA polymerase I subunit RPA4 | RPA14_YEAST 2rf4 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 41 residues in model #1.2 to IUPAC-IUB standards. Opened (LIVE) MDFF potential as #1.1.1.5, grid size 34,34,34, pixel 0.766,0.761,0.727, shown at level 0.205, step 1, values float32 > alphafold match #1 Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json Fetching compressed AlphaFold P46669 from https://alphafold.ebi.ac.uk/files/AF-P46669-F1-model_v2.cif Fetching compressed AlphaFold P50106 from https://alphafold.ebi.ac.uk/files/AF-P50106-F1-model_v2.cif 2 AlphaFold models found using UniProt identifiers: P46669 (chains A,A,C,C,E,E), P50106 (chains B,B,D,D,F,F) AlphaFold chains matching 2rf4 --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id B | RPA14_YEAST | P50106 | 1.71 | 52 | 61 | 100 B | RPA14_YEAST | P50106 | 1.57 | 35 | 61 | 100 D | RPA14_YEAST | P50106 | 1.59 | 52 | 60 | 100 D F | RPA14_YEAST | P50106 | 1.65 | 35 | 60 | 100 F | RPA14_YEAST | P50106 | 1.69 | 52 | 60 | 100 A | RPA43_YEAST | P46669 | 1.66 | 171 | 174 | 100 A | RPA43_YEAST | P46669 | 3.00 | 42 | 174 | 100 C | RPA43_YEAST | P46669 | 1.48 | 171 | 172 | 100 C | RPA43_YEAST | P46669 | 3.25 | 42 | 172 | 100 E | RPA43_YEAST | P46669 | 1.58 | 171 | 175 | 100 E | RPA43_YEAST | P46669 | 3.75 | 42 | 175 | 100 Opened 12 AlphaFold models > show #2 > select /A,B 4213 atoms, 4302 bonds, 2 pseudobonds, 535 residues, 6 models selected > close #1.3#1-2#1.1-2 Deleting Crystallographic maps (2rf4-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_sharp_32 Deleting (LIVE) MDFF potential > open 3brw structureFactors true Summary of feedback from opening 3brw fetched from pdb --- warnings | Unknown polymer entity '5' near line 10839 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. notes | Fetching compressed mmCIF 3brw from http://files.rcsb.org/download/3brw.cif Fetching CCD BEF from http://ligand-expo.rcsb.org/reports/B/BEF/BEF.cif Fetching compressed 3brw structure factors from http://files.rcsb.org/download/3brw-sf.cif Resolution: 3.400053747470817 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 38,28,22, pixel 1.09,1.09,1.13, shown at level 0.155, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 38,28,22, pixel 1.09,1.09,1.13, shown at level -0.0584,0.0584, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_40 as #1.1.1.4, grid size 38,28,22, pixel 1.09,1.09,1.13, shown at level 0.332, step 1, values float32 3brw title: Structure of the Rap-RapGAP complex [more info...] Chain information for 3brw --- Chain | Description | UniProt 1.2/A 1.2/B 1.2/C | Rap1 GTPase-activating protein 1 | RPGP1_HUMAN 1.2/D | Ras-related protein Rap-1b | RAP1B_HUMAN Non-standard residues in 3brw #1.2 --- BEF — beryllium trifluoride ion MG — magnesium ion 3brw mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 133 residues in model #1.2 to IUPAC-IUB standards. Opened (LIVE) MDFF potential as #1.1.1.5, grid size 38,28,22, pixel 1.09,1.09,1.13, shown at level 0.152, step 1, values float32 > alphafold match #1 Fetching compressed AlphaFold P47736 from https://alphafold.ebi.ac.uk/files/AF-P47736-F1-model_v2.cif Fetching compressed AlphaFold P61224 from https://alphafold.ebi.ac.uk/files/AF-P61224-F1-model_v2.cif 2 AlphaFold models found using UniProt identifiers: P47736 (chains A,B,C), P61224 (chain D) AlphaFold chains matching 3brw --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id D | RAP1B_HUMAN | P61224 | 0.83 | 167 | 167 | 100 A | RPGP1_HUMAN | P47736 | 1.85 | 341 | 336 | 99 B | RPGP1_HUMAN | P47736 | 1.27 | 341 | 337 | 99 C | RPGP1_HUMAN | P47736 | 1.80 | 341 | 332 | 99 Opened 4 AlphaFold models > show #2 > isolde restrain distances #1/A templateAtoms #2/A adjustForConfidence true > displayThreshold 0.5 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 68 residues in model #2.1 to IUPAC-IUB standards. Fetching compressed Alphafold P47736 PAE from https://alphafold.ebi.ac.uk/files/AF-P47736-F1-predicted_aligned_error_v1.json RMSD between 330 pruned atom pairs is 1.430 angstroms; (across all 336 pairs: 1.835) RMSD between 5 pruned atom pairs is 2.688 angstroms; (across all 6 pairs: 3.841) > isolde restrain distances #1/B templateAtoms #2/B adjustForConfidence true > displayThreshold 0.5 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 68 residues in model #2.2 to IUPAC-IUB standards. RMSD between 334 pruned atom pairs is 1.071 angstroms; (across all 337 pairs: 1.249) > select #1/A,B 5418 atoms, 5551 bonds, 676 residues, 1 model selected > hide #!2 models > select clear > show #!2 models > addh Summary of feedback from adding hydrogens to multiple structures --- warnings | Not adding hydrogens to 3brw #1.2/A THR 76 CB because it is missing heavy-atom bond partners Not adding hydrogens to 3brw #1.2/A LEU 411 CB because it is missing heavy- atom bond partners Not adding hydrogens to 3brw #1.2/B LYS 78 CB because it is missing heavy-atom bond partners Not adding hydrogens to 3brw #1.2/C LYS 78 CB because it is missing heavy-atom bond partners Not adding hydrogens to 3brw #1.2/C LEU 411 CB because it is missing heavy- atom bond partners notes | Termini for 3brw (#1.2) chain A determined from SEQRES records Termini for 3brw (#1.2) chain B determined from SEQRES records Termini for 3brw (#1.2) chain C determined from SEQRES records Termini for 3brw (#1.2) chain D determined from SEQRES records Chain-initial residues that are actual N termini: 3brw #1.2/D MET 1 Chain-initial residues that are not actual N termini: 3brw #1.2/A THR 76, 3brw #1.2/B LYS 78, 3brw #1.2/C LYS 78, 3brw #1.2/C PRO 330 Chain-final residues that are actual C termini: 3brw #1.2/D ARG 167 Chain-final residues that are not actual C termini: 3brw #1.2/A LEU 411, 3brw #1.2/B ASP 414, 3brw #1.2/C GLY 325, 3brw #1.2/C GLY 413 Traceback (most recent call last): File ""C:\Program Files\ChimeraX-daily\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 302, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX-daily\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX-daily\bin\lib\site- packages\chimerax\addh\cmd.py"", line 62, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File ""C:\Program Files\ChimeraX-daily\bin\lib\site- packages\chimerax\addh\cmd.py"", line 161, in hbond_add_hydrogens hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info, File ""C:\Program Files\ChimeraX-daily\bin\lib\site- packages\chimerax\addh\cmd.py"", line 168, in hbond_add_hydrogens _make_shared_data(session, structures, in_isolation) File ""C:\Program Files\ChimeraX-daily\bin\lib\site- packages\chimerax\addh\cmd.py"", line 365, in _make_shared_data from chimerax.atom_search import AtomSearchTree File ""C:\Program Files\ChimeraX-daily\bin\lib\site- packages\chimerax\atom_search\\__init__.py"", line 15, in import chimerax.atom_search_lib ModuleNotFoundError: No module named 'chimerax.atom_search_lib' ModuleNotFoundError: No module named 'chimerax.atom_search_lib' File ""C:\Program Files\ChimeraX-daily\bin\lib\site- packages\chimerax\atom_search\\__init__.py"", line 15, in import chimerax.atom_search_lib See log for complete Python traceback. > ui tool show Shell C:\Program Files\ChimeraX-daily\bin\lib\site- packages\jedi\inference\compiled\subprocess\functions.py:22: UserWarning: Module chimerax.atom_search.ast not importable in path ['C:\\\Users\\\tristan\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\1.4\\\site- packages', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\python39.zip', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\DLLs', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib', 'C:\\\Program Files\\\ChimeraX- daily\\\bin', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site- packages', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site- packages\\\win32', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site- packages\\\win32\\\lib', 'C:\\\Program Files\\\ChimeraX- daily\\\bin\\\lib\\\site-packages\\\Pythonwin', '.', 'C:\\\Program Files\\\ChimeraX-daily\\\bin\\\lib\\\site-packages\\\IPython\\\extensions']. return access.load_module(inference_state, **kwargs) OpenGL version: 3.3.0 NVIDIA 497.29 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Locale: en_GB.cp1252 Qt version: PyQt5 5.15.2, Qt 5.15.2 Qt platform: windows Manufacturer: Notebook Model: P7xxTM1 OS: Microsoft Windows 10 Education (Build 19041) Memory: 68,654,501,888 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.5.2 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.36.2 ChimeraX-AtomicLibrary: 6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.18.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.1 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202203030220 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4.dev0 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.2 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.8 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.7.7 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16.2 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.5.1 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.29.1 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.26 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.9.2 kiwisolver: 1.3.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.0 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 9.0.0 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.28 psutil: 5.9.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 303 pyzmq: 22.3.0 qtconsole: 5.2.2 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.8 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Structure Analysis fixed all ChimeraX