id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14836 Residue addition problem Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC) Description Looks like something has changed in the way residue addition is handled, breaking ISOLDE's ""isolde add aa"" command (aliased as simply ""aa {residue ID}"" here). The new residues are going in with garbled (and contradictory) order... The residue that triggered the traceback was added to the model, but in a somewhat bizarre location well away from the others. After deleting that, if I select the two new residues and the two preceding, then do in the log: m = session.isolde.selected_model from chimerax.atomic import selected_residues m.residues.indices(selected_residues(session)) array([55, 56, 59, 58]) m.atoms.selecteds=False m.residues[57].atoms.selected=True m.residues.indices(selected_residues(session)) array([58]) ... so the last added residue is somehow both index 57 and 58 in `m.residues` For what it's worth, the code I'm using to add the residues is at https://github.com/tristanic/isolde/blob/ead1b3f7d64869b42efe9b6f2720675656d720e1/isolde/src/atomic/building/build_utils.py#L131 (which calls https://github.com/tristanic/isolde/blob/ead1b3f7d64869b42efe9b6f2720675656d720e1/isolde/src/atomic/building/place_ligand.py#L159 to add the new residue). As far as I can tell, this seems to work correctly in ChimeraX 1.7. 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: 1.8.dev202403220040 (2024-03-22) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6zp4 Summary of feedback from opening 6zp4 fetched from pdb --- note | Fetching compressed mmCIF 6zp4 from http://files.rcsb.org/download/6zp4.cif 6zp4 title: SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2 [more info...] Chain information for 6zp4 #1 --- Chain | Description | UniProt 1 | tRNA | 2 | 18S ribosomal RNA | 4 | Eukaryotic translation initiation factor 2 subunit 2 | IF2B_HUMAN 1-333 A | Eukaryotic translation initiation factor 3 subunit A | EIF3A_HUMAN 1-1406 B | Eukaryotic translation initiation factor 3 subunit B | EIF3B_HUMAN 1-814 C | Eukaryotic translation initiation factor 3 subunit C | EIF3C_HUMAN 1-913 D | 40S ribosomal protein S15a | RS15A_HUMAN 1-130 E | Eukaryotic translation initiation factor 3 subunit E | EIF3E_HUMAN 1-445 F | Eukaryotic translation initiation factor 3 subunit F | EIF3F_HUMAN 1-357 G | Eukaryotic translation initiation factor 1A, X-chromosomal | IF1AX_HUMAN 1-144 H | Eukaryotic translation initiation factor 3 subunit H | EIF3H_HUMAN 1-352 I | Eukaryotic translation initiation factor 3 subunit I | EIF3I_HUMAN 1-325 J | Non-structural protein 1 | R1AB_SARS2 1-180 K | Eukaryotic translation initiation factor 3 subunit K | EIF3K_HUMAN 1-218 L | Eukaryotic translation initiation factor 3 subunit L | EIF3L_HUMAN 1-564 M | Eukaryotic translation initiation factor 3 subunit M | EIF3M_HUMAN 1-374 N | Eukaryotic translation initiation factor 3 subunit D | EIF3D_HUMAN 1-548 O | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 0-314 P | 40S ribosomal protein S25 | RS25_HUMAN 1-125 Q | 40S ribosomal protein S26 | RS26_HUMAN 1-115 R | 40S ribosomal protein S27 | RS27_HUMAN 1-84 S | 40S ribosomal protein S28 | RS28_HUMAN 1-69 T | 40S ribosomal protein S30 | RS30_HUMAN 1-59 U | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 1-156 V | Receptor of activated protein C kinase 1 | RACK1_HUMAN 1-317 W | 60S ribosomal protein L41 | RL41_HUMAN 1-25 X | Unknown factor | Y | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472 Z | Eukaryotic translation initiation factor 1 | EIF1_HUMAN 1-113 a | 40S ribosomal protein SA | RSSA_HUMAN 1-295 b | 40S ribosomal protein S3 | RS3_HUMAN 1-243 c | 40S ribosomal protein S9 | RS9_HUMAN 1-194 d | 40S ribosomal protein S2 | RS2_HUMAN 1-293 e | 40S ribosomal protein S5 | RS5_HUMAN 1-204 g | 40S ribosomal protein S16 | RS16_HUMAN 1-146 h | 40S ribosomal protein S20 | RS20_HUMAN 1-119 i | 40S ribosomal protein S14 | RS14_HUMAN 1-151 j | 40S ribosomal protein S23 | RS23_HUMAN 1-143 k | 40S ribosomal protein S18 | RS18_HUMAN 1-152 l | 40S ribosomal protein S29 | RS29_HUMAN 1-56 m | 40S ribosomal protein S13 | RS13_HUMAN 1-151 n | 40S ribosomal protein S11 | RS11_HUMAN 1-158 o | 40S ribosomal protein S15 | RS15_HUMAN 1-145 p | 40S ribosomal protein S3a | RS3A_HUMAN 1-264 q | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263 r | 40S ribosomal protein S6 | RS6_HUMAN 1-249 s | 40S ribosomal protein S7 | RS7_HUMAN 1-194 t | 40S ribosomal protein S8 | RS8_HUMAN 1-208 u | 40S ribosomal protein S10 | RS10_HUMAN 1-165 v | 40S ribosomal protein S12 | RS12_HUMAN 1-132 w | 40S ribosomal protein S17 | RS17_HUMAN 1-135 x | 40S ribosomal protein S19 | RS19_HUMAN 1-145 y | 40S ribosomal protein S21 | RS21_HUMAN 1-83 z | 40S ribosomal protein S24 | RS24_HUMAN 1-133 Non-standard residues in 6zp4 #1 --- GTP — guanosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > view :GTP > clipper init > cofr centerOfView showPivot true > camera ortho > lighting simple > cartoon > style stick Changed 117784 atom styles > color byhetero > log metadata #1 Metadata for 6zp4 #1 --- Title | SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2 Citation | Thoms, M., Buschauer, R., Ameismeier, M., Koepke, L., Denk, T., Hirschenberger, M., Kratzat, H., Hayn, M., Mackens-Kiani, T., Cheng, J., Straub, J.H., Sturzel, C.M., Frohlich, T., Berninghausen, O., Becker, T., Kirchhoff, F., Sparrer, K.M.J., Beckmann, R. (2020). Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 369, 1249-1255. PMID: 32680882. DOI: 10.1126/science.abc8665 Non-standard residues | GTP — guanosine-5'-triphosphate MG — magnesium ion ZN — zinc ion Sources (natural) | Severe acute respiratory syndrome coronavirus 2 (2019-ncov) Homo sapiens (human) CryoEM Map | EMDB 11335 — open map Experimental method | Electron microscopy Resolution | 2.9Å > open 11335 fromDatabase emdb Summary of feedback from opening 11335 fetched from emdb --- notes | Fetching compressed map 11335 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11335/map/emd_11335.map.gz Fetching map header 11335 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11335/header/emd-11335.xml Opened emdb 11335 as #2, grid size 360,360,360, pixel 1.06, shown at level 0.03, step 2, values float32, fit PDB 6zp4 > volume #2 step 1 > volume #2 level 0.0434 > close > cd ""C:/Users/Tristan Croll/Documents/Structures/anti- > isrib/8qzz_eif2_gamma_gtp"" Current working directory is: C:\Users\Tristan Croll\Documents\Structures\anti-isrib\8qzz_eif2_gamma_gtp > open ""C:/Users/Tristan Croll/Documents/Structures/anti- > isrib/8qzz_eif2_gamma_gtp/8qzz_partial_rebuild.pdb"" Chain information for 8qzz_partial_rebuild.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > open ""C:/Users/Tristan Croll/Downloads/ChimeraX/PDB-SF/8qzz-sf.cif"" Summary of feedback from opening C:/Users/Tristan Croll/Downloads/ChimeraX/PDB-SF/8qzz-sf.cif --- warning | No mmCIF models found. > clipper open ""C:/Users/Tristan Croll/Downloads/ChimeraX/PDB-SF/8qzz-sf.cif"" > structureModel #1 overSampling 2.5 Resolution: 3.350277671680785 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, intensity_meas, intensity_sigma, pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma Automatically choosing ""F_meas_au, F_meas_sigma_au"". Launching live xmap mgr took 1.2190792560577393 seconds. Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 38,38,38, pixel 0.67,0.67,0.659, shown at level 0.0823, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 38,38,38, pixel 0.67,0.67,0.659, shown at level -0.0658,0.0658, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_39 as #1.1.1.4, grid size 38,38,38, pixel 0.67,0.67,0.659, shown at level 0.267, step 1, values float32 Chain information for 8qzz_partial_rebuild.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Opened (LIVE) MDFF potential as #1.1.1.5, grid size 38,38,38, pixel 0.67,0.67,0.659, shown at level 0.237, step 1, values float32 Done loading forcefield > 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 > save working.cxs > st > select #1 8498 atoms, 8564 bonds, 3 pseudobonds, 556 residues, 28 models selected > isolde sim start /A-C Loading residue template for GNP from internal database ISOLDE: started sim > select clear > isolde pepflip /A:11 > st [Repeated 1 time(s)] > isolde sim pause > st [Repeated 17 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 8 time(s)] > isolde sim resume > isolde sim pause > isolde sim resume > isolde pepflip /A:334 > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > isolde pepflip /A:151 > isolde sim pause > isolde sim resume > isolde pepflip /A:334 > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > st [Repeated 2 time(s)] > select clear > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > st [Repeated 3 time(s)] > isolde sim stop Sim termination reason: None Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > al MG > select #1 8499 atoms, 8564 bonds, 3 pseudobonds, 557 residues, 34 models selected > isolde sim start /A-C ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > delete sel > aw > isolde sim start /A:502 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > delete sel > st > select #1 8498 atoms, 8564 bonds, 3 pseudobonds, 556 residues, 34 models selected > isolde sim start /A-C ISOLDE: started sim > select clear > isolde sim pause > isolde sim resume > isolde sim pause > st [Repeated 16 time(s)] > isolde sim resume > isolde pepflip /A:65 > isolde sim stop Sim termination reason: None Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > sequence chain #1/A Alignment identifier is 1.2/A > alphafold match #1 trim false Fetching compressed AlphaFold A0A6I9J801 from https://alphafold.ebi.ac.uk/files/AF-A0A6I9J801-F1-model_v4.cif Fetching compressed AlphaFold G3QTZ7 from https://alphafold.ebi.ac.uk/files/AF-G3QTZ7-F1-model_v4.cif 3 AlphaFold models found using sequence similarity searches: A0A6I9J801 (chain A), A0A096NVP0 (chain B), G3QTZ7 (chain C) AlphaFold prediction matching 8qzz_partial_rebuild.pdb --- Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id B | A0A096NVP0 | A0A096NVP0_PAPAN | 0.99 | 315 | 113 | 100 A | A0A6I9J801 | A0A6I9J801_CHRAS | 1.86 | 472 | 433 | 100 C | G3QTZ7 | G3QTZ7_GORGO | 2.21 | 682 | 9 | 100 Opened 3 AlphaFold models > hide #!2 models > aa VAL > isolde sim start #1.2/A:67 ISOLDE: started sim > isolde pepflip #1.2/A:67 [Repeated 1 time(s)] > isolde pepflip #1.2/A:66 [Repeated 2 time(s)] > isolde sim stop Sim termination reason: None Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > aa ARG > isolde sim start #1.2/A:65,68,134 ISOLDE: started sim > isolde sim stop Sim termination reason: None Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > aa PHE Traceback (most recent call last): File ""C:\Program Files\ChimeraX-daily\bin\Lib\site- packages\chimerax\cmd_line\tool.py"", line 319, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX-daily\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 2925, in run result = ci.function(session, *args, optional=optional, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX-daily\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3464, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX-daily\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\chimerax\isolde\atomic\building\cmd.py"", line 132, in add_aa_cmd add_amino_acid_residue(structure, resname.upper(), prev_res=prev_res, next_res=next_res, File ""C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\chimerax\isolde\atomic\building\build_utils.py"", line 210, in add_amino_acid_residue add_bond(r.find_atom('N'), prev_res.find_atom('C')) File ""C:\Program Files\ChimeraX-daily\bin\Lib\site- packages\chimerax\atomic\struct_edit.py"", line 242, in add_bond a1.structure.reorder_residues(new_residues) File ""C:\Program Files\ChimeraX-daily\bin\Lib\site- packages\chimerax\atomic\molobject.py"", line 1940, in reorder_residues f(self._c_pointer, [r._c_pointer.value for r in new_order]) TypeError: Duplicate residue in new residue order TypeError: Duplicate residue in new residue order File ""C:\Program Files\ChimeraX-daily\bin\Lib\site- packages\chimerax\atomic\molobject.py"", line 1940, in reorder_residues f(self._c_pointer, [r._c_pointer.value for r in new_order]) See log for complete Python traceback. > select up 20 atoms, 20 bonds, 1 residue, 1 model selected > delete sel > sequence chain #1/A Alignment identifier is 1.2/A > st > sequence chain #1/A Destroying pre-existing alignment with identifier 1.2/A Alignment identifier is 1.2/A > sequence chain #2/A Alignment identifier is 2.1/A > cartoon #1 > ui tool show Shell 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. > select clear OpenGL version: 3.3.0 NVIDIA 529.19 OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_GB.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: windows Manufacturer: HP Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC OS: Microsoft Windows 11 Pro (Build 22631) Memory: 34,007,068,672 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.5.1 build: 1.1.1 certifi: 2024.2.2 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.56 ChimeraX-AtomicLibrary: 14.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 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: 2.12.1 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: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.0 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: 1.8.dev202403220040 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4.2 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: 1.1.1 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-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.9 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.3 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.3 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-Segmentations: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.37.1 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: 0.2.2 comtypes: 1.3.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.9 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.50.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2024.2.26 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.3 matplotlib-inline: 0.1.6 msgpack: 1.0.8 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.0 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pillow: 10.2.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.2.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.0 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: 0.6.1 tables: 3.9.2 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 WMI: 1.5.1 }}} " defect closed normal Structure Editing fixed all ChimeraX