id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4981 Bad AlphaFold model trimming Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17 ChimeraX Version: 1.3.dev202107240347 (2021-07-24 03:47:26 UTC) Description Something going wrong with the model trimming when fetching the AlphaFold prediction for 7ck3 - the trimmed model contains almost nothing (quite a bit of it wrong), while the untrimmed version shows most of the structure is correctly predicted with high confidence. Log: > alias preview_toolshed toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu; toolshed reload available > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu; > toolshed reload available > 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} pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color bychain; color byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.3.dev202107240347 (2021-07-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7o4f 7o4f title: The DYW domain of A. thaliana OTP86 in its active state [more info...] Chain information for 7o4f #1 --- Chain | Description | UniProt A B D G | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic | PP296_ARATH Non-standard residues in 7o4f #1 --- ZN — zinc ion 7o4f mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > open #1 fromDatabase AlphaFold Summary of feedback from opening #1 fetched from AlphaFold --- notes | Fetching compressed AlphaFold Q9M1V3 from https://alphafold.ebi.ac.uk/files/AF-Q9M1V3-F1-model_v1.cif 7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2 Matchmaker 7o4f, chain A (#1) with AlphaFold Q9M1V3, chain A (#), sequence alignment score = 654.4 RMSD between 102 pruned atom pairs is 0.619 angstroms; (across all 135 pairs: 4.767) 7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2 Matchmaker 7o4f, chain B (#1) with AlphaFold Q9M1V3, chain B (#), sequence alignment score = 646.3 RMSD between 103 pruned atom pairs is 0.590 angstroms; (across all 135 pairs: 4.891) 7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2 Matchmaker 7o4f, chain D (#1) with AlphaFold Q9M1V3, chain D (#), sequence alignment score = 654.4 RMSD between 103 pruned atom pairs is 0.611 angstroms; (across all 135 pairs: 4.759) 7522 atoms, 960 residues, atom bfactor range 24.7 to 98.2 Matchmaker 7o4f, chain G (#1) with AlphaFold Q9M1V3, chain G (#), sequence alignment score = 647.2 RMSD between 103 pruned atom pairs is 0.592 angstroms; (across all 135 pairs: 4.901) Chain information for UniProt Q9M1V3 chain A #2.1 --- Chain | Description | UniProt A | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic | PP296_ARATH Chain information for UniProt Q9M1V3 chain B #2.2 --- Chain | Description B | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic Chain information for UniProt Q9M1V3 chain D #2.3 --- Chain | Description D | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic Chain information for UniProt Q9M1V3 chain G #2.4 --- Chain | Description G | Pentatricopeptide repeat-containing protein At3g63370, chloroplastic Opened 4 AlphaFold chain models > ui tool show Shell > save 7o4f.pdb #1 Fetching compressed Alphafold Q9M1V3 PAE from https://alphafold.ebi.ac.uk/files/AF-Q9M1V3-F1-predicted_aligned_error_v1.json > color byattribute r:isolde_domain #2.4 target ra palette rainbow [Repeated 1 time(s)]1101 atoms, 135 residues, atom isolde_domain range -1 to 4 > hide #2.1 models > hide #2.2 models > hide #2.3 models > color byattribute r:isolde_domain #2.4 target ra palette rainbow 1101 atoms, 135 residues, atom isolde_domain range -1 to 13 > color byattribute r:isolde_domain #2.4 target ra palette rainbow 1101 atoms, 135 residues, atom isolde_domain range -1 to 23 > color byattribute r:isolde_domain #2.4 target ra palette rainbow 1101 atoms, 135 residues, atom isolde_domain range -1 to 0 > color byattribute r:isolde_domain #2.4 target ra palette rainbow 1101 atoms, 135 residues, atom isolde_domain range -1 to 87 > close #1-2 > open 7cfd 7cfd title: Drosophila melanogaster Krimper eTud2-AubR15me2 complex [more info...] Chain information for 7cfd #1 --- Chain | Description | UniProt A B C D E F G H | FI20010p1 | A1ZAC4_DROME I J K L M N O Z | Protein aubergine | AUB_DROME 7cfd mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly 5| author_defined_assembly 6| author_defined_assembly 7| author_defined_assembly 8| author_defined_assembly > cartoon > hide > open #1 fromDatabase AlphaFold Summary of feedback from opening #1 fetched from AlphaFold --- error | Fewer than 3 residues aligned; cannot match 7cfd, chain O with AlphaFold O76922, chain O notes | 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8 Matchmaker 7cfd, chain B (#1) with AlphaFold A1ZAC4, chain B (#), sequence alignment score = 929 RMSD between 125 pruned atom pairs is 0.984 angstroms; (across all 178 pairs: 2.118) Fetching compressed AlphaFold O76922 from https://alphafold.ebi.ac.uk/files/AF-O76922-F1-model_v1.cif 6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8 Matchmaker 7cfd, chain I (#1) with AlphaFold O76922, chain I (#), sequence alignment score = 48.2 RMSD between 4 pruned atom pairs is 0.867 angstroms; (across all 4 pairs: 0.867) 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8 Matchmaker 7cfd, chain C (#1) with AlphaFold A1ZAC4, chain C (#), sequence alignment score = 935 RMSD between 141 pruned atom pairs is 1.018 angstroms; (across all 179 pairs: 1.674) 6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8 Matchmaker 7cfd, chain J (#1) with AlphaFold O76922, chain J (#), sequence alignment score = 51.8 RMSD between 6 pruned atom pairs is 1.261 angstroms; (across all 7 pairs: 1.648) 6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8 Matchmaker 7cfd, chain K (#1) with AlphaFold O76922, chain K (#), sequence alignment score = 53 RMSD between 8 pruned atom pairs is 1.551 angstroms; (across all 8 pairs: 1.551) 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8 Matchmaker 7cfd, chain D (#1) with AlphaFold A1ZAC4, chain D (#), sequence alignment score = 925.4 RMSD between 136 pruned atom pairs is 0.934 angstroms; (across all 178 pairs: 1.734) 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8 Matchmaker 7cfd, chain E (#1) with AlphaFold A1ZAC4, chain E (#), sequence alignment score = 905.6 RMSD between 155 pruned atom pairs is 1.177 angstroms; (across all 180 pairs: 1.888) 6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8 Matchmaker 7cfd, chain L (#1) with AlphaFold O76922, chain L (#), sequence alignment score = 48.2 RMSD between 4 pruned atom pairs is 1.100 angstroms; (across all 4 pairs: 1.100) 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8 Matchmaker 7cfd, chain F (#1) with AlphaFold A1ZAC4, chain F (#), sequence alignment score = 936.2 RMSD between 143 pruned atom pairs is 1.059 angstroms; (across all 182 pairs: 1.673) 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8 Matchmaker 7cfd, chain A (#1) with AlphaFold A1ZAC4, chain A (#), sequence alignment score = 931.4 RMSD between 131 pruned atom pairs is 1.015 angstroms; (across all 176 pairs: 1.780) 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8 Matchmaker 7cfd, chain G (#1) with AlphaFold A1ZAC4, chain G (#), sequence alignment score = 933.8 RMSD between 147 pruned atom pairs is 1.263 angstroms; (across all 181 pairs: 1.573) 6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8 Matchmaker 7cfd, chain N (#1) with AlphaFold O76922, chain N (#), sequence alignment score = 50.6 RMSD between 5 pruned atom pairs is 1.368 angstroms; (across all 6 pairs: 1.962) 5902 atoms, 746 residues, atom bfactor range 21.6 to 96.8 Matchmaker 7cfd, chain H (#1) with AlphaFold A1ZAC4, chain H (#), sequence alignment score = 870.2 RMSD between 151 pruned atom pairs is 1.283 angstroms; (across all 181 pairs: 1.594) 6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8 Matchmaker 7cfd, chain M (#1) with AlphaFold O76922, chain M (#), sequence alignment score = 50.6 RMSD between 5 pruned atom pairs is 0.710 angstroms; (across all 6 pairs: 1.685) 6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8 Matchmaker 7cfd, chain Z (#1) with AlphaFold O76922, chain Z (#), sequence alignment score = 47 RMSD between 3 pruned atom pairs is 0.729 angstroms; (across all 3 pairs: 0.729) 6914 atoms, 866 residues, atom bfactor range 20.2 to 98.8 Matchmaker 7cfd, chain O (#1) with AlphaFold O76922, chain O (#), sequence alignment score = 44.6 Chain information for UniProt A1ZAC4 chain B #2.1 --- Chain | Description B | FI20010p1 Chain information for UniProt O76922 chain I #2.2 --- Chain | Description I | Protein aubergine Chain information for UniProt A1ZAC4 chain C #2.3 --- Chain | Description C | FI20010p1 Chain information for UniProt O76922 chain J #2.4 --- Chain | Description J | Protein aubergine Chain information for UniProt O76922 chain K #2.5 --- Chain | Description K | Protein aubergine Chain information for UniProt A1ZAC4 chain D #2.6 --- Chain | Description D | FI20010p1 Chain information for UniProt A1ZAC4 chain E #2.7 --- Chain | Description E | FI20010p1 Chain information for UniProt O76922 chain L #2.8 --- Chain | Description L | Protein aubergine Chain information for UniProt A1ZAC4 chain F #2.9 --- Chain | Description F | FI20010p1 Chain information for UniProt A1ZAC4 chain A #2.10 --- Chain | Description | UniProt A | FI20010p1 | A1ZAC4_DROME Chain information for UniProt A1ZAC4 chain G #2.11 --- Chain | Description G | FI20010p1 Chain information for UniProt O76922 chain N #2.12 --- Chain | Description N | Protein aubergine Chain information for UniProt A1ZAC4 chain H #2.13 --- Chain | Description H | FI20010p1 Chain information for UniProt O76922 chain M #2.14 --- Chain | Description M | Protein aubergine Chain information for UniProt O76922 chain Z #2.15 --- Chain | Description Z | Protein aubergine Chain information for UniProt O76922 chain O #2.16 --- Chain | Description O | Protein aubergine Opened 16 AlphaFold chain models > hide #2.16 models > show #2.16 models > select #2.1 1521 atoms, 1562 bonds, 185 residues, 1 model selected Fetching compressed Alphafold A1ZAC4 PAE from https://alphafold.ebi.ac.uk/files/AF-A1ZAC4-F1-predicted_aligned_error_v1.json > color byattribute r:isolde_domain #2.1 target ra palette rainbow 1521 atoms, 185 residues, atom isolde_domain range -1 to 110 > color byattribute r:isolde_domain #2.1 target ra palette rainbow 1521 atoms, 185 residues, atom isolde_domain range -1 to 9 > hide ~sel models > show #!2 models > select clear > color byattribute r:isolde_domain #2.1 target ra palette rainbow 1521 atoms, 185 residues, atom isolde_domain range -1 to 16 > color byattribute r:isolde_domain #2.1 target ra palette rainbow 1521 atoms, 185 residues, atom isolde_domain range -1 to 17 > save 7cfd.pdb #1 > save AF_A1ZAC4_cluster_0.pdb #2.1 selectedOnly true > save AF_A1ZAC4_cluster_1.pdb #2.1 selectedOnly true > select clear > open 7cfb 7cfb title: Drosophila melanogaster Krimper eTud1 apo structure [more info...] Chain information for 7cfb #3 --- Chain | Description | UniProt A B | FI20010p1 | A1ZAC4_DROME Non-standard residues in 7cfb #3 --- SO4 — sulfate ion 7cfb mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > matchmaker #3 to #1 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 7cfd, chain H (#1) with 7cfb, chain B (#3), sequence alignment score = 114.8 RMSD between 83 pruned atom pairs is 1.228 angstroms; (across all 143 pairs: 5.190) > matchmaker #3 to #2.1 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 UniProt A1ZAC4 chain B, chain B (#2.1) with 7cfb, chain B (#3), sequence alignment score = 99.8 RMSD between 76 pruned atom pairs is 1.068 angstroms; (across all 143 pairs: 5.602) > save 7cfb.pdb #3 > close #1-2#3 > open 7ciw 7ciw title: Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with Ac-Agm and CoA [more info...] Chain information for 7ciw #1 --- Chain | Description | UniProt A | Agmatine N-acetyltransferase | Q9W469_DROME Non-standard residues in 7ciw #1 --- COA — coenzyme A G0R — N-(4-carbamimidamidobutyl)ethanamide > open #1 fromDatabase AlphaFold Summary of feedback from opening #1 fetched from AlphaFold --- notes | Fetching compressed AlphaFold Q9W469 from https://alphafold.ebi.ac.uk/files/AF-Q9W469-F1-model_v1.cif 1673 atoms, 216 residues, atom bfactor range 40.4 to 98.9 Matchmaker 7ciw, chain A (#1) with AlphaFold Q9W469, chain A (#), sequence alignment score = 1100.6 RMSD between 208 pruned atom pairs is 0.547 angstroms; (across all 216 pairs: 3.620) Chain information for UniProt Q9W469 chain A --- Chain | Description | UniProt 2.1/A | Agmatine N-acetyltransferase | Q9W469_DROME Opened 1 AlphaFold chain models > close #1#2 > open 7ck3 7ck3 title: Crystal structure of Arabidopsis CESA3 catalytic domain [more info...] Chain information for 7ck3 #1 --- Chain | Description | UniProt A B | Cellulose synthase A catalytic subunit 3 [UDP-forming],Cellulose synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH 7ck3 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > open #1 fromDatabase AlphaFold Summary of feedback from opening #1 fetched from AlphaFold --- notes | 8430 atoms, 1065 residues, atom bfactor range 23 to 97.8 Matchmaker 7ck3, chain A (#1) with AlphaFold Q941L0, chain A (#), sequence alignment score = 1592 RMSD between 50 pruned atom pairs is 0.916 angstroms; (across all 98 pairs: 9.484) 8430 atoms, 1065 residues, atom bfactor range 23 to 97.8 Matchmaker 7ck3, chain B (#1) with AlphaFold Q941L0, chain B (#), sequence alignment score = 1598.3 RMSD between 51 pruned atom pairs is 0.926 angstroms; (across all 98 pairs: 9.558) Chain information for UniProt Q941L0 chain A #2.1 --- Chain | Description | UniProt A | Cellulose synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH Chain information for UniProt Q941L0 chain B #2.2 --- Chain | Description B | Cellulose synthase A catalytic subunit 3 [UDP-forming] Opened 2 AlphaFold chain models > open #1 fromDatabase AlphaFold trim false Summary of feedback from opening #1 fetched from AlphaFold --- notes | 8430 atoms, 1065 residues, atom bfactor range 23 to 97.8 Matchmaker 7ck3, chain A (#1) with AlphaFold Q941L0, chain A (#), sequence alignment score = 1890.2 RMSD between 268 pruned atom pairs is 0.836 angstroms; (across all 369 pairs: 5.904) 8430 atoms, 1065 residues, atom bfactor range 23 to 97.8 Matchmaker 7ck3, chain B (#1) with AlphaFold Q941L0, chain B (#), sequence alignment score = 1903.7 RMSD between 270 pruned atom pairs is 0.856 angstroms; (across all 369 pairs: 5.907) Chain information for UniProt Q941L0 chain A #3.1 --- Chain | Description | UniProt A | Cellulose synthase A catalytic subunit 3 [UDP-forming] | CESA3_ARATH Chain information for UniProt Q941L0 chain B #3.2 --- Chain | Description B | Cellulose synthase A catalytic subunit 3 [UDP-forming] Opened 2 AlphaFold chain models > hide #!2 models > hide #!3 models > show #!2 models > show #2 > hide #2 > show #!3 models > color bfactor #3 16860 atoms, 2130 residues, atom bfactor range 23 to 97.8 > select #3&@@bfactor>50 13038 atoms, 13380 bonds, 1632 residues, 2 models selected > select #3&@@bfactor>70 12158 atoms, 12492 bonds, 1518 residues, 2 models selected > select clear > hide #!3 models > show #!3 models > hide #!2 models OpenGL version: 3.3.0 NVIDIA 465.19.01 OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 13G 35G 306M 13G 48G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia Locale: ('en_GB', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.0 chardet: 4.0.0 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.27.1 ChimeraX-AtomicLibrary: 4.0 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.3.2 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202107240347 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.4 ChimeraX-DistUI: 1.0 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 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3.dev32 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 1.2.1 ChimeraX-MDcrds: 2.4 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.2 ChimeraX-ModelPanel: 1.1 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: 1.6.2 ChimeraX-PDB: 2.4.4 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 0.3 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-Sample: 0.1 ChimeraX-SaveCommand: 1.4.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.1 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: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.10.1 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-Voyager: 0.1 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: 1.0 cycler: 0.10.0 Cython: 0.29.23 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.3.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.20 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 2.11.3 jupyter-client: 6.1.12 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 3.3.0 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 1.1.1 matplotlib: 3.4.2 matplotlib-inline: 0.1.2 msgpack: 1.0.2 netCDF4: 1.5.6 networkx: 2.6.2 numexpr: 2.7.3 numpy: 1.21.0 numpydoc: 1.1.0 OpenMM: 7.6.0 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.2.0 pip: 21.1.1 pkginfo: 1.7.0 prompt-toolkit: 3.0.19 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.9.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.1.0 qtconsole: 5.1.0 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.25.1 scipy: 1.6.3 setuptools: 57.0.0 sfftk-rw: 0.7.0.post1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.0.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.26.6 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.2 wheel-filename: 1.3.0 }}} " defect closed normal Input/Output fixed all ChimeraX