id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14755 tug after session restore: openmm.OpenMMException: Particle coordinate is NaN maja.divjak@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description (Describe the actions that caused this problem to occur here) I split out a domain from a model, repositioned it and then performed a tug to pull one split end towards the new position, combined and added a bond, then tried to tug the remaining split end towards a copy of the repositioned domain. This error occurred in the tug Log: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1CombineAddBondProtonate5ciu.cxs Log from Wed Mar 13 11:37:21 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1.cxs Log from Wed Mar 13 08:51:37 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY.cxs Log from Wed Mar 13 08:01:34 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciu.cxs Log from Wed Mar 6 11:14:39 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciu.cxs Log from Wed Mar 6 10:04:03 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciu.cxs Log from Mon Mar 4 11:21:25 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFold.cxs Log from Fri Mar 1 15:48:22 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_14.cxs Log from Thu Feb 29 11:27:46 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd2x6s01_10.cxs Log from Wed Feb 28 11:39:23 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd2x6s01_9.cxs Log from Tue Feb 27 14:31:41 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_6.cxs Log from Thu Aug 31 14:18:46 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_3.cxs Log from Thu Aug 31 11:00:29 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add8PEO.cxs Log from Wed Aug 30 17:36:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3.cxs Log from Thu Aug 24 17:47:44 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd5CIU.cxs Log from Wed Aug 23 15:48:27 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomains.cxs Log from Tue Aug 22 15:47:49 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/6PA7Model.cxs Log from Tue Aug 22 14:32:23 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:quickstart > open 6pa7 Summary of feedback from opening 6pa7 fetched from pdb --- notes | Fetching compressed mmCIF 6pa7 from http://files.rcsb.org/download/6pa7.cif Fetching CCD CL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif Fetching CCD SAH from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/SAH/SAH.cif 6pa7 title: The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. [more info...] Chain information for 6pa7 #1 --- Chain | Description | UniProt A E | Histone H3.2 | H32_XENLA 1-135 B F | Histone H4 | H4_XENLA 0-102 C G | Histone H2A type 1 | H2A1_XENLA 1-129 D H | Histone H2B 1.1 | H2B11_XENLA 1-122 I | DNA (167-MER) | J | DNA (167-MER) | K P | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 224-912 N S | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 1-770 Non-standard residues in 6pa7 #1 --- CL — chloride ion SAH — S-adenosyl-L-homocysteine > sequence chain #1/K#1/P Alignment identifier is 1 > select /K,P:627 14 atoms, 14 bonds, 2 residues, 1 model selected > select /K,P:627-638 194 atoms, 196 bonds, 24 residues, 1 model selected > select /K/P 4718 atoms, 4844 bonds, 2 pseudobonds, 578 residues, 2 models selected > surface (#!1 & sel) > select /N/S 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > surface (#!1 & sel) > sequence chain #1/K#1/P Alignment identifier is 2 > select clear > select /K/P 4718 atoms, 4844 bonds, 2 pseudobonds, 578 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide (#!1 & sel) target a > cartoon (#!1 & sel) > cartoon style (#!1 & sel) xsection oval modeHelix default > select clear > select /K,P:614 16 atoms, 14 bonds, 2 residues, 1 model selected > select /K,P:614-626 216 atoms, 226 bonds, 26 residues, 1 model selected > select /K,P:613 20 atoms, 20 bonds, 2 residues, 1 model selected > select /K,P:613 20 atoms, 20 bonds, 2 residues, 1 model selected > select /K,P:613-643 508 atoms, 526 bonds, 62 residues, 1 model selected > select clear > select /K,P:613 20 atoms, 20 bonds, 2 residues, 1 model selected > select /K,P:613 20 atoms, 20 bonds, 2 residues, 1 model selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/6PA7Model.cxs ——— End of log from Tue Aug 22 14:32:23 2023 ——— opened ChimeraX session > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/PDBs/AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb title: Alphafold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (Q9Y6K1) [more info...] Chain information for AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb #2 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 1-912 > hide #!1 models > show #!1 models > ui tool show Matchmaker > matchmaker #2 to #1/K pairing bs Parameters --- Chain pairing | bs 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 6pa7, chain K (#1) with AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb, chain A (#2), sequence alignment score = 2995.3 RMSD between 276 pruned atom pairs is 0.673 angstroms; (across all 288 pairs: 1.153) > matchmaker #2 to #1/K pairing bs Parameters --- Chain pairing | bs 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 6pa7, chain K (#1) with AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb, chain A (#2), sequence alignment score = 2995.3 RMSD between 276 pruned atom pairs is 0.673 angstroms; (across all 288 pairs: 1.153) > hide #!1 models > hide #2 models > show #!1 models > show #2 models > show #!1 target m > show #2 target m > view #2 clip false > select #2/A 7146 atoms, 7323 bonds, 912 residues, 1 model selected > surface sel > surface hidePatches (#!2 & sel) > color (#!2 & sel) red > hide #!1 models > show #!1 models > log metadata #2 Metadata for AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb #2 --- Title | Alphafold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (Q9Y6K1) Source (natural) | Homo sapiens > log chains #2 Chain information for AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb #2 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 1-912 > sequence chain #2/A Alignment identifier is 2/A > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-5 35 atoms, 36 bonds, 5 residues, 1 model selected > select #2/A:912 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:912 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-5 35 atoms, 36 bonds, 5 residues, 1 model selected > help help:quickstart > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWithDNMT3AAlphafold.cxs > select #2/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:278-429 1208 atoms, 1247 bonds, 152 residues, 1 model selected > select clear > select #2/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > color (#!2 & sel) hot pink > label (#!2 & sel) atoms attribute name > ui tool show ""Selection Inspector"" > select > #2/A:176-178,200-228,313-316,341-343,347-351,356-359,363-379,392-411,418-422,426-429,473-484,490-492,515-524,560-566,571-577,601-609,628-630,645-652,667-676,687-689,692-698,710-712,728-740,763-772,782-784,815-817,837-840,861-868,882-891,895-907 1994 atoms, 2004 bonds, 240 residues, 1 model selected > select clear > select > #2/A:176-178,200-228,313-316,341-343,347-351,356-359,363-379,392-411,418-422,426-429,473-484,490-492,515-524,560-566,571-577,601-609,628-630,645-652,667-676,687-689,692-698,710-712,728-740,763-772,782-784,815-817,837-840,861-868,882-891,895-907 1994 atoms, 2004 bonds, 240 residues, 1 model selected > select #2/A:477 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:477 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:477 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:477-614 1086 atoms, 1108 bonds, 138 residues, 1 model selected > color (#!2 & sel) cornflower blue > color (#!2 & sel) yellow > select #2/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:628-912 2301 atoms, 2355 bonds, 285 residues, 1 model selected > color (#!2 & sel) purple > color (#!2 & sel) magenta > color (#!2 & sel) orange > color (#!2 & sel) magenta > name frozen CatalyticDomain sel [Repeated 1 time(s)] > select clear > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select clear > select #2/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:628-912 2301 atoms, 2355 bonds, 285 residues, 1 model selected > name frozen CatalyticDomain sel [Repeated 1 time(s)] > select clear > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select clear > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWithDNMT3AAlphafold.cxs > select #2/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > surface (#!2 & sel) > color (#!2 & sel) orange > color (#!2 & sel) magenta > select > #2/A:176-178,200-228,313-316,341-343,347-351,356-359,363-379,392-411,418-422,426-429,473-484,490-492,515-524,560-566,571-577,601-609,628-630,645-652,667-676,687-689,692-698,710-712,728-740,763-772,782-784,815-817,837-840,861-868,882-891,895-907 1994 atoms, 2004 bonds, 240 residues, 1 model selected > select #2/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > color (#!2 & sel) orange > surface (#!2 & sel) > select #2/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:628-912 2301 atoms, 2355 bonds, 285 residues, 1 model selected > color (#!2 & sel) cornflower blue > surface (#!2 & sel) > select clear > select #2/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:628-912 2301 atoms, 2355 bonds, 285 residues, 1 model selected > select #2/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > surface (#!2 & sel) > select clear > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-443 3394 atoms, 3479 bonds, 443 residues, 1 model selected > select 28165 atoms, 29465 bonds, 425 pseudobonds, 3017 residues, 5 models selected > select clear > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-2 15 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:1-2,912 23 atoms, 22 bonds, 3 residues, 1 model selected > select #2/A:1-570,912 4382 atoms, 4484 bonds, 571 residues, 1 model selected > select #2/A:571 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:571-890 2586 atoms, 2651 bonds, 320 residues, 1 model selected > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-420 3199 atoms, 3276 bonds, 420 residues, 1 model selected > select #2/A:1-750 5816 atoms, 5958 bonds, 750 residues, 1 model selected > select #2/A 7146 atoms, 7323 bonds, 912 residues, 1 model selected > surface (#!2 & sel) > surface hidePatches (#!2 & sel) > select clear > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select clear > select #2/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > surface (#!2 & sel) > select clear > select #2/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > surface (#!2 & sel) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWithDNMT3AAlphafoldDefineDomains.cxs > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/PDBs/AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb title: Alphafold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (Q9Y6K1) [more info...] Chain information for AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb #3 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 1-912 > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > ui tool show Matchmaker > matchmaker #3 to #1/P pairing bs Parameters --- Chain pairing | bs 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 6pa7, chain P (#1) with AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb, chain A (#3), sequence alignment score = 2995.3 RMSD between 276 pruned atom pairs is 0.673 angstroms; (across all 288 pairs: 1.153) > hide #!2 models > show #!2 models > show #3 target m [Repeated 1 time(s)] > log metadata #3 Metadata for AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb #3 --- Title | Alphafold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (Q9Y6K1) Source (natural) | Homo sapiens > log chains #3 Chain information for AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb #3 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 1-912 > sequence chain #3/A Alignment identifier is 3/A > sequence chain #3/A Destroying pre-existing alignment with identifier 3/A Alignment identifier is 3/A > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:278-279 12 atoms, 11 bonds, 2 residues, 1 model selected > select #3/A:427 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:427 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > color sel magenta > select #3/A:477 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:477 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:614-615 17 atoms, 16 bonds, 2 residues, 1 model selected > select #3/A:477-614 1086 atoms, 1108 bonds, 138 residues, 1 model selected > select #3/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > color sel orange > select > #3/A:176-178,200-228,313-316,341-343,347-351,356-359,363-379,392-411,418-422,426-429,473-484,490-492,515-524,560-566,571-577,601-609,628-630,645-652,667-676,687-689,692-698,710-712,728-740,763-772,782-784,815-817,837-840,861-868,882-891,895-907 1994 atoms, 2004 bonds, 240 residues, 1 model selected > select #3/A:629 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:629 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/A:628-912 2301 atoms, 2355 bonds, 285 residues, 1 model selected > color sel cornflower blue > select #3/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > name frozen ADD_2 sel > select clear > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > surface sel > color (#!3 & sel) orange > surface hidePatches (#!3 & sel) > surface (#!3 & sel) > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:427 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > name frozen PWWP_2 sel > select clear > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select clear > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > name frozen PWWP_2 sel [Repeated 1 time(s)] > select clear > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select clear > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:427 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > name frozen PWWP_2 sel > select clear > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select clear > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > help help:user/menu.html#named-selections > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomains.cxs ——— End of log from Tue Aug 22 15:47:49 2023 ——— opened ChimeraX session > select add #2/A 8243 atoms, 8442 bonds, 1051 residues, 2 models selected > select clear > select #1/K 2359 atoms, 2422 bonds, 1 pseudobond, 289 residues, 2 models selected > cartoon hide (#!1 & sel) > select #1/P 2359 atoms, 2422 bonds, 1 pseudobond, 289 residues, 2 models selected > cartoon hide (#!1 & sel) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomains.cxs > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > open 4u7p Summary of feedback from opening 4u7p fetched from pdb --- notes | Fetching compressed mmCIF 4u7p from http://files.rcsb.org/download/4u7p.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 4u7p title: Crystal structure of DNMT3A-DNMT3L complex [more info...] Chain information for 4u7p #4 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 455-912 B | DNA (cytosine-5)-methyltransferase 3-like | DNM3L_HUMAN 178-379 Non-standard residues in 4u7p #4 --- SAH — S-adenosyl-L-homocysteine ZN — zinc ion > select add #1 21019 atoms, 22142 bonds, 425 pseudobonds, 2105 residues, 4 models selected > select subtract #1 4 models selected > select add #1 21019 atoms, 22142 bonds, 425 pseudobonds, 2105 residues, 3 models selected > select subtract #1 4 models selected > hide #!3 models > hide #!2 models > hide #!1 models > ui tool show ""Selection Inspector"" > show #!3 models > show #!2 models > show #!1 models > ui tool show Matchmaker > matchmaker #4/A to #1/K pairing ss 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 6pa7, chain K (#1) with 4u7p, chain A (#4), sequence alignment score = 2072.7 RMSD between 272 pruned atom pairs is 0.661 angstroms; (across all 287 pairs: 1.369) > hide #!3 models > hide #!2 models > show #!3 models > show #!2 models > hide #!1 models > show #!1 models > hide #4.2 models > show #4.2 models > hide #4.1 models > show #4.1 models > hide #!4 models > show #!4 models > sequence chain #4/A Alignment identifier is 4/A > sequence chain #4/A Destroying pre-existing alignment with identifier 4/A Alignment identifier is 4/A > sequence chain #4/B Alignment identifier is 4/B > sequence chain #4/B Destroying pre-existing alignment with identifier 4/B Alignment identifier is 4/B > select #4/B:201-202 18 atoms, 17 bonds, 2 residues, 1 model selected > select #4/B:201-303 841 atoms, 870 bonds, 103 residues, 1 model selected > select #4/B 1621 atoms, 1673 bonds, 1 pseudobond, 197 residues, 2 models selected > select #4/B 1621 atoms, 1673 bonds, 1 pseudobond, 197 residues, 2 models selected > select #4/B:179-180 20 atoms, 20 bonds, 2 residues, 1 model selected > select #4/B 1621 atoms, 1673 bonds, 1 pseudobond, 197 residues, 2 models selected > color (#!4 & sel) forest green > select clear > select > #4/A:474-485,489-493,514-528,560-567,570-576,600-609,644-654,666-677,691-698,710-714,729-740,762-774,783-785,814-818,860-869,881-891,894-906 1321 atoms, 1330 bonds, 160 residues, 1 model selected > select #4/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > color sel orange > select #4/A:627-628 12 atoms, 12 bonds, 2 residues, 1 model selected > select #4/A:627-628 12 atoms, 12 bonds, 2 residues, 1 model selected > select #4/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:628-776 1190 atoms, 1215 bonds, 149 residues, 1 model selected > select #4/A:628-912 2200 atoms, 2253 bonds, 1 pseudobond, 272 residues, 2 models selected > color (#!4 & sel) cornflower blue > cartoon hide (#!4 & sel) > hide sel atoms > hide #!2 models > hide #!3 models > select #4/A:474 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/A:474-481 76 atoms, 76 bonds, 8 residues, 1 model selected > select #4/A:474 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/A:474-475 18 atoms, 17 bonds, 2 residues, 1 model selected > select #4/A:474-756 2257 atoms, 2311 bonds, 283 residues, 1 model selected > select #4/A:474-912 3422 atoms, 3505 bonds, 1 pseudobond, 426 residues, 2 models selected > select #4/A:867 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/A:867-912 379 atoms, 391 bonds, 46 residues, 1 model selected > select #4/A:860 14 atoms, 15 bonds, 1 residue, 1 model selected > select #4/A:860-866 64 atoms, 65 bonds, 7 residues, 1 model selected > select #4/A:902-903 16 atoms, 16 bonds, 2 residues, 1 model selected > select #4/A:902-912 90 atoms, 93 bonds, 11 residues, 1 model selected > select #4/A:628-629 14 atoms, 13 bonds, 2 residues, 1 model selected > select #4/A:628-633 50 atoms, 50 bonds, 6 residues, 1 model selected > select #4/A:610-611 13 atoms, 12 bonds, 2 residues, 1 model selected > select #4/A:610-621 99 atoms, 102 bonds, 12 residues, 1 model selected > show #!3 models > show #!2 models > select > #4/A:504-505,512-513,546-548,557-559,591-592,595-596,634-639,657-663,681-684,703-707,752-758,778-781,791-796,824-825,850-851,856-857 488 atoms, 485 bonds, 59 residues, 1 model selected > select #4/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:628-912 2200 atoms, 2253 bonds, 1 pseudobond, 272 residues, 2 models selected > select #3/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:1-79 594 atoms, 605 bonds, 79 residues, 1 model selected > select backbone 20518 atoms, 20826 bonds, 6 pseudobonds, 4547 residues, 6 models selected > select clear > hide #!4 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > show #!4 models > show #!4 target m > select add #1 21019 atoms, 22142 bonds, 425 pseudobonds, 2105 residues, 3 models selected > select subtract #1 4 models selected > select add #1 21019 atoms, 22142 bonds, 425 pseudobonds, 2105 residues, 3 models selected > select subtract #1 4 models selected > help help:user > show sequence 6pa7 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show seq 6pa7 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > help help:user > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K #1/P Alignment identifier is 1 > ui tool show ""Show Sequence Viewer"" > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #3/A Alignment identifier is 1 > select #2/A:628 #3/A:628 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:628 #3/A:628 10 atoms, 8 bonds, 2 residues, 2 models selected DNA (cytosine-5)-methyltransferase 3A [ID: 1] region 2 chains [628] RMSD: 56.745 > select #2/A:628 #3/A:628 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:628-912 #3/A:628-912 4602 atoms, 4710 bonds, 570 residues, 2 models selected DNA (cytosine-5)-methyltransferase 3A [ID: 1] region 2 chains [628-912] RMSD: 52.122 > cartoon hide (#!2-3 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K #1/P Alignment identifier is 1 > select #1/K,P:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/K,P:628-912 4416 atoms, 4522 bonds, 2 pseudobonds, 546 residues, 2 models selected > cartoon (#!1 & sel) > color (#!1 & sel) cornflower blue > select clear > select add #1 21019 atoms, 22142 bonds, 425 pseudobonds, 2105 residues, 3 models selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd4U7P.cxs > surface hidePatches (#!1 & sel) > select subtract #1 4 models selected > select #1/K,P:627 14 atoms, 14 bonds, 2 residues, 1 model selected > select #1/K,P:627-912 4430 atoms, 4538 bonds, 2 pseudobonds, 548 residues, 2 models selected > style (#!1 & sel) sphere Changed 4430 atom styles > show (#!1 & sel) target ab > select clear > select add #2 7146 atoms, 7323 bonds, 912 residues, 2 models selected > select subtract #2 1 model selected > select add #3 7146 atoms, 7323 bonds, 912 residues, 1 model selected > select subtract #3 1 model selected > select add #2 7146 atoms, 7323 bonds, 912 residues, 2 models selected > select subtract #2 1 model selected > select add #3 7146 atoms, 7323 bonds, 912 residues, 1 model selected > select subtract #3 1 model selected > select add #4 5072 atoms, 5206 bonds, 14 pseudobonds, 627 residues, 3 models selected > select subtract #4 Nothing selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd4U7P.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K #1/P Alignment identifier is 1 > select #1/K,P:627 14 atoms, 14 bonds, 2 residues, 1 model selected > select #1/K,P:627 14 atoms, 14 bonds, 2 residues, 1 model selected > select #1/K,P:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/K,P:628-912 4416 atoms, 4522 bonds, 2 pseudobonds, 546 residues, 2 models selected > hide (#!1 & sel) target a > cartoon hide (#!1 & sel) > cartoon (#!1 & sel) > open 4u7p 4u7p title: Crystal structure of DNMT3A-DNMT3L complex [more info...] Chain information for 4u7p #5 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 455-912 B | DNA (cytosine-5)-methyltransferase 3-like | DNM3L_HUMAN 178-379 Non-standard residues in 4u7p #5 --- SAH — S-adenosyl-L-homocysteine ZN — zinc ion > hide #!4 models > show #!4 models > ui tool show Matchmaker [Repeated 1 time(s)] > matchmaker #5/A to #1/P pairing ss 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 6pa7, chain P (#1) with 4u7p, chain A (#5), sequence alignment score = 2072.7 RMSD between 272 pruned atom pairs is 0.661 angstroms; (across all 287 pairs: 1.369) > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A Alignment identifier is 5/A > select > #5/A:474-485,489-493,514-528,560-567,570-576,600-609,644-654,666-677,691-698,710-714,729-740,762-774,783-785,814-818,860-869,881-891,894-906 1321 atoms, 1330 bonds, 160 residues, 1 model selected > select #5/A:474 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:474 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > color sel orange > select #5/A:633 7 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:633 7 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5/A:628-912 2200 atoms, 2253 bonds, 1 pseudobond, 272 residues, 2 models selected > cartoon hide (#!5 & sel) > hide (#!5 & sel) target a > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7P.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #5/B Alignment identifier is 5/B > select #5/B 1621 atoms, 1673 bonds, 1 pseudobond, 197 residues, 2 models selected > color (#!5 & sel) forest green > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7P.cxs > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K Alignment identifier is 1/K > select #1/K:634 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/K:634-638 40 atoms, 39 bonds, 5 residues, 1 model selected > select #1/K:627 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/K:627 7 atoms, 7 bonds, 1 residue, 1 model selected > hide (#!1 & sel) target a > ui tool show ""Show Sequence Viewer"" > sequence chain #1/P Alignment identifier is 1/P > select #1/P:627 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/P:627 7 atoms, 7 bonds, 1 residue, 1 model selected > hide (#!1 & sel) target a > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7P.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A #5/A Alignment identifier is 1 > select #4/A:474 #5/A:474 22 atoms, 20 bonds, 2 residues, 2 models selected > select #4/A:474 #5/A:474 22 atoms, 20 bonds, 2 residues, 2 models selected DNA (cytosine-5)-methyltransferase 3A [ID: 1] region 2 chains [28] RMSD: 99.042 > select #4/A:476 #5/A:476 22 atoms, 20 bonds, 2 residues, 2 models selected > select #4/A:476 #5/A:476 22 atoms, 20 bonds, 2 residues, 2 models selected DNA (cytosine-5)-methyltransferase 3A [ID: 1] region 2 chains [30] RMSD: 102.238 > select #4/A:614 #5/A:614 16 atoms, 14 bonds, 2 residues, 2 models selected > select #4/A:476-614 #5/A:476-614 2194 atoms, 2238 bonds, 278 residues, 2 models selected DNA (cytosine-5)-methyltransferase 3A [ID: 1] region 2 chains [30-168] RMSD: 95.079 > surface sel > color (#!4-5 & sel) orange > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7P.cxs > select clear > open 5ciu Summary of feedback from opening 5ciu fetched from pdb --- notes | Fetching compressed mmCIF 5ciu from http://files.rcsb.org/download/5ciu.cif Fetching CCD M3L from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/M3L/M3L.cif Fetching CCD GOL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif 5ciu title: Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain [more info...] Chain information for 5ciu #6 --- Chain | Description | UniProt A B | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 206-355 C D | Histone H3.2 | Non-standard residues in 5ciu #6 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 5ciu mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > select add #6 2266 atoms, 2162 bonds, 3 pseudobonds, 426 residues, 2 models selected > select subtract #6 Nothing selected > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > ui tool show Matchmaker [Repeated 1 time(s)] > matchmaker #6/A to #2/A pairing ss 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 AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb, chain A (#2) with 5ciu, chain A (#6), sequence alignment score = 443.2 RMSD between 125 pruned atom pairs is 0.628 angstroms; (across all 127 pairs: 0.695) > ui tool show ""Show Sequence Viewer"" > sequence chain #6/C Alignment identifier is 6/C > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show sel target ab > hide sel target a > surface sel > select #6/A:345 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/A:345 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > name frozen H3K36me3 sel > select clear > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #6/B Alignment identifier is 6/B > sequence chain #6/D Alignment identifier is 6/D > ui tool show Matchmaker > matchmaker #6/B to #3/A pairing ss 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 AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb, chain A (#3) with 5ciu, chain B (#6), sequence alignment score = 415.6 RMSD between 120 pruned atom pairs is 0.771 angstroms; (across all 121 pairs: 0.797) > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > surface sel > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select clear > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > ui tool show Matchmaker > matchmaker #6/A to #2/A pairing ss 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 AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb, chain A (#2) with 5ciu, chain A (#6), sequence alignment score = 443.2 RMSD between 125 pruned atom pairs is 0.628 angstroms; (across all 127 pairs: 0.695) > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > surface hidePatches (#!6 & sel) > cartoon hide (#!6 & sel) > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > cartoon hide (#!6 & sel) > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #6/D:32-37 43 atoms, 42 bonds, 6 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > hide (#!6 & sel) target a > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > name frozen H3K36me3_ sel > select clear > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > name frozen PWWP_H3K36me3_ sel > select clear > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > surface (#!6 & sel) > surface hidePatches (#!6 & sel) > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > surface (#!6 & sel) > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > cartoon hide (#!6 & sel) > hide (#!6 & sel) target a > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > color (#!6 & sel) white > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > color (#!6 & sel) white > select clear > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd5CIU.cxs ——— End of log from Wed Aug 23 15:48:27 2023 ——— opened ChimeraX session > open 5ciu 5ciu title: Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain [more info...] Chain information for 5ciu #7 --- Chain | Description | UniProt A B | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 206-355 C D | Histone H3.2 | Non-standard residues in 5ciu #7 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 5ciu mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > ui tool show Matchmaker > matchmaker #7/B to #3/A pairing ss 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 AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb, chain A (#3) with 5ciu, chain B (#7), sequence alignment score = 415.6 RMSD between 120 pruned atom pairs is 0.771 angstroms; (across all 121 pairs: 0.797) > ui tool show ""Show Sequence Viewer"" > sequence chain #7/B Alignment identifier is 7/B > sequence chain #7/C Alignment identifier is 7/C > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > color (#!7 & sel) white > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > color sel white > surface sel > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIU.cxs > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select clear > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > help help:user > help help:user/menu.html#named-selections > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select add #6 2266 atoms, 2162 bonds, 3 pseudobonds, 426 residues, 2 models selected > select subtract #6 3 models selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > name frozen H3K36me3 sel > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select clear > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #7/A Alignment identifier is 7/A > select #7/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > cartoon hide (#!7 & sel) > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > name frozen PWWP_H3K36me3 sel > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select add #7 3241 atoms, 3166 bonds, 5 pseudobonds, 547 residues, 4 models selected > select add #6 4532 atoms, 4324 bonds, 6 pseudobonds, 852 residues, 5 models selected > select subtract #6 2266 atoms, 2162 bonds, 3 pseudobonds, 426 residues, 6 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #7/A Alignment identifier is 7/A > select #7/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #7/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3_ 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select clear > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > name frozen PWWP_H3K36me3_ sel > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3_ 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIU.cxs > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select clear > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > hide #!3 models > show #!3 models > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:278 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:427 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > select clear > select #3/A:427 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:278-427 1190 atoms, 1229 bonds, 150 residues, 1 model selected > name frozen PWWP_2 sel > select clear > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select clear > ui tool show ""Show Sequence Viewer"" > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select #3/A:479 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:479 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select clear > select #3/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > name frozen ADD_1 sel > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select clear > select #2/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > name frozen ADD_1 sel > select clear > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 7146 atoms, 2355 bonds, 912 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3_ 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIU.cxs > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/P Alignment identifier is 1/P > select #1/P:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/P:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > select clear > select #1/P:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/P:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > name frozen CatalyticDomain sel > select clear > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3_ 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIU.cxs > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K Alignment identifier is 1/K > select clear > select #1/K:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/K:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3_ 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_2 7146 atoms, 1229 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3_ 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select clear [Repeated 1 time(s)] > select #1/K:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/K:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > name frozen CatalyticDomain_1 sel > select clear > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIU.cxs > open 4u7t Summary of feedback from opening 4u7t fetched from pdb --- note | Fetching compressed mmCIF 4u7t from http://files.rcsb.org/download/4u7t.cif 4u7t title: Crystal structure of DNMT3A-DNMT3L in complex with histone H3 [more info...] Chain information for 4u7t #8 --- Chain | Description | UniProt A C | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 476-912 B D | DNA (cytosine-5)-methyltransferase 3-like | DNM3L_HUMAN 178-379 F G | peptide from Histone H3.3 | H33_HUMAN 1-12 Non-standard residues in 4u7t #8 --- SAH — S-adenosyl-L-homocysteine ZN — zinc ion > select clear > hide #!4 models > show #!4 models > hide #!4 models > hide #!5 models > show #!5 models > show #!4 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!4 models > hide #!5 models > show #!5 models > show #!4 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!1 models > show #!1 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > ui tool show Matchmaker > matchmaker #8/A to #2/A pairing ss 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 AF-Q9Y6K1-F1-model_v4_DNMT3A_AlphaFoldModel.pdb, chain A (#2) with 4u7t, chain A (#8), sequence alignment score = 2228.6 RMSD between 411 pruned atom pairs is 0.506 angstroms; (across all 417 pairs: 1.559) > ui tool show ""Show Sequence Viewer"" > sequence chain #8/F Alignment identifier is 8/F > sequence chain #8/G Alignment identifier is 8/G > select #8/F:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/F 79 atoms, 78 bonds, 10 residues, 1 model selected > surface sel > select #8/G:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/G 79 atoms, 78 bonds, 10 residues, 1 model selected > surface sel > hide #!2 models > hide #!3 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T.cxs > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/E Alignment identifier is 1/E > select #1/A:37-135 817 atoms, 829 bonds, 99 residues, 1 model selected > surface sel > select #1/E 805 atoms, 817 bonds, 98 residues, 1 model selected > surface sel > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T.cxs > select #1/A:37-135 817 atoms, 829 bonds, 99 residues, 1 model selected > select #1/E 805 atoms, 817 bonds, 98 residues, 1 model selected > hide #!1 models > show #!1 models > hide #!8 models > show #!8 models > hide #!8 models > show #!3 models > show #!2 models > hide #!3 models > hide #!2 models > show #!8 models > show #!3 models > show #!2 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #6/B Alignment identifier is 6/B > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #6/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > hide (#!6 & sel) target a > ui tool show ""Show Sequence Viewer"" [Repeated 1 time(s)] > sequence chain #8/A #8/C Alignment identifier is 1 > ui tool show ""Show Sequence Viewer"" > sequence chain #8/B Alignment identifier is 8/B > sequence chain #8/D Alignment identifier is 8/D > select #8/B 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > select clear > select #8/B 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > show #!3 models > show #!2 models > select clear > select #8/B 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > select clear > select #8/B 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > name frozen DNMT3L_1 sel > select clear > select DNMT3L_1 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > select clear > select #8/D:177-379 1579 atoms, 1629 bonds, 2 pseudobonds, 191 residues, 2 models selected > name frozen DNMT3L_2 sel > select clear > select DNMT3L_2 1579 atoms, 1629 bonds, 2 pseudobonds, 191 residues, 2 models selected > select DNMT3L_1 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > hide #!3 models > hide #!2 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T.cxs > hide target m > show target m > hide (#!8 & sel) target a > select DNMT3L_1 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > style (#!8 & sel) sphere Changed 1531 atom styles > show (#!8 & sel) target ab > hide (#!8 & sel) target a > select DNMT3L_2 1579 atoms, 1629 bonds, 2 pseudobonds, 191 residues, 2 models selected > hide (#!8 & sel) target a > hide #!3 models > hide #!2 models > select DNMT3L_1 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > cartoon (#!8 & sel) > select DNMT3L_2 1579 atoms, 1629 bonds, 2 pseudobonds, 191 residues, 2 models selected > cartoon (#!8 & sel) > select clear > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > sequence chain #8/C Alignment identifier is 8/C > select #8/C:474-887 3149 atoms, 3221 bonds, 2 pseudobonds, 393 residues, 2 models selected > select #8/C:474 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/C:474-475 20 atoms, 20 bonds, 2 residues, 1 model selected > select #8/C:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:476-610 1063 atoms, 1084 bonds, 135 residues, 1 model selected > hide sel target a > surface sel > color (#!8 & sel) orange > surface (#!8 & sel) > hide (#!8 & sel) target a > name frozen ADDwithH3K4me0 sel > select clear > select ADDwithH3K4me0 3354 atoms, 1084 bonds, 418 residues, 1 model selected > select clear > select #8/C:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > hide (#!8 & sel) target a > surface (#!8 & sel) > select ADDwithH3K4me0 3354 atoms, 1084 bonds, 418 residues, 1 model selected > surface (#!8 & sel) > select clear > select #8/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:476-610 1063 atoms, 1084 bonds, 135 residues, 1 model selected > hide sel target a > surface sel > color (#!8 & sel) orange > select clear > select #8/A:476-610 1063 atoms, 1084 bonds, 135 residues, 1 model selected > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > show #!3 models > show #!2 models > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > hide #!3 models > show #!3 models > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > hide #!3 models > hide #!2 models > select #8/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:476-610 1063 atoms, 1084 bonds, 135 residues, 1 model selected > name frozen ADDwithH3K4me0_1 sel > select clear > select ADDwithH3K4me0_1 3347 atoms, 1084 bonds, 417 residues, 1 model selected > select clear > select #8/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/A:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > hide (#!8 & sel) target a > surface (#!8 & sel) > select ADDwithH3K4me0_1 3347 atoms, 1084 bonds, 417 residues, 1 model selected > surface (#!8 & sel) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_2.cxs > select #8/A:474 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:474-475 20 atoms, 20 bonds, 2 residues, 1 model selected > select #8/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:474 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:474-475 20 atoms, 20 bonds, 2 residues, 1 model selected > hide #!5 models > hide #!4 models > show #!4 models > show #!5 models > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!8 models > show #!8 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_2.cxs > hide #!8 models > hide #!5 models > hide #!4 models > show #!4 models > show #!5 models > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K #1/P Alignment identifier is 1 > select #1/K,P:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/K,P:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/K,P:912 14 atoms, 12 bonds, 2 residues, 1 model selected > select #1/K,P:628-912 4416 atoms, 4522 bonds, 2 pseudobonds, 546 residues, 2 models selected > hide sel cartoons > show sel atoms > show #!8 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_2.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #7/D Alignment identifier is 7/D > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide sel cartoons > hide #!6 models > show #!6 models > hide #!8 models > show #!8 models > hide #!1 models > show #!1 models > hide #!6 models > hide #!7 models > show #!7 models > show #!6 models > hide #!8 models > show #!8 models > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > show #!2 models > show #!3 models > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > hide #!3 models > hide #!2 models > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > hide sel atoms > show sel atoms > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > hide sel atoms > show sel atoms > select DNMT3L_1 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > select DNMT3L_2 1579 atoms, 1629 bonds, 2 pseudobonds, 191 residues, 2 models selected > select H3K36me3 50 atoms, 50 bonds, 7 residues, 1 model selected > select H3K36me3_ 50 atoms, 50 bonds, 7 residues, 1 model selected > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select PWWP_H3K36me3_ 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > hide #!8 models > show #!8 models > hide #!8 models > hide #!1 models > hide #!5 models > hide #!4 models > show #!4 models > show #!5 models > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A Alignment identifier is 4/A > sequence chain #5/A Alignment identifier is 5/A > select #5/A:474-912 3422 atoms, 3505 bonds, 1 pseudobond, 426 residues, 2 models selected > select #5/A:474 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:474 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:476 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > show #!8 models > hide #!8 models > show #!2 models > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > show #!3 models > hide #!3 models > hide #!2 models > select clear > show #!2 models > hide #!2 models > show #!3 models > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > hide #!3 models > select clear > select #5/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > name frozen Inactive_ADD_2 sel > select clear > select Inactive_ADD_2 3422 atoms, 1119 bonds, 426 residues, 1 model selected > select clear [Repeated 1 time(s)] > select #4/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:477-614 1086 atoms, 1108 bonds, 138 residues, 1 model selected > select #4/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > name frozen Inactive_ADD_1 sel > select clear > select Inactive_ADD_1 3422 atoms, 1119 bonds, 426 residues, 1 model selected > surface hidePatches (#!4 & sel) > surface (#!4 & sel) > surface hidePatches (#!4 & sel) > select Inactive_ADD_2 3422 atoms, 1119 bonds, 426 residues, 1 model selected > select Inactive_ADD_1 3422 atoms, 1119 bonds, 426 residues, 1 model selected > surface (#!4 & sel) > surface hidePatches (#!4 & sel) > select #4/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:474-614 1115 atoms, 1137 bonds, 141 residues, 1 model selected > surface (#!4 & sel) > name frozen Inactive_ADD_1 sel [Repeated 1 time(s)] > select clear > select Inactive_ADD_2 3422 atoms, 1119 bonds, 426 residues, 1 model selected > select Inactive_ADD_1 3422 atoms, 1137 bonds, 426 residues, 1 model selected > select Inactive_ADD_1 3422 atoms, 1137 bonds, 426 residues, 1 model selected > select Inactive_ADD_2 3422 atoms, 1119 bonds, 426 residues, 1 model selected > surface (#!5 & sel) > select #5/A:615 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:615 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:474-614 1115 atoms, 1137 bonds, 141 residues, 1 model selected > select #5/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > select #5/A:474-912 3422 atoms, 3505 bonds, 1 pseudobond, 426 residues, 2 models selected > surface hidePatches (#!5 & sel) > select #5/A:615 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:615 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:614 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:476-614 1097 atoms, 1119 bonds, 139 residues, 1 model selected > surface (#!5 & sel) > select clear > show #!1 models > show #!8 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_2.cxs > hide #!8 models > hide #!7 models > show #!7 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > show #!8 models > hide #!8 models > hide #!5 models > hide #!4 models > hide #!7 models > hide #!6 models > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > select clear > show #!7 models > show #!6 models > show #!5 models > show #!4 models > show #!3 models > hide #!3 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_2.cxs > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > hide sel atoms > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > hide sel atoms > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/N #1/S Alignment identifier is 1 > select #1/N,S 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > select #1/N,S 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > name frozen DNMT3B sel > select clear > select DNMT3B 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > hide sel atoms > show sel atoms > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_2.cxs > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > select DNMT3B 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > hide sel atoms > lighting simple > lighting soft > lighting full > lighting soft > lighting full > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > show sel atoms > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > show sel atoms > select DNMT3B 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > show sel atoms > show #!7 models > show #!6 models > show #!5 models > show #!4 models > show #!8 models > hide #!8 models > show #!8 models > hide #!1 models > show #!1 models > hide #!8 models > hide #!7 models > hide #!6 models > show #!6 models > show #!7 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!7 models > hide #!6 models > show #!8 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > hide #!3 models > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > hide sel atoms > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > hide sel atoms > show #!6 models > show #!7 models > open 5yx2 Summary of feedback from opening 5yx2 fetched from pdb --- notes | Fetching compressed mmCIF 5yx2 from http://files.rcsb.org/download/5yx2.cif Fetching CCD PYO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/PYO/PYO.cif 5yx2 title: Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites [more info...] Chain information for 5yx2 #9 --- Chain | Description | UniProt A D | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 628-912 B C | DNA (cytosine-5)-methyltransferase 3-like | DNM3L_HUMAN 178-385 E F | DNA (25-MER) | Non-standard residues in 5yx2 #9 --- GOL — glycerol (glycerin; propane-1,2,3-triol) SAH — S-adenosyl-L-homocysteine > ui tool show Matchmaker > matchmaker #9/A to #8/A pairing ss 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 4u7t, chain A (#8) with 5yx2, chain A (#9), sequence alignment score = 1415.8 RMSD between 263 pruned atom pairs is 0.653 angstroms; (across all 273 pairs: 1.090) > ui tool show Matchmaker [Repeated 2 time(s)] > matchmaker #9/A to #8/A pairing ss 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 4u7t, chain A (#8) with 5yx2, chain A (#9), sequence alignment score = 1415.8 RMSD between 263 pruned atom pairs is 0.653 angstroms; (across all 273 pairs: 1.090) > ui tool show Matchmaker > matchmaker #9/C to #8/A pairing ss 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 4u7t, chain A (#8) with 5yx2, chain C (#9), sequence alignment score = 300.9 RMSD between 89 pruned atom pairs is 0.935 angstroms; (across all 163 pairs: 11.460) > ui tool show Matchmaker > matchmaker #9/A to #8/A pairing ss 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 4u7t, chain A (#8) with 5yx2, chain A (#9), sequence alignment score = 1415.8 RMSD between 263 pruned atom pairs is 0.653 angstroms; (across all 273 pairs: 1.090) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #9/B #9/C Alignment identifier is 1 > select #9/B:178 5 atoms, 4 bonds, 1 residue, 1 model selected > select #9/B:178-379/C:187-378 2661 atoms, 2740 bonds, 7 pseudobonds, 362 residues, 2 models selected > hide sel atoms > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > hide sel atoms > show sel atoms > hide sel atoms > hide #!8 models > show #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #9/E #9/F Alignment identifier is 1 > select #9/E-F:422 36 atoms, 40 bonds, 2 residues, 1 model selected > select #9/E-F:422-446 1020 atoms, 1144 bonds, 52 pseudobonds, 50 residues, 2 models selected > surface (#!9 & sel) > surface hidePatches (#!9 & sel) > hide sel atoms > show sel cartoons > show (#!9 & sel) target ab > style sel ball Changed 1020 atom styles > ui tool show ""Show Sequence Viewer"" > sequence chain #9/A #9/D Alignment identifier is 1 > hide #!8 models > show #!8 models > hide #!8 models > hide #!7 models > hide #!6 models > select #9/A,D:912 12 atoms, 10 bonds, 2 residues, 1 model selected > select #9/A,D:628-912 4536 atoms, 4644 bonds, 570 residues, 1 model selected > hide sel atoms > surface sel > hide (#!9 & sel) target a > show #!8 models > show #!7 models > show #!6 models > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > hide #!8 models > show #!8 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2.cxs > select clear > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A #8/C Alignment identifier is 2 > ui tool show ""Show Sequence Viewer"" > hide #!8 models > show #!8 models > sequence chain #8/A #8/C Alignment identifier is 1 > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:912 14 atoms, 12 bonds, 2 residues, 1 model selected > select #8/A,C:628-912 4416 atoms, 4522 bonds, 2 pseudobonds, 546 residues, 2 models selected > select clear > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:628-912 4416 atoms, 4522 bonds, 2 pseudobonds, 546 residues, 2 models selected > name frozen CatalyticDomains4U7T sel > select clear > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > surface hidePatches (#!8 & sel) > surface (#!8 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > sequence chain #8/C Alignment identifier is 8/C > select clear > show #!2 models > show #!3 models > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > select ADD_2 1097 atoms, 1119 bonds, 139 residues, 1 model selected > hide #!3 models > hide #!2 models > select clear > select #8/A:474-622 1099 atoms, 1120 bonds, 1 pseudobond, 139 residues, 2 models selected > select #8/C:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:912 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/C:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > select clear > select #8/C:912 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/C:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > name frozen CatalyticDomain4U7T_2 sel > select clear > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > surface hidePatches (#!8 & sel) > surface (#!8 & sel) > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > show #!4 models > show #!5 models > hide #!5 models > hide #!4 models > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!8 models > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > show #!8 models > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > select #8/C:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > surface hidePatches (#!8 & sel) > cartoon (#!8 & sel) > hide #!9 models > show #!9 models > hide #!9 models > select #8/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/A:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > surface hidePatches (#!8 & sel) > show sel cartoons > select clear > show #!9 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2.cxs > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #9/A #9/D Alignment identifier is 1 > select #9/A,D:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #9/A,D:628-912 4536 atoms, 4644 bonds, 570 residues, 1 model selected > show sel cartoons > surface hidePatches (#!9 & sel) > name frozen CatalyticDomains5YX2 sel > hide sel cartoons > hide #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #9/E #9/F Alignment identifier is 2 > select #9/E-F:423 38 atoms, 40 bonds, 2 residues, 1 model selected > select #9/E-F:423 38 atoms, 40 bonds, 2 residues, 1 model selected > select #9/E-F:427 38 atoms, 40 bonds, 2 residues, 1 model selected > select #9/E-F:427 38 atoms, 40 bonds, 2 residues, 1 model selected > style sel sphere Changed 38 atom styles > show #!8 models > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > select CatalyticDomains5YX2 4536 atoms, 4644 bonds, 570 residues, 1 model selected > surface (#!9 & sel) > hide #!9 models > show #!9 models > select clear > select CatalyticDomains5YX2 4536 atoms, 4644 bonds, 570 residues, 1 model selected > surface hidePatches (#!9 & sel) > show sel cartoons > select clear > hide #!8 models > show #!8 models > show #!4 models > hide #!4 models > hide #!8 models > show #!8 models > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > select clear > ui tool show ""Show Sequence Viewer"" > hide #!8 models > show #!8 models > sequence chain #8/A #8/C Alignment identifier is 1 > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:628-660 520 atoms, 524 bonds, 66 residues, 1 model selected > select #8/A,C:628-912 4416 atoms, 4522 bonds, 2 pseudobonds, 546 residues, 2 models selected > select clear > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:628-912 4416 atoms, 4522 bonds, 2 pseudobonds, 546 residues, 2 models selected > name frozen CatalyticDomains4U7T sel > select clear > ui tool show ""Selection Inspector"" > select CatalyticDomains5YX2 4536 atoms, 4644 bonds, 570 residues, 1 model selected > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:628 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/A,C:628-912 4416 atoms, 4522 bonds, 2 pseudobonds, 546 residues, 2 models selected > hide #!4 target m > show #!4 target m > hide #!4 models > hide sel cartoons > show sel cartoons > select clear > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2.cxs > hide #!9 models > hide #!8 models > show #!5 models > show #!4 models > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > show sel cartoons > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > show sel atoms > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > show (#!1 & sel) target ab > surface (#!1 & sel) > hide sel cartoons > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > hide sel atoms > surface (#!1 & sel) > select DNMT3B 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > hide sel atoms > show sel cartoons > surface (#!1 & sel) > select clear > set bgColor white > set bgColor #ffffff00 > hide #!5 models > show #!5 models > hide #!7 models > hide #!6 models > show #!6 models > show #!7 models > color #7 magenta > color #6 magenta > set bgColor black > set bgColor transparent > show #!9 models > show #!8 models > hide #!5 models > hide #!4 models > show #!4 models > show #!5 models > hide #!8 models > hide #!9 models > show #!9 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > show #!1 models > hide #!1 models > show #!8 models > show #!1 models > hide #!8 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!9 models > show #!9 models > show #!1 models > hide #!9 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide sel atoms > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > surface hidePatches (#!1 & sel) > select DNMT3B 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide sel cartoons > select DNMT3B 3406 atoms, 3498 bonds, 2 pseudobonds, 422 residues, 2 models selected > surface (#!1 & sel) > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > surface (#!1 & sel) > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > surface (#!1 & sel) > show #!8 models > hide #!8 models > show #!7 models > show #!6 models > show #!5 models > show #!4 models > set bgColor white > set bgColor #ffffff00 > select clear > set bgColor black > set bgColor transparent > show #!8 models > hide #!5 models > hide #!4 models > hide #!8 models > hide #!1 models > show #!1 models > show #!5 models > hide #!5 models > show #!4 models > show #!3 models > hide #!3 models > show #!5 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K #1/P Alignment identifier is 1 > select #1/K,P:615 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/K,P:615-626 200 atoms, 210 bonds, 24 residues, 1 model selected > select #1/K,P:615 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/K,P:615-628 224 atoms, 236 bonds, 28 residues, 1 model selected > color (#!1 & sel) light gray > color (#!1 & sel) gray > color (#!1 & sel) light gray > color (#!1 & sel) dark gray > ui tool show ""Show Sequence Viewer"" > sequence chain #6/C #6/D Alignment identifier is 1 > select #6/C-D:32-38 100 atoms, 100 bonds, 14 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #6/C #6/D Alignment identifier is 2 > sequence chain #7/C #7/D Alignment identifier is 3 > select #7/C-D:32-38 100 atoms, 100 bonds, 14 residues, 1 model selected > select #7/C-D:32-38 100 atoms, 100 bonds, 14 residues, 1 model selected > color (#!7 & sel) #e5f1fbff > color (#!7 & sel) #ccccccff > color (#!7 & sel) #3d5a90ff > color (#!7 & sel) #75aeffff > color (#!7 & sel) #253b1fff > color (#!7 & sel) #121d0fff > color (#!7 & sel) #46713cff > color (#!7 & sel) #63a055ff > color (#!7 & sel) #eaffceff > color (#!7 & sel) #f7ffdaff > color (#!7 & sel) #dfffc3ff > color (#!7 & sel) #e5f1fbff > color (#!7 & sel) #ccccccff > color (#!7 & sel) #f0f0f0ff > color (#!7 & sel) #606452ff > color (#!7 & sel) #676b58ff > color (#!7 & sel) #558a49ff > color (#!7 & sel) #91e97bff > color (#!7 & sel) #98f581ff > color (#!7 & sel) #a4ff8cff > color (#!7 & sel) #eaffceff > color (#!7 & sel) #b2ff98ff > color (#!7 & sel) #a6ff8eff > color (#!7 & sel) #96f280ff > color (#!7 & sel) #86d872ff > color (#!7 & sel) #90e87bff > color (#!7 & sel) #96f280ff > color (#!7 & sel) #8ce278ff > color (#!7 & sel) #7ac568ff > color (#!7 & sel) #66a557ff > color (#!7 & sel) #7bc669ff > color (#!7 & sel) #86d972ff > color (#!7 & sel) #92ec7dff > color (#!7 & sel) #9dfd86ff > color (#!7 & sel) #a0ff89ff > color (#!7 & sel) #8bdf76ff > color (#!7 & sel) #7ac568ff > color (#!7 & sel) #76be64ff > color (#!7 & sel) #9af983ff > color (#!7 & sel) #95f180ff > color (#!7 & sel) #97f481ff > color (#!7 & sel) #aeff95ff > color (#!7 & sel) #88dc74ff > color (#!7 & sel) #94ee7eff > color (#!7 & sel) #a2ff8aff > color (#!7 & sel) #aaff91ff > color (#!7 & sel) #a9ff90ff > color (#!7 & sel) #87da73ff > color (#!7 & sel) #96f280ff > color (#!7 & sel) #9dfd86ff > select #6/C-D:32-38 100 atoms, 100 bonds, 14 residues, 1 model selected > select #6/C-D:32-38 100 atoms, 100 bonds, 14 residues, 1 model selected > select #7/C-D:32-38 100 atoms, 100 bonds, 14 residues, 1 model selected > select #6/C-D:32-38 100 atoms, 100 bonds, 14 residues, 1 model selected > select add #6 2266 atoms, 2162 bonds, 3 pseudobonds, 426 residues, 4 models selected > select subtract #6 3 models selected > select #6/C-D:32-38 100 atoms, 100 bonds, 14 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pale green > show #!8 models > show #!9 models > hide #!9 models > select clear > hide #!5 models > hide #!4 models > show #!4 models > show #!5 models > hide #!5 models > hide #!4 models > hide #!8 models > show #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/F #8/G Alignment identifier is 1 > select #8/F-G:1 10 atoms, 8 bonds, 2 residues, 1 model selected > select #8/F-G 158 atoms, 156 bonds, 20 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pale green > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_2.cxs > hide #!8 models > show #!5 models > show #!4 models > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > surface (#!7 & sel) > select PWWP_H3K36me3_ 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > surface (#!6 & sel) > show #!8 models > surface hidePatches (#!6 & sel) > hide #!8 models > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > surface hidePatches (#!7 & sel) > select clear > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > show #!8 models > hide #!5 models > hide #!4 models > show #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!4 models > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > show #!9 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > show #!1 models > select CatalyticDomain 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > surface hidePatches (#!1 & sel) > select CatalyticDomain_1 2333 atoms, 2261 bonds, 1 pseudobond, 288 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!8 models > show #!8 models > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > hide sel cartoons > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > select clear > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > select clear > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > hide sel cartoons > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #9/E #9/F Alignment identifier is 1 > select #9/E-F:427 38 atoms, 40 bonds, 2 residues, 1 model selected > select #9/E-F:427 38 atoms, 40 bonds, 2 residues, 1 model selected > color (#!9 & sel) red > select clear > hide #!1 models > select add #9 8380 atoms, 8616 bonds, 59 pseudobonds, 1065 residues, 3 models selected > select clear > show #!1 models > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > hide #!9 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > surface (#!8 & sel) > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > surface (#!8 & sel) > select CatalyticDomain4U7T_2 3354 atoms, 2261 bonds, 1 pseudobond, 418 residues, 2 models selected > surface (#!8 & sel) > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > surface (#!8 & sel) > select clear > show #!9 models > hide #!8 models > show #!8 models > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > surface hidePatches (#!8 & sel) > surface (#!8 & sel) > select clear > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > select CatalyticDomains4U7T 6701 atoms, 4522 bonds, 2 pseudobonds, 835 residues, 2 models selected > surface hidePatches (#!8 & sel) > surface (#!8 & sel) > select clear > hide #!9 models > show #!9 models > hide #!9 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3.cxs ——— End of log from Thu Aug 24 17:47:44 2023 ——— opened ChimeraX session > open 8peo 8peo title: H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex [more info...] Chain information for 8peo #10 --- Chain | Description | UniProt A E | Histone H3 | A0A310TTQ1_XENLA 1-135 B F | Histone H4 | H4_XENLA 1-102 C G | Histone H2A | Q6AZJ8_XENLA 1-129 D H | Histone H2B 1.1 | H2B11_XENLA 1-122 I | Widom 601 DNA (147-MER) | J | Widom 601 DNA (147-MER) | K | PC4 and SFRS1-interacting protein | PSIP1_HUMAN 1-530 Non-standard residues in 8peo #10 --- M2L — (2R)-2-amino-3-(2-dimethylaminoethylsulfanyl)propanoic acid > ui tool show Matchmaker > matchmaker #10/I to #1/I pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 8peo #10/I to 6pa7 #1/I Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 6pa7, chain I (#1) with 8peo, chain I (#10), sequence alignment score = 568.4 RMSD between 118 pruned atom pairs is 1.106 angstroms; (across all 147 pairs: 2.041) > ui tool show ""Show Sequence Viewer"" > sequence chain #10/K Alignment identifier is 10/K > select #10/K:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" [Repeated 1 time(s)] > select #10/I 2996 atoms, 3357 bonds, 147 residues, 1 model selected > hide sel atoms > select #10/J 3031 atoms, 3403 bonds, 147 residues, 1 model selected > hide sel atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #10/A #10/E Alignment identifier is 1 > sequence chain #10/B #10/F Alignment identifier is 2 > sequence chain #10/D #10/H Alignment identifier is 3 > select #10/A:35-134/E 1618 atoms, 1641 bonds, 1 pseudobond, 196 residues, 2 models selected > hide sel atoms > select #10/B,F 1351 atoms, 1366 bonds, 168 residues, 1 model selected > hide sel atoms > select #10/D,H 1472 atoms, 1494 bonds, 188 residues, 1 model selected > hide sel atoms > hide #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #10/C Alignment identifier is 10/C > sequence chain #10/G Alignment identifier is 10/G > select #10/C 823 atoms, 833 bonds, 107 residues, 1 model selected > hide sel atoms > select #10/G 823 atoms, 833 bonds, 107 residues, 1 model selected > hide sel atoms > show #!1 models > select #10/K:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > select #10/K:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > hide sel atoms > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #10/A Alignment identifier is 10/A > sequence chain #10/E Alignment identifier is 10/E > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > show sel cartoons [Repeated 1 time(s)] > hide #!1 models > show #!1 models > surface (#!10 & sel) > select #10/K:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > color (#!10 & sel) magenta > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add8PEO.cxs ——— End of log from Wed Aug 30 17:36:42 2023 ——— opened ChimeraX session > open 8peo 8peo title: H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex [more info...] Chain information for 8peo #11 --- Chain | Description | UniProt A E | Histone H3 | A0A310TTQ1_XENLA 1-135 B F | Histone H4 | H4_XENLA 1-102 C G | Histone H2A | Q6AZJ8_XENLA 1-129 D H | Histone H2B 1.1 | H2B11_XENLA 1-122 I | Widom 601 DNA (147-MER) | J | Widom 601 DNA (147-MER) | K | PC4 and SFRS1-interacting protein | PSIP1_HUMAN 1-530 Non-standard residues in 8peo #11 --- M2L — (2R)-2-amino-3-(2-dimethylaminoethylsulfanyl)propanoic acid > ui tool show Matchmaker > matchmaker #11/I to #1/I pairing ss Using Nucleic matrix instead of BLOSUM-62 to match 8peo #11/I to 6pa7 #1/I Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 6pa7, chain I (#1) with 8peo, chain I (#11), sequence alignment score = 568.4 RMSD between 118 pruned atom pairs is 1.106 angstroms; (across all 147 pairs: 2.041) > hide #!11 models > hide #!1 models > show #!1 models > show #!11 models > ui tool show ""Show Sequence Viewer"" > sequence chain #11/I Alignment identifier is 11/I > sequence chain #11/J Alignment identifier is 11/J > select #11/I:-73 21 atoms, 23 bonds, 1 residue, 1 model selected > select #11/I 2996 atoms, 3357 bonds, 147 residues, 1 model selected > hide sel atoms > select #11/J:-73 21 atoms, 23 bonds, 1 residue, 1 model selected > select #11/J 3031 atoms, 3403 bonds, 147 residues, 1 model selected > hide sel cartoons > hide sel atoms > hide #!1 models > show #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #11/B Alignment identifier is 11/B > sequence chain #11/C Alignment identifier is 11/C > sequence chain #11/D Alignment identifier is 11/D > sequence chain #11/F Alignment identifier is 11/F > sequence chain #11/G Alignment identifier is 11/G > sequence chain #11/H Alignment identifier is 11/H > select #11/H 736 atoms, 747 bonds, 94 residues, 1 model selected > hide sel atoms [Repeated 1 time(s)] > select #11/G 823 atoms, 833 bonds, 107 residues, 1 model selected > hide sel atoms > select #11/F 694 atoms, 702 bonds, 86 residues, 1 model selected > hide sel atoms > select #11/D 736 atoms, 747 bonds, 94 residues, 1 model selected > hide sel atoms > select #11/C 823 atoms, 833 bonds, 107 residues, 1 model selected > hide sel atoms > select #11/B 657 atoms, 664 bonds, 82 residues, 1 model selected > hide sel atoms > hide #!10 models > hide #!1 models > show #!1 models > hide #!1 models > show #!10 models > hide #!10 models > hide #!11 models > show #!11 models > show #!10 models > hide #!10 models > show #!10 models > hide #!11 models > hide #!10 models > show #!11 models > ui tool show Matchmaker > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add8PEOx2.cxs > ui tool show Matchmaker > matchmaker #10/E to #11/A pairing ss 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 8peo, chain A (#11) with 8peo, chain E (#10), sequence alignment score = 614.7 RMSD between 96 pruned atom pairs is 0.311 angstroms; (across all 97 pairs: 0.373) > show #!10 models > show #!1 models > hide #!1 models > hide #!7 models > hide #!6 models > hide #!10 models > ui tool show ""Show Sequence Viewer"" > sequence chain #11/E Alignment identifier is 11/E > sequence chain #11/A Alignment identifier is 11/A > select #11/E:38-120 682 atoms, 693 bonds, 83 residues, 1 model selected > hide sel atoms > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > hide sel atoms > surface (#!11 & sel) > show #!10 models > ui tool show ""Show Sequence Viewer"" > sequence chain #11/K Alignment identifier is 11/K > select #11/K:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #11/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > select #11/K:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #11/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > show sel cartoons > hide sel atoms > color (#!11 & sel) magenta > show #!9 models > hide #!9 models > show #!7 models > hide #!7 models > hide #!8 models > show #!8 models > show #!5 models > hide #!5 models > show #!1 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_2.cxs > select clear > hide #!8 models > show #!8 models > hide #!1 models > show #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/F Alignment identifier is 8/F > sequence chain #8/G Alignment identifier is 8/G > select #8/F:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/F 79 atoms, 78 bonds, 10 residues, 1 model selected > ui tool show ""Color Actions"" > color sel plum > select #8/G:1-2 16 atoms, 15 bonds, 2 residues, 1 model selected > select #8/G 79 atoms, 78 bonds, 10 residues, 1 model selected > color sel plum > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_2.cxs > set bgColor white > set bgColor #ffffff00 > show #!9 models > hide #!8 models > show #!8 models > hide #!9 models > set bgColor black > set bgColor transparent > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_2.cxs > hide #!1 models > hide #!11 models > hide #!10 models > show #!4 models > hide #!4 models > show #!1 models > show #!10 models > show #!11 models > show #!7 models > hide #!7 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > hide #!8 models > show #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/B Alignment identifier is 8/B > sequence chain #8/D Alignment identifier is 8/D > select #8/B 1531 atoms, 1575 bonds, 4 pseudobonds, 187 residues, 2 models selected > hide sel cartoons > select #8/D:177-379 1579 atoms, 1629 bonds, 2 pseudobonds, 191 residues, 2 models selected > hide sel cartoons > hide #!1 models > show #!1 models > select clear > hide #!1 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > show #!9 models > hide #!9 models > show #!1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > hide #!8 models > hide #!1 models > show #!1 models > show #!8 models > show #!5 models > show #!4 models > hide #!8 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K #1/P Alignment identifier is 1 > select #1/K,P:613-912 4666 atoms, 4788 bonds, 2 pseudobonds, 576 residues, 2 models selected > show sel cartoons [Repeated 1 time(s)] > hide sel cartoons > surface (#!1 & sel) > select clear > hide #!5 models > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > show #!5 models > hide #!1 models > show #!1 models > hide #!4 models > show #!4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #4/B #5/B #8/B #8/D Alignment identifier is 2 > select #4/B #5/B #8/B/D:177-379 6352 atoms, 6550 bonds, 8 pseudobonds, 772 residues, 6 models selected > hide sel & #!4-5 cartoons > hide #!1 models > show #!1 models > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > hide #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #10/A #10/E #11/A #11/E Alignment identifier is 1 > select #10/A:35-134/E #11/A:35-134/E 3236 atoms, 3282 bonds, 2 pseudobonds, 392 residues, 4 models selected > show #!1 models > ui tool show ""Color Actions"" > color sel pale green > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/E Alignment identifier is 2 > select #10/A:35-134/E #11/A:35-134/E 3236 atoms, 3282 bonds, 2 pseudobonds, 392 residues, 4 models selected > surface hidePatches (#!10-11 & sel) > show sel atoms > hide sel atoms > show sel atoms > ui tool show ""Color Actions"" > color sel plum > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #1/C #1/G #10/C #10/G #11/C #11/G Alignment identifier is 3 > select #10/A:35-134/E #11/A:35-134/E 3236 atoms, 3282 bonds, 2 pseudobonds, 392 residues, 4 models selected > select #1/C:11-118/G #10/C,G #11/C,G 4965 atoms, 5025 bonds, 647 residues, 3 models selected > select #1/A:37-135/E 1622 atoms, 1646 bonds, 197 residues, 1 model selected > select #1/A:37-135/E 1622 atoms, 1646 bonds, 197 residues, 1 model selected > select #10/A:35-134/E #11/A:35-134/E 3236 atoms, 3282 bonds, 2 pseudobonds, 392 residues, 4 models selected > select #1/A:37-135/E 1622 atoms, 1646 bonds, 197 residues, 1 model selected > select #1/C:11-118/G #10/C,G #11/C,G 4965 atoms, 5025 bonds, 647 residues, 3 models selected > ui tool show ""Color Actions"" > color sel aquamarine > color sel salmon > color sel pale violet red > color sel medium purple > color sel teal > color sel turquoise > select clear > select #1/A:37-135/E 1622 atoms, 1646 bonds, 197 residues, 1 model selected > select #10/A:35-134/E #11/A:35-134/E 3236 atoms, 3282 bonds, 2 pseudobonds, 392 residues, 4 models selected > hide sel atoms > select #1/A:37-135/E 1622 atoms, 1646 bonds, 197 residues, 1 model selected > select clear > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_3.cxs ——— End of log from Thu Aug 31 11:00:29 2023 ——— opened ChimeraX session > show #!6 models > show #!7 models > hide #!5 models > hide #!4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #6/C Alignment identifier is 6/C > sequence chain #6/D Alignment identifier is 6/D > sequence chain #7/C Alignment identifier is 7/C > sequence chain #7/D Alignment identifier is 7/D > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > surface hidePatches (#!6 & sel) > show sel atoms > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > surface hidePatches (#!7 & sel) > show sel atoms > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show sel atoms > show sel cartoons > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show sel cartoons > show sel atoms > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show sel atoms > hide sel cartoons > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show sel cartoons > show sel atoms > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show sel cartoons > show sel atoms > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show sel atoms > show sel cartoons > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show sel cartoons > show sel atoms > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide #!10 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > show #!10 models > hide #!1 models > hide #!10 models > show #!10 models > hide #!11 models > show #!11 models > hide #!10 models > show #!10 models > hide #!11 models > show #!11 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #10/E Alignment identifier is 10/E > sequence chain #11/E Alignment identifier is 11/E > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select #11/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select clear > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #10/A Alignment identifier is 10/A > sequence chain #11/A Alignment identifier is 11/A > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #10/E Alignment identifier is 10/E > sequence chain #11/E Alignment identifier is 11/E > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > show sel atoms [Repeated 1 time(s)] > hide sel atoms > show sel cartoons > select #11/E 801 atoms, 813 bonds, 97 residues, 1 model selected > show sel cartoons > hide sel cartoons > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > hide sel atoms > select #11/E 801 atoms, 813 bonds, 97 residues, 1 model selected > hide sel cartoons > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > hide sel cartoons > hide #!10 models > show #!10 models > hide #!11 models > show #!11 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select #11/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > surface (#!10 & sel) > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > surface (#!11 & sel) > show #!1 models > hide #!1 models > surface hidePatches (#!11 & sel) > surface (#!11 & sel) > color (#!11 & sel) black > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > color (#!11 & sel) light gray > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > color sel light gray > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > select clear > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > color (#!10 & sel) light gray > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select #11/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > ui tool show ""Color Actions"" > color sel plum > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > show #!1 models > hide #!11 models > hide #!10 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/E Alignment identifier is 1/E > select #1/A:37-135 817 atoms, 829 bonds, 99 residues, 1 model selected > ui tool show ""Color Actions"" > color sel plum [Repeated 2 time(s)] > select #1/E 805 atoms, 817 bonds, 98 residues, 1 model selected > ui tool show ""Color Actions"" > color sel plum > surface hidePatches (#!1 & sel) > select #1/A:37-135 817 atoms, 829 bonds, 99 residues, 1 model selected > surface hidePatches (#!1 & sel) > hide #!1 models > show #!10 models > show #!11 models > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light green > color sel pale green > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > color sel pale green > show #!1 models > select clear > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_4.cxs > hide #!1 models > hide #!11 models > show #!11 models > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > color sel byelement > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > color (#!6 & sel) byelement > select clear > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > color (#!6 & sel) yellow > color (#!6 & sel) byelement > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > color sel yellow > color sel byelement > hide #!6 models > hide #!7 models > show #!7 models > show #!6 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_4.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #11/A Alignment identifier is 11/A > sequence chain #11/E Alignment identifier is 11/E > select #11/E 801 atoms, 813 bonds, 97 residues, 1 model selected > surface sel > surface hidePatches (#!11 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #10/A Alignment identifier is 10/A > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #11/E Alignment identifier is 11/E > sequence chain #10/E Alignment identifier is 10/E > select #11/E 801 atoms, 813 bonds, 97 residues, 1 model selected > surface (#!11 & sel) > select #10/E 801 atoms, 813 bonds, 97 residues, 1 model selected > surface sel > surface hidePatches (#!10 & sel) > select #11/E 801 atoms, 813 bonds, 97 residues, 1 model selected > surface hidePatches (#!11 & sel) > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > ui tool show Matchmaker > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_4.cxs > select clear > ui tool show Matchmaker > matchmaker #6/C to #11/A pairing ss 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 8peo, chain A (#11) with 5ciu, chain C (#6), sequence alignment score = 56.8 RMSD between 3 pruned atom pairs is 0.196 angstroms; (across all 3 pairs: 0.196) > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide #!6 models > show #!6 models > ui tool show Matchmaker > matchmaker #7/D to #10/A pairing ss 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 8peo, chain A (#10) with 5ciu, chain D (#7), sequence alignment score = 61 RMSD between 3 pruned atom pairs is 0.443 angstroms; (across all 3 pairs: 0.443) > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > show sel cartoons > surface hidePatches (#!11 & sel) > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > surface hidePatches (#!10 & sel) > show sel cartoons > hide #!10 models > show #!10 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > hide sel cartoons > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > show sel cartoons > show sel atoms [Repeated 1 time(s)] > hide sel atoms > style sel stick Changed 817 atom styles > show sel atoms > color (#!11 & sel) byelement > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > show sel atoms > style sel stick Changed 817 atom styles > color (#!10 & sel) byelement > hide #!6 models > hide #!7 models > show #!7 models > show #!6 models > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > sequence chain #7/B Alignment identifier is 7/B > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > hide sel cartoons > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > hide sel cartoons > hide sel atoms > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > hide sel atoms > select #6/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > hide sel atoms > hide sel cartoons > select #7/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > hide sel cartoons > hide sel atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #6/D Alignment identifier is 6/D > sequence chain #7/C Alignment identifier is 7/C > select #6/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #7/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > show #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > show #!8 models > show #!9 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > show #!7 models > show #!6 models > show #!5 models > show #!4 models > show #!8 models > hide #!8 models > hide #!1 models > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > surface (#!11 & sel) > select #10/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > surface (#!10 & sel) > show #!1 models > ui tool show ""Color Actions"" > color sel pale green > select #11/A:35-134 817 atoms, 828 bonds, 1 pseudobond, 99 residues, 2 models selected > color sel pale green > select #1/A:37-135 817 atoms, 829 bonds, 99 residues, 1 model selected > select clear > hide #!4 models > show #!4 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > hide #!10 models > show #!10 models > hide #!11 models > show #!11 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_5.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/E Alignment identifier is 1/E > select #1/A:37-135 817 atoms, 829 bonds, 99 residues, 1 model selected > hide sel atoms > select #1/E 805 atoms, 817 bonds, 98 residues, 1 model selected > hide sel atoms > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > select #1/E 805 atoms, 817 bonds, 98 residues, 1 model selected > show sel atoms > hide sel cartoons > hide sel atoms > show #!8 models > hide #!5 models > hide #!4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K Alignment identifier is 1/K > sequence chain #1/P Alignment identifier is 1/P > select #1/K:613 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/P:613-912 2333 atoms, 2394 bonds, 1 pseudobond, 288 residues, 2 models selected > surface hidePatches (#!1 & sel) > show sel cartoons [Repeated 1 time(s)] > hide sel cartoons > select #1/K:613-912 2333 atoms, 2394 bonds, 1 pseudobond, 288 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide #!8 models > show #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/F Alignment identifier is 8/F > sequence chain #8/G Alignment identifier is 8/G > select #8/F:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/F 79 atoms, 78 bonds, 10 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pale green > select #8/G:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/G 79 atoms, 78 bonds, 10 residues, 1 model selected > color sel pale green > set bgColor white > set bgColor #ffffff00 > show #!9 models > hide #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #9/E Alignment identifier is 9/E > sequence chain #9/F Alignment identifier is 9/F > select #9/E:427 19 atoms, 20 bonds, 1 residue, 1 model selected > select #9/E:427 19 atoms, 20 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel mint cream > color sel pale turquoise > color sel light goldenrod yellow > color sel pale turquoise > color sel light goldenrod yellow > color sel green yellow > color sel light goldenrod yellow > color sel khaki > color sel pale goldenrod > color sel light goldenrod yellow > hide sel atoms > style sel ball Changed 19 atom styles > style sel ball Changed 19 atom styles > ui tool show ""Color Actions"" [Repeated 1 time(s)] > color sel goldenrod > color sel white smoke > color sel mint cream > color sel light goldenrod yellow > select #9/E:422 18 atoms, 20 bonds, 1 residue, 1 model selected > select #9/E:422-446 510 atoms, 572 bonds, 25 residues, 1 model selected > color sel light goldenrod yellow > select clear > select #9/E:422 18 atoms, 20 bonds, 1 residue, 1 model selected > select #9/E:422-446 510 atoms, 572 bonds, 25 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pale green > color sel pale turquoise > color sel mint cream > color sel azure > color sel cornsilk > color sel lemon chiffon > color sel papaya whip > color sel light cyan > color sel pale goldenrod > color sel khaki > color sel pale goldenrod > color sel light cyan > color sel light goldenrod yellow > color sel dark khaki > color sel light goldenrod yellow > set bgColor black > set bgColor transparent > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > show #!8 models > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > sequence chain #8/C Alignment identifier is 8/C > select #8/C:474-912 3354 atoms, 3434 bonds, 2 pseudobonds, 418 residues, 2 models selected > surface hidePatches (#!8 & sel) > undo > select #8/C:474-912 3354 atoms, 3434 bonds, 2 pseudobonds, 418 residues, 2 models selected > surface (#!8 & sel) > ui tool show ""Show Sequence Viewer"" > select #8/C:607 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:607-608 19 atoms, 19 bonds, 2 residues, 1 model selected > select #8/C:630 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/C:630 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/C:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > surface hidePatches (#!8 & sel) > select > #8/A:476-485,489-493,514-525,560-567,570-578,600-609,627-631,644-654,666-678,686-698,729-742,762-773,783-785,814-819,860-868,881-892,894-908 1379 atoms, 1388 bonds, 167 residues, 1 model selected > select #8/A:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/A:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > surface hidePatches (#!8 & sel) > select #9/F:427 19 atoms, 20 bonds, 1 residue, 1 model selected > select #9/F:427 19 atoms, 20 bonds, 1 residue, 1 model selected > select #9/F:422 18 atoms, 20 bonds, 1 residue, 1 model selected > select #9/F:422-426 100 atoms, 112 bonds, 5 residues, 1 model selected > select #9/F:422-426,428-446 491 atoms, 550 bonds, 24 residues, 1 model selected > hide sel atoms > select #9/E:422 18 atoms, 20 bonds, 1 residue, 1 model selected > select #9/E:422-446 510 atoms, 572 bonds, 25 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #9/F:422-424 58 atoms, 65 bonds, 3 residues, 1 model selected > select #9/F:422-426 100 atoms, 112 bonds, 5 residues, 1 model selected > hide sel cartoons > select #9/F:428 22 atoms, 24 bonds, 1 residue, 1 model selected > select #9/F:428-446 391 atoms, 438 bonds, 19 residues, 1 model selected > hide sel cartoons > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > select #8/A:474-782 2372 atoms, 2424 bonds, 1 pseudobond, 299 residues, 2 models selected > select #9/E:422 18 atoms, 20 bonds, 1 residue, 1 model selected > select #9/E:422-446 510 atoms, 572 bonds, 25 residues, 1 model selected > show sel cartoons > select #9/F:422 18 atoms, 20 bonds, 1 residue, 1 model selected > select #9/F:422-446 510 atoms, 572 bonds, 25 residues, 1 model selected > show sel cartoons > show sel atoms > select #9/E:422 18 atoms, 20 bonds, 1 residue, 1 model selected > select #9/E:422-446 510 atoms, 572 bonds, 25 residues, 1 model selected > show sel atoms > hide #!9 models > select #1/P:613-912 2333 atoms, 2394 bonds, 1 pseudobond, 288 residues, 2 models selected > surface (#!1 & sel) > select #1/K:613-912 2333 atoms, 2394 bonds, 1 pseudobond, 288 residues, 2 models selected > surface (#!1 & sel) > hide #!1 models > show #!1 models > set bgColor white > set bgColor #ffffff00 > select clear > hide #!1 models > show #!1 models > hide #!8 models > show #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > sequence chain #8/C Alignment identifier is 8/C > select #8/C:628 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:628-912 2208 atoms, 2261 bonds, 1 pseudobond, 273 residues, 2 models selected > surface (#!8 & sel) > select #8/C:627 7 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:474-627 1146 atoms, 1172 bonds, 1 pseudobond, 145 residues, 2 models selected > surface (#!8 & sel) > hide #!8 models > show #!8 models > select #8/C:474-912 3354 atoms, 3434 bonds, 2 pseudobonds, 418 residues, 2 models selected > surface (#!8 & sel) > select #8/A:474-912 3347 atoms, 3426 bonds, 2 pseudobonds, 417 residues, 2 models selected > surface (#!8 & sel) > select #1/E 805 atoms, 817 bonds, 98 residues, 1 model selected > show sel atoms > select #1/A:37-135 817 atoms, 829 bonds, 99 residues, 1 model selected > show sel atoms > select clear > hide #!8 models > show #!5 models > show #!4 models > show #!9 models > hide #!9 models > show #!8 models > hide #!8 models > show #!8 models > set bgColor black > set bgColor transparent > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEO_6.cxs ——— End of log from Thu Aug 31 14:18:46 2023 ——— opened ChimeraX session > open 6s01 6s01 title: Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome [more info...] Chain information for 6s01 #12 --- Chain | Description | UniProt A E | Histone H3 | A0A310TTQ1_XENLA 1-135 B F | Histone H4 | H4_XENLA 1-102 C G | Histone H2A | Q6AZJ8_XENLA 1-129 D H | Histone H2B 1.1 | H2B11_XENLA 1-122 I | Wisdom 601 DNA (165-MER) | J | Wisdom 601 DNA (165-MER) | K | PC4 and SFRS1-interacting protein | PSIP1_HUMAN 1-530 > ui tool show Matchmaker > matchmaker #!12 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 6pa7, chain I (#1) with 6s01, chain I (#12), sequence alignment score = 811.2 RMSD between 132 pruned atom pairs is 1.006 angstroms; (across all 150 pairs: 2.263) > hide #!1 models > hide #!12 models > show #!1 models > show #!12 models > select PWWP_H3K36me3 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > hide #!12 models > select PWWP_H3K36me3_ 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select clear > select ADD_1 7146 atoms, 1119 bonds, 912 residues, 1 model selected > show #!12 models > hide #!1 models > hide #!11 models > hide #!10 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!8 models > hide #!7 models > select #12/I#12/J 6150 atoms, 6898 bonds, 350 pseudobonds, 300 residues, 2 models selected > select subtract #12/A 6150 atoms, 6898 bonds, 350 pseudobonds, 300 residues, 2 models selected > select subtract #12/E 6150 atoms, 6898 bonds, 350 pseudobonds, 300 residues, 2 models selected > delete atoms (#!12 & sel) > delete bonds (#!12 & sel) > select clear > select subtract #12/A Nothing selected > surface #12 > select clear > select #12/A 829 atoms, 841 bonds, 100 residues, 1 model selected > select #12/E 801 atoms, 813 bonds, 97 residues, 1 model selected > select clear > select add #12/D 736 atoms, 747 bonds, 94 residues, 1 model selected > select add #12/H 1472 atoms, 1494 bonds, 188 residues, 2 models selected > delete atoms (#!12 & sel) > delete bonds (#!12 & sel) > select add #12/C 823 atoms, 833 bonds, 107 residues, 1 model selected > delete atoms (#!12 & sel) > delete bonds (#!12 & sel) > select add #12/G 823 atoms, 833 bonds, 107 residues, 1 model selected > delete atoms (#!12 & sel) > delete bonds (#!12 & sel) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd6s01_7.cxs > select add #12/B 657 atoms, 664 bonds, 82 residues, 1 model selected > delete atoms (#!12 & sel) > delete bonds (#!12 & sel) > select add #12/F 694 atoms, 702 bonds, 86 residues, 1 model selected > delete atoms (#!12 & sel) > delete bonds (#!12 & sel) > show #!11 models > show #!10 models > hide #!10 models > hide #!11 models > show #!11 models > show #!10 models > hide #!11 models > hide #!10 models > show #!1 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd6s01_7.cxs > hide #!1 models > select add #12/E 801 atoms, 813 bonds, 97 residues, 1 model selected > hide (#!12 & sel) target a > surface hidePatches (#!12 & sel) > show #!1 models > open 6s01 6s01 title: Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome [more info...] Chain information for 6s01 #13 --- Chain | Description | UniProt A E | Histone H3 | A0A310TTQ1_XENLA 1-135 B F | Histone H4 | H4_XENLA 1-102 C G | Histone H2A | Q6AZJ8_XENLA 1-129 D H | Histone H2B 1.1 | H2B11_XENLA 1-122 I | Wisdom 601 DNA (165-MER) | J | Wisdom 601 DNA (165-MER) | K | PC4 and SFRS1-interacting protein | PSIP1_HUMAN 1-530 > ui tool show Matchmaker > matchmaker #!13 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 6pa7, chain I (#1) with 6s01, chain I (#13), sequence alignment score = 811.2 RMSD between 132 pruned atom pairs is 1.006 angstroms; (across all 150 pairs: 2.263) > select clear > hide #!1 models > select add #10/A#10/E#11/A#11/E#12/A#12/E#13/A#13/E 6518 atoms, 6614 bonds, 2 pseudobonds, 788 residues, 6 models selected > select clear > select add #13/I#13/J 6150 atoms, 6898 bonds, 350 pseudobonds, 300 residues, 2 models selected > delete atoms (#!13 & sel) > delete bonds (#!13 & sel) > hide #!12 models > select clear > select #13/A 829 atoms, 841 bonds, 100 residues, 1 model selected > select #13/E 801 atoms, 813 bonds, 97 residues, 1 model selected > delete atoms sel > delete bonds sel > select add #13/C 823 atoms, 833 bonds, 107 residues, 1 model selected > select add #13/G 1646 atoms, 1666 bonds, 214 residues, 1 model selected > delete atoms sel > delete bonds sel > select add #13/D 736 atoms, 747 bonds, 94 residues, 1 model selected > select add #13/H 1472 atoms, 1494 bonds, 188 residues, 1 model selected > delete atoms sel > delete bonds sel > select add #13/B 657 atoms, 664 bonds, 82 residues, 1 model selected > select add #13/F 1351 atoms, 1366 bonds, 168 residues, 1 model selected > delete atoms sel > delete bonds sel > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd6s01_8.cxs > show #!1 models > hide #!1 models > select #13/A 829 atoms, 841 bonds, 100 residues, 1 model selected > select #13/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > show #!11 models > hide #!11 models > show #!10 models > show #!12 models > hide #!12 models > show #!1 models > hide #!1 models > ui tool show Matchmaker > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd6s01_8.cxs > ui tool show Matchmaker No reference and/or match structure/chain chosen > show #!1 models > select #1/A 818 atoms, 829 bonds, 100 residues, 1 model selected > select #1/E 805 atoms, 817 bonds, 98 residues, 1 model selected > hide #!1 models > ui tool show Matchmaker > matchmaker #!13 to #1/A pairing bs Parameters --- Chain pairing | bs 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 6pa7, chain A (#1) with 6s01, chain A (#13), sequence alignment score = 590.3 RMSD between 97 pruned atom pairs is 0.593 angstroms; (across all 98 pairs: 0.786) > show #!12 models > hide #!10 models > hide #!12 models > show #!12 models > show #!1 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd2x6s01_9.cxs ——— End of log from Tue Feb 27 14:31:41 2024 ——— opened ChimeraX session > hide #!1 models > select #13/A 829 atoms, 841 bonds, 100 residues, 1 model selected > select #12/E 801 atoms, 813 bonds, 97 residues, 1 model selected > surface (#!12 & sel) > select #12/E 801 atoms, 813 bonds, 97 residues, 1 model selected > delete atoms (#!12 & sel) > delete bonds (#!12 & sel) > select #12/A 829 atoms, 841 bonds, 100 residues, 1 model selected > select #13/A 829 atoms, 841 bonds, 100 residues, 1 model selected > surface sel > hide (#!13 & sel) target a > select #13/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > hide (#!13 & sel) target a > cartoon (#!13 & sel) > select #12/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > surface hidePatches (#!12 & sel) > hide (#!12 & sel) target a > cartoon style (#!12 & sel) xsection oval modeHelix default > select #12/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > cartoon (#!12 & sel) > show #!11 models > show #!10 models > hide #!10 models > hide #!11 models > show #!1 models > select clear > show #!2 models > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > hide #!1 models > hide #!4 models > show #!6 models > hide #!6 models > hide #!2 models > hide #!3 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > hide #!8 models > hide #!9 models > show #!9 models > show #!8 models > hide #!8 models > hide #!7 models > hide #!6 models > show #!6 models > show #!7 models > show #!5 models > hide #!5 models > show #!8 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!1 models > hide #!8 models > hide #!6 models > hide #!7 models > hide #!9 models > hide #!1 models > select #12/A 829 atoms, 841 bonds, 100 residues, 1 model selected > surface hidePatches (#!12 & sel) > hide (#!12 & sel) target a > cartoon (#!12 & sel) > show #!6 models > hide #!6 models > show (#!12 & sel) target ab > hide (#!12 & sel) target a > style (#!12 & sel) stick Changed 829 atom styles > show (#!12 & sel) target ab > hide (#!12 & sel) target a > select clear > select #12/A 829 atoms, 841 bonds, 100 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #13/A Alignment identifier is 13/A > sequence chain #12/A Alignment identifier is 12/A > select #12/A:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #12/A:37-38 16 atoms, 16 bonds, 2 residues, 1 model selected > select #12/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #12/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > style sel stick Changed 12 atom styles > show (#!12 & sel) target ab > style (#!12 & sel) ball Changed 12 atom styles > select #13/A:35-65 271 atoms, 275 bonds, 31 residues, 1 model selected > select #13/A 829 atoms, 841 bonds, 100 residues, 1 model selected > select #12/A 829 atoms, 841 bonds, 100 residues, 1 model selected > select #12/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #12/A:36-37 21 atoms, 20 bonds, 2 residues, 1 model selected > select #12/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > select #12/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #12/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > select #12/A:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #12/A:37-134 810 atoms, 822 bonds, 98 residues, 1 model selected > surface (#!12 & sel) > select #12/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > select #12/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > surface (#!12 & sel) > surface hidePatches (#!12 & sel) > select #13/A 829 atoms, 841 bonds, 100 residues, 1 model selected > surface hidePatches (#!13 & sel) > cartoon (#!13 & sel) > select #13/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #13/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > show (#!13 & sel) target ab > style (#!13 & sel) ball Changed 12 atom styles > select #13/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > select #13/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > show #!6 models > show #!7 models > hide #!6 models > hide #!7 models > show #!11 models > hide #!11 models > show #!9 models > hide #!9 models > show #!8 models > show #!5 models > hide #!5 models > show #!3 models > show #!2 models > show #!1 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!1 models > hide #!8 models > hide #!2 models > show #!2 models > show #!1 models > show #!4 models > hide #!4 models > show #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd2x6s01_10.cxs > ui tool show ""Show Sequence Viewer"" > sequence chain #1/C Alignment identifier is 1/C > sequence chain #1/G Alignment identifier is 1/G > select #1/C:11-15 29 atoms, 28 bonds, 5 residues, 1 model selected > ui tool show ""Model Panel"" > ui tool show ""Show Sequence Viewer"" > sequence chain #1/C Alignment identifier is 1/C > sequence chain #1/G Alignment identifier is 1/G > select #1/C:22 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/C:22-25 32 atoms, 32 bonds, 4 residues, 1 model selected > select #1/C:103-104 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/C:103-118 114 atoms, 115 bonds, 16 residues, 1 model selected > select #1/C:42-43,77-78,100-102 59 atoms, 56 bonds, 7 residues, 1 model selected > select #1/C:103 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/C:103-118 114 atoms, 115 bonds, 16 residues, 1 model selected > select #1/C:11-15 29 atoms, 28 bonds, 5 residues, 1 model selected > select #1/C:103-104 14 atoms, 13 bonds, 2 residues, 1 model selected > select #1/C:103-118 114 atoms, 115 bonds, 16 residues, 1 model selected > select #1/G:10-15 46 atoms, 45 bonds, 6 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/D Alignment identifier is 1/D > sequence chain #1/H Alignment identifier is 1/H > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/E Alignment identifier is 1/E > select #1/A:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:37 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B Alignment identifier is 1/B > sequence chain #1/F Alignment identifier is 1/F > ui tool show ""Show Sequence Viewer"" > sequence chain #1/K Alignment identifier is 1/K > sequence chain #1/N Alignment identifier is 1/N > sequence chain #1/P Alignment identifier is 1/P > sequence chain #1/S Alignment identifier is 1/S > hide #!8 models > show #!8 models > hide #!8 models > hide #!3 models > hide #!2 models > select #1/K:613-641 242 atoms, 251 bonds, 29 residues, 1 model selected > select #1/K:613-912 2333 atoms, 2394 bonds, 1 pseudobond, 288 residues, 2 models selected > select #1/N:542-543 17 atoms, 16 bonds, 2 residues, 1 model selected > select #1/N 1703 atoms, 1749 bonds, 1 pseudobond, 211 residues, 2 models selected > hide #!1 models > show #!2 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:224 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:224-612 3037 atoms, 3119 bonds, 389 residues, 1 model selected > select clear > select #2/A:192-223 270 atoms, 276 bonds, 32 residues, 1 model selected > select #2/A:1-223 1683 atoms, 1714 bonds, 223 residues, 1 model selected > select #2/A:1-32 235 atoms, 238 bonds, 32 residues, 1 model selected > select #2/A:1-222 1679 atoms, 1710 bonds, 222 residues, 1 model selected > select > #2/A:176-178,200-228,313-316,341-343,347-351,356-359,363-379,392-411,418-422,426-429,473-484,490-492,515-524,560-566,571-577,601-609,628-630,645-652,667-676,687-689,692-698,710-712,728-740,763-772,782-784,815-817,837-840,861-868,882-891,895-907 1994 atoms, 2004 bonds, 240 residues, 1 model selected > select #2/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:1-223 1683 atoms, 1714 bonds, 223 residues, 1 model selected > hide #!3 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > show #!3 models > select #2/A:612 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:224-612 3037 atoms, 3119 bonds, 389 residues, 1 model selected > show #!1 models > hide #!3 models > hide #!2 models > select #1/K:613 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/K:613-912 2333 atoms, 2394 bonds, 1 pseudobond, 288 residues, 2 models selected > show #!2 models > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > hide #!4 models > show #!8 models > hide #!8 models > select #2/A:612 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:224-612 3037 atoms, 3119 bonds, 389 residues, 1 model selected > select #2/A:224 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:224-240 127 atoms, 127 bonds, 17 residues, 1 model selected > select #2/A:241 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:241-304 463 atoms, 475 bonds, 64 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #12/K Alignment identifier is 12/K > select #1/K:613 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/K:613-912 2333 atoms, 2394 bonds, 1 pseudobond, 288 residues, 2 models selected > select #12/K:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #12/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > select #2/A:224 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:224-304 590 atoms, 603 bonds, 81 residues, 1 model selected > select #2/A:305 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/A:305-311 65 atoms, 69 bonds, 7 residues, 1 model selected > hide #!1 models > select #12/K:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #12/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > select #2/A:106 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:83-106 177 atoms, 180 bonds, 24 residues, 1 model selected > ui tool show Matchmaker > ui tool show ""Show Sequence Viewer"" > toolshed show > start match align Unknown command: start match align > start match > align Unknown command: start match > align > start match > align Unknown command: start match > align > ui tool show ""Modeller Comparative"" > help help:user/tools/modeller.html > toolshed show > ui tool show ""Show Sequence Viewer"" > sequence chain #12/K Destroying pre-existing alignment with identifier 12/K Alignment identifier is 12/K > sequence chain #13/K Alignment identifier is 13/K > select #13/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > select #13/K 710 atoms, 736 bonds, 1 pseudobond, 86 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #12/A Alignment identifier is 12/A > select #12/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #12/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > color (#!12 & sel) byelement > ui tool show ""Show Sequence Viewer"" > sequence chain #13/A Alignment identifier is 13/A > select #13/A:36-37 21 atoms, 20 bonds, 2 residues, 1 model selected > select #13/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #13/A:44-55,63-75,85-114,120-131 540 atoms, 543 bonds, 67 residues, 1 model selected > select #13/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #13/A:36 12 atoms, 11 bonds, 1 residue, 1 model selected > color (#!13 & sel) byelement > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > sequence chain #12/K Alignment identifier is 12/K > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7PAdd2x5CIUAdd4U7T_Add5YX2_3_Add2x8PEOAdd2x6s01_10.cxs ——— End of log from Wed Feb 28 11:39:23 2024 ——— opened ChimeraX session > hide #!3 models > hide #!2 models > select add #6/A 1119 atoms, 1053 bonds, 1 pseudobond, 224 residues, 2 models selected > select add #6/B 2154 atoms, 2062 bonds, 3 pseudobonds, 400 residues, 3 models selected > select add #7/A 3273 atoms, 3115 bonds, 4 pseudobonds, 624 residues, 5 models selected > select add #7/B 4308 atoms, 4124 bonds, 6 pseudobonds, 800 residues, 5 models selected > cartoon #12-13 [Repeated 1 time(s)] > show #!6 models > show #!7 models > select add #6/A 4308 atoms, 4124 bonds, 6 pseudobonds, 800 residues, 6 models selected > select add #6/B 4308 atoms, 4124 bonds, 6 pseudobonds, 800 residues, 6 models selected > select add #7/A 4308 atoms, 4124 bonds, 6 pseudobonds, 800 residues, 6 models selected > select add #7/B 4308 atoms, 4124 bonds, 6 pseudobonds, 800 residues, 6 models selected > delete atoms (#!6-7 & sel) > delete bonds (#!6-7 & sel) > select #6/C 54 atoms, 50 bonds, 11 residues, 1 model selected > select #6/D 58 atoms, 50 bonds, 15 residues, 1 model selected > delete atoms (#!6 & sel) > delete bonds (#!6 & sel) > select #7/C 54 atoms, 50 bonds, 11 residues, 1 model selected > delete atoms (#!7 & sel) > delete bonds (#!7 & sel) > select #6/C 54 atoms, 50 bonds, 11 residues, 1 model selected > select #7/D 58 atoms, 50 bonds, 15 residues, 1 model selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7Add4U7T_Add5YX2_3_Add2x8PEOAdd2x6s01Delete5ciu_11.cxs > hide sel target a > ui tool show ""Show Sequence Viewer"" > sequence chain #6/C Alignment identifier is 6/C > sequence chain #7/D Alignment identifier is 7/D > select #7/D:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #7/D:36 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide sel target a > select #7/D:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #7/D:36-37 21 atoms, 20 bonds, 2 residues, 1 model selected > select #7/D:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #7/D:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #7/D:36 12 atoms, 11 bonds, 1 residue, 1 model selected > style sel stick Changed 12 atom styles > show sel target ab > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide (#!6 & sel) target a > select #6/C:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #6/C:36 12 atoms, 11 bonds, 1 residue, 1 model selected > show (#!6 & sel) target ab > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelWith2xDNMT3AAlphafoldDefineDomainsAdd2x4U7Add4U7T_Add5YX2_3_Add2x8PEOAdd2x6s01Delete5ciu_11.cxs > open 5ciu Summary of feedback from opening 5ciu fetched from pdb --- note | Fetching compressed mmCIF 5ciu from http://files.rcsb.org/download/5ciu.cif 5ciu title: Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain [more info...] Chain information for 5ciu #14 --- Chain | Description | UniProt A B | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 206-355 C D | Histone H3.2 | Non-standard residues in 5ciu #14 --- GOL — glycerol (glycerin; propane-1,2,3-triol) M3L — N-trimethyllysine 5ciu mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > ui tool show Matchmaker > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #12/A Alignment identifier is 12/A > sequence chain #13/A Alignment identifier is 13/A > select #12/A:35-97 531 atoms, 539 bonds, 63 residues, 1 model selected > select #13/A:35-129 786 atoms, 798 bonds, 95 residues, 1 model selected > select clear > select #12/A:35-63 254 atoms, 258 bonds, 29 residues, 1 model selected > select #13/A:35 7 atoms, 6 bonds, 1 residue, 1 model selected > select #13/A:62-63 19 atoms, 18 bonds, 2 residues, 1 model selected > select #13/A:62-134 594 atoms, 601 bonds, 73 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > matchmaker #!7 to #13/A pairing bs Parameters --- Chain pairing | bs 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 6s01, chain A (#13) with 5ciu, chain D (#7), sequence alignment score = 62.2 RMSD between 4 pruned atom pairs is 0.323 angstroms; (across all 4 pairs: 0.323) > matchmaker #!7 to #13/A pairing bs Parameters --- Chain pairing | bs 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 6s01, chain A (#13) with 5ciu, chain D (#7), sequence alignment score = 62.2 RMSD between 4 pruned atom pairs is 0.323 angstroms; (across all 4 pairs: 0.323) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Delete5ciuAlign6s01H3Tail_12.cxs > ui tool show Matchmaker > select #13/A:63-126 516 atoms, 523 bonds, 64 residues, 1 model selected > select #13/A:63-127 521 atoms, 528 bonds, 65 residues, 1 model selected > select #12/A:35-94 511 atoms, 519 bonds, 60 residues, 1 model selected > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > matchmaker #!6 to #12/A pairing bs Parameters --- Chain pairing | bs 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 6s01, chain A (#12) with 5ciu, chain C (#6), sequence alignment score = 58 RMSD between 4 pruned atom pairs is 0.389 angstroms; (across all 4 pairs: 0.389) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Delete5ciuAlign6s01H3Tail_12.cxs > hide #!13 models > hide #!12 models > show #!12 models > show #!13 models > ui tool show ""Show Sequence Viewer"" > sequence chain #14/A Alignment identifier is 14/A > sequence chain #14/B Alignment identifier is 14/B > ui tool show Matchmaker > select clear > select #6/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > matchmaker #!14 to #6/C pairing bs Parameters --- Chain pairing | bs 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 5ciu, chain C (#6) with 5ciu, chain C (#14), sequence alignment score = 61.6 RMSD between 7 pruned atom pairs is 0.000 angstroms; (across all 7 pairs: 0.000) > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #14/A:216-351 1022 atoms, 1053 bonds, 1 pseudobond, 127 residues, 2 models selected > select #14/A 1119 atoms, 1053 bonds, 1 pseudobond, 224 residues, 2 models selected > delete atoms (#!14 & sel) > delete bonds (#!14 & sel) > select #14/D 58 atoms, 50 bonds, 15 residues, 1 model selected > delete atoms sel > delete bonds sel > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_13.cxs > open 5ciu 5ciu title: Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain [more info...] Chain information for 5ciu #15 --- Chain | Description | UniProt A B | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 206-355 C D | Histone H3.2 | Non-standard residues in 5ciu #15 --- GOL — glycerol (glycerin; propane-1,2,3-triol) M3L — N-trimethyllysine 5ciu mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > ui tool show Matchmaker > select clear > select #7/D:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select clear > matchmaker #!15 to #7/D pairing bs Parameters --- Chain pairing | bs 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 5ciu, chain D (#7) with 5ciu, chain C (#15), sequence alignment score = 61.6 RMSD between 7 pruned atom pairs is 0.595 angstroms; (across all 7 pairs: 0.595) > matchmaker #!15 to #7/D pairing bs Parameters --- Chain pairing | bs 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 5ciu, chain D (#7) with 5ciu, chain C (#15), sequence alignment score = 61.6 RMSD between 7 pruned atom pairs is 0.595 angstroms; (across all 7 pairs: 0.595) > select #15/B 1035 atoms, 1009 bonds, 2 pseudobonds, 176 residues, 2 models selected > select #15/A 1119 atoms, 1053 bonds, 1 pseudobond, 224 residues, 2 models selected > delete atoms (#!15 & sel) > delete bonds (#!15 & sel) > select #15/C 54 atoms, 50 bonds, 11 residues, 1 model selected > select #15/D 58 atoms, 50 bonds, 15 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!1 models > hide #!1 models > hide #!13 models > hide #!12 models > hide #!14 models > hide #!15 models > hide #!7 models > hide #!6 models > show #!14 models > show #!15 models > ui tool show ""Show Sequence Viewer"" > sequence chain #14/B Destroying pre-existing alignment with identifier 14/B Alignment identifier is 14/B > sequence chain #14/C Alignment identifier is 14/C > sequence chain #15/B Alignment identifier is 15/B > sequence chain #15/C Alignment identifier is 15/C > select #14/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide sel target a [Repeated 1 time(s)] > select #14/C:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #14/C:36 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > style sel ball Changed 12 atom styles > select #15/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide sel target a > select #15/C:36 12 atoms, 11 bonds, 1 residue, 1 model selected > select #15/C:36 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > style sel ball Changed 12 atom styles > select #15/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > hide (#!15 & sel) target a > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > hide (#!14 & sel) target a Drag select of 6 atoms, 5 bonds > delete atoms sel > delete bonds sel Drag select of 1 atoms [Repeated 2 time(s)] > delete atoms sel > delete bonds sel Drag select of 7 atoms, 5 bonds > delete atoms sel > delete bonds sel Drag select of 1 atoms > delete atoms sel > delete bonds sel > show #!1 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_13.cxs > show #!13 models > show #!12 models > hide #!12 models > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #14/B:216-348 951 atoms, 979 bonds, 2 pseudobonds, 118 residues, 2 models selected > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > surface (#!14 & sel) > select #15/B:216-239 203 atoms, 211 bonds, 24 residues, 1 model selected > select #15/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > surface (#!15 & sel) > hide #!13 models > hide #!1 models > lighting simple > lighting full > lighting simple > show #!13 models > show #!12 models > surface hidePatches (#!15 & sel) > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > surface hidePatches (#!14 & sel) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_13.cxs > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > show #!14 models > show #!15 models > show #!1 models > lighting soft > lighting full > lighting soft > select #14/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > color (#!14 & sel) magenta > show #!2 models > show #!3 models > ui tool show ""Color Actions"" > select clear > select #15/B:216-351 975 atoms, 1004 bonds, 2 pseudobonds, 121 residues, 2 models selected > color (#!15 & sel) magenta > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!1 models > show #!2 models > show #!3 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #!9 models > hide #!3 models > hide #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > show #!6 models > show #!7 models > hide #!7 models > hide #!6 models > show #!8 models > hide #!8 models > hide #!9 models > show #!9 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > show #!10 models > hide #!10 models > show #!12 models > hide #!12 models > show #!13 models > hide #!13 models > show #!2 models > show #!3 models > hide #!1 models > hide #!3 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!6 models > hide #!6 models > select clear > show #!6 models > hide #!6 models > show #!7 models > show #!6 models > select #14/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > select #15/C:32-38 50 atoms, 50 bonds, 7 residues, 1 model selected > hide #!6 models > hide #!7 models > show #!8 models > hide #!8 models > hide #!9 models > show #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > hide #!13 models > select clear > hide #!9 models > show #!1 models > hide #!1 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_14.cxs ——— End of log from Thu Feb 29 11:27:46 2024 ——— opened ChimeraX session > show #!2 models > show #!3 models > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/PDBs/AF-Q9UBC3-F1-model_v4.pdb AF-Q9UBC3-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3B (Q9UBC3) [more info...] Chain information for AF-Q9UBC3-F1-model_v4.pdb #16 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 1-853 > hide #16 models > show #16 models > ui tool show Matchmaker > matchmaker #16 to #1/N pairing bs Parameters --- Chain pairing | bs 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 6pa7, chain N (#1) with AF-Q9UBC3-F1-model_v4.pdb, chain A (#16), sequence alignment score = 3014.1 RMSD between 144 pruned atom pairs is 1.093 angstroms; (across all 211 pairs: 6.166) > show #!1 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_AddDNMT3BAlphaFold.cxs > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/PDBs/AF-Q9UBC3-F1-model_v4.pdb AF-Q9UBC3-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3B (Q9UBC3) [more info...] Chain information for AF-Q9UBC3-F1-model_v4.pdb #17 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 1-853 > ui tool show Matchmaker > matchmaker #17 to #1/S pairing bs Parameters --- Chain pairing | bs 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 6pa7, chain S (#1) with AF-Q9UBC3-F1-model_v4.pdb, chain A (#17), sequence alignment score = 3024.9 RMSD between 146 pruned atom pairs is 1.004 angstroms; (across all 211 pairs: 6.825) > matchmaker #17 to #1/S pairing bs Parameters --- Chain pairing | bs 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 6pa7, chain S (#1) with AF-Q9UBC3-F1-model_v4.pdb, chain A (#17), sequence alignment score = 3024.9 RMSD between 146 pruned atom pairs is 1.004 angstroms; (across all 211 pairs: 6.825) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFold.cxs ——— End of log from Fri Mar 1 15:48:22 2024 ——— opened ChimeraX session > show #!4 models > show #!5 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!4 models > hide #!5 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #16/A Alignment identifier is 16/A > sequence chain #17/A Alignment identifier is 17/A > select #16/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #16/A:1-204 1560 atoms, 1587 bonds, 204 residues, 1 model selected > select #16/A:206 9 atoms, 8 bonds, 1 residue, 1 model selected > select #16/A:1-206 1576 atoms, 1603 bonds, 206 residues, 1 model selected > select #16/A:355 7 atoms, 7 bonds, 1 residue, 1 model selected > select #16/A:206-355 1178 atoms, 1213 bonds, 150 residues, 1 model selected > color sel orange > show #!2 models > hide #!2 models > color sel magenta > select #16/A:555 4 atoms, 3 bonds, 1 residue, 1 model selected > select #16/A:423-555 1045 atoms, 1066 bonds, 133 residues, 1 model selected > color sel orange > select #16/A:569 5 atoms, 4 bonds, 1 residue, 1 model selected > select #16/A:569-853 2289 atoms, 2341 bonds, 285 residues, 1 model selected > ui tool show ""Color Actions"" > color sel lemon chiffon > color sel pale goldenrod > color sel mint cream > color sel light goldenrod yellow > color sel old lace > color sel lemon chiffon > color sel khaki > color sel wheat > color sel beige > color sel light goldenrod yellow > color sel old lace > color sel cornsilk > color sel lemon chiffon > hide #!1 models > select #16/A:205 7 atoms, 6 bonds, 1 residue, 1 model selected > select #16/A:1-205 1567 atoms, 1594 bonds, 205 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #14/B Alignment identifier is 14/B > sequence chain #15/B Alignment identifier is 15/B > select #14/B:216-267 426 atoms, 442 bonds, 52 residues, 1 model selected > select #14/B:314 4 atoms, 3 bonds, 1 residue, 1 model selected > select #14/B:314-315 13 atoms, 12 bonds, 2 residues, 1 model selected > select #15/B:314 4 atoms, 3 bonds, 1 residue, 1 model selected > select #15/B:314-315 13 atoms, 12 bonds, 2 residues, 1 model selected > select #15/B:330-331 16 atoms, 16 bonds, 2 residues, 1 model selected > select #15/B:330-337 70 atoms, 73 bonds, 8 residues, 1 model selected > select #17/A:355 7 atoms, 7 bonds, 1 residue, 1 model selected > select #17/A:206-355 1178 atoms, 1213 bonds, 150 residues, 1 model selected > select #16/A:325-355 242 atoms, 249 bonds, 31 residues, 1 model selected > select #16/A:206-355 1178 atoms, 1213 bonds, 150 residues, 1 model selected > ui tool show ""Build Structure"" [Repeated 2 time(s)] > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/PDBs/PWWP_DomainFromDNMT3B_AlphaFoldChain16.pdb > models #16 selectedOnly true > select clear > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColour.cxs > open > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/PDBs/PWWP_DomainFromDNMT3B_AlphaFoldChain16.pdb Summary of feedback from opening D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/PDBs/PWWP_DomainFromDNMT3B_AlphaFoldChain16.pdb --- warnings | Start residue of secondary structure not found: HELIX 8 8 ARG A 417 ALA A 425 1 9 Start residue of secondary structure not found: HELIX 9 9 LEU A 431 ASP A 433 1 3 Start residue of secondary structure not found: HELIX 10 10 GLN A 456 LEU A 465 1 10 Start residue of secondary structure not found: HELIX 11 11 VAL A 501 CYS A 503 1 3 Start residue of secondary structure not found: HELIX 12 12 LEU A 504 LEU A 507 1 4 29 messages similar to the above omitted PWWP_DomainFromDNMT3B_AlphaFoldChain16.pdb title: Alphafold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3B (Q9UBC3) [more info...] Chain information for PWWP_DomainFromDNMT3B_AlphaFoldChain16.pdb #18 --- Chain | Description | UniProt A | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 1-853 > ui tool show Matchmaker > matchmaker #18 to #16/A pairing bs Parameters --- Chain pairing | bs 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 AF-Q9UBC3-F1-model_v4.pdb, chain A (#16) with PWWP_DomainFromDNMT3B_AlphaFoldChain16.pdb, chain A (#18), sequence alignment score = 3420.6 RMSD between 150 pruned atom pairs is 0.000 angstroms; (across all 150 pairs: 0.000) > matchmaker #18 to #15/B pairing bs Parameters --- Chain pairing | bs 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 5ciu, chain B (#15) with PWWP_DomainFromDNMT3B_AlphaFoldChain16.pdb, chain A (#18), sequence alignment score = 708.8 RMSD between 121 pruned atom pairs is 0.593 angstroms; (across all 121 pairs: 0.593) > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciu.cxs ——— End of log from Mon Mar 4 11:21:25 2024 ——— opened ChimeraX session > hide #18 models > hide #!15 models > show #!15 models > hide #!14 models > show #!14 models > select add #16/A:350 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel lime > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciu.cxs ——— End of log from Wed Mar 6 10:04:03 2024 ——— opened ChimeraX session > select clear > select #15/B:216 9 atoms, 8 bonds, 1 residue, 1 model selected > select #16/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel light sea green > select add #15/B:216 21 atoms, 20 bonds, 2 residues, 2 models selected > color (#16#!15 & sel) light sea green > select clear [Repeated 1 time(s)] > select add #15/B:351 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!15 & sel) yellow > select #16/A:350 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > hide #17 models > select #16/A:351 8 atoms, 7 bonds, 1 residue, 1 model selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciu.cxs ——— End of log from Wed Mar 6 11:14:39 2024 ——— opened ChimeraX session > show #17 models > hide #17 models > hide #!15 models > hide #!14 models > show #!14 models > show #!15 models > hide #!14 models > hide #!15 models > show #!15 models > show #!14 models > select #16/A:350 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel magenta > select #16/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > select #15/B:351 8 atoms, 7 bonds, 1 residue, 1 model selected > select #16/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > select #15/B:351 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #16/A:217 20 atoms, 19 bonds, 2 residues, 3 models selected > color (#16#!15 & sel) magenta > select #16/A:216 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel cyan > select clear > select #15/B:351 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!15 & sel) yellow > select #16/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > select #15/B:216 9 atoms, 8 bonds, 1 residue, 1 model selected > select #16/A:216 9 atoms, 8 bonds, 1 residue, 1 model selected > select #16/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > select #16/A:215 6 atoms, 5 bonds, 1 residue, 1 model selected > hide #16 models > select #15/C:36 12 atoms, 11 bonds, 1 residue, 1 model selected > color sel byelement > select #14/C:36 12 atoms, 11 bonds, 1 residue, 1 model selected > color sel byelement > select #14/B:351 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!14 & sel) yellow > select #14/B:216 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!14 & sel) cyan > show #16 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY.cxs > hide #16 models > show #17 models > select #17/A:128 9 atoms, 8 bonds, 1 residue, 1 model selected > select #17/A:128-260 1025 atoms, 1054 bonds, 133 residues, 1 model selected > show #16 models > hide #16 models > select #17/A:206 9 atoms, 8 bonds, 1 residue, 1 model selected > select #17/A:206 9 atoms, 8 bonds, 1 residue, 1 model selected > select #17/A:326-355 234 atoms, 241 bonds, 30 residues, 1 model selected > select #17/A:206-355 1178 atoms, 1213 bonds, 150 residues, 1 model selected > color sel magenta > show #16 models > select #17/A:423 8 atoms, 7 bonds, 1 residue, 1 model selected > select #17/A:423-424 15 atoms, 14 bonds, 2 residues, 1 model selected > select #17/A:525-555 262 atoms, 268 bonds, 31 residues, 1 model selected > select #17/A:423-555 1045 atoms, 1066 bonds, 133 residues, 1 model selected > color sel orange > select #17/A:569 5 atoms, 4 bonds, 1 residue, 1 model selected > select #17/A:569 5 atoms, 4 bonds, 1 residue, 1 model selected > select #17/A:853 10 atoms, 9 bonds, 1 residue, 1 model selected > select #17/A:569-853 2289 atoms, 2341 bonds, 285 residues, 1 model selected > ui tool show ""Color Actions"" > color sel lemon chiffon > select clear > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY.cxs > hide #16 models > hide #!15 models > select #17/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > select #17/A:351 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > select #17/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel cyan > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY.cxs > hide #17 models > show #16 models > show #!15 models > hide #!14 models > select #17/A:574-575 15 atoms, 15 bonds, 2 residues, 1 model selected > select #17/A:574-795 1767 atoms, 1804 bonds, 222 residues, 1 model selected > select #16/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > select #16/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > select #16/A:350-351 15 atoms, 15 bonds, 2 residues, 1 model selected > select #16/A:217-351 1074 atoms, 1108 bonds, 135 residues, 1 model selected > select clear > select #16/A:351 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > select #16/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel magenta > hide #16 models > hide #!15 models > show #!14 models > show #17 models > select #17/A:216 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel cyan > select #17/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel orange red > color sel magenta > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY.cxs ——— End of log from Wed Mar 13 08:01:34 2024 ——— opened ChimeraX session > color sel cyan > select #17/A:216 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel magenta > select #17/A:216 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel cyan > select #17/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel magenta > hide #17 models > show #16 models > show #!15 models > hide #!14 models > hide #16 models > hide #!15 models > show #!14 models > show #17 models > hide #17 models > show #16 models > show #!15 models > hide #!14 models > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY.cxs > split #16 atoms : 217-351 Split AF-Q9UBC3-F1-model_v4.pdb (#16) into 2 models Chain information for AF-Q9UBC3-F1-model_v4.pdb 1 #16.1 --- Chain | Description A | No description available Chain information for AF-Q9UBC3-F1-model_v4.pdb 2 #16.2 --- Chain | Description A | No description available > hide #16.1 models > show #16.1 models > ui tool show Matchmaker > hide #16.1 models > show #16.1 models > matchmaker #16.1/A to #15/B pairing ss 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 5ciu, chain B (#15) with AF-Q9UBC3-F1-model_v4.pdb 1, chain A (#16.1), sequence alignment score = 652.3 RMSD between 120 pruned atom pairs is 0.582 angstroms; (across all 120 pairs: 0.582) > matchmaker #16.1/A to #15/B pairing ss 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 5ciu, chain B (#15) with AF-Q9UBC3-F1-model_v4.pdb 1, chain A (#16.1), sequence alignment score = 652.3 RMSD between 120 pruned atom pairs is 0.582 angstroms; (across all 120 pairs: 0.582) > hide #!15 models > select #16.2/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > select #16.1/A:351 8 atoms, 7 bonds, 1 residue, 1 model selected > select #16.1/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel cyan > select #16.2/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel yellow > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciu.cxs > show #!14 models > hide #!14 models > show #!15 models > hide #!15 models > ui tool show ""Add Hydrogens"" > hide #16.1 models > show #16.1 models > select #16.1/A:351 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select add #16.2/A:352 16 atoms, 14 bonds, 2 residues, 2 models selected > select add #16.2/A:216 25 atoms, 22 bonds, 3 residues, 2 models selected > select add #16.1/A:217 37 atoms, 34 bonds, 4 residues, 2 models selected > select clear > select #16.1/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel magenta > select clear > select #16.2/A:352 8 atoms, 7 bonds, 1 residue, 1 model selected > select #16.1/A:351 8 atoms, 7 bonds, 1 residue, 1 model selected > select #16.2/A:216 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > style sel ball Changed 9 atom styles > select add #16.2/A:352 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #16.1/A:351 25 atoms, 22 bonds, 3 residues, 2 models selected > show sel target ab > style sel ball Changed 25 atom styles > select #16.1/A:217 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel cyan > select #16.1/A:351 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #16.1/A:217 20 atoms, 19 bonds, 2 residues, 1 model selected > select add #16.2/A:216@CA 21 atoms, 19 bonds, 3 residues, 2 models selected > select add #16.2/A:352 29 atoms, 26 bonds, 4 residues, 2 models selected > show sel target ab > style sel ball Changed 29 atom styles > color sel byelement > select clear > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtoms.cxs > hide #16.2 models > show #16.2 models > ui tool show ""Add Hydrogens"" > addh #16.1-2 Summary of feedback from adding hydrogens to multiple structures --- notes | No usable SEQRES records for AF-Q9UBC3-F1-model_v4.pdb 1 (#16.1) chain A; guessing termini instead Chain-initial residues that are actual N termini: AF-Q9UBC3-F1-model_v4.pdb 1 #16.1/A TYR 217 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: AF-Q9UBC3-F1-model_v4.pdb 1 #16.1/A ASN 351 127 hydrogen bonds AF-Q9UBC3-F1-model_v4.pdb 1 #16.1/A ASN 351 is not terminus, removing H atom from 'C' No usable SEQRES records for AF-Q9UBC3-F1-model_v4.pdb 2 (#16.2) chain A; guessing termini instead Chain-initial residues that are actual N termini: AF-Q9UBC3-F1-model_v4.pdb 2 #16.2/A MET 1 Chain-initial residues that are not actual N termini: AF-Q9UBC3-F1-model_v4.pdb 2 #16.2/A ASN 352 Chain-final residues that are actual C termini: AF-Q9UBC3-F1-model_v4.pdb 2 #16.2/A GLU 853 Chain-final residues that are not actual C termini: AF-Q9UBC3-F1-model_v4.pdb 2 #16.2/A GLU 216 464 hydrogen bonds Adding 'H' to AF-Q9UBC3-F1-model_v4.pdb 2 #16.2/A ASN 352 AF-Q9UBC3-F1-model_v4.pdb 2 #16.2/A GLU 216 is not terminus, removing H atom from 'C' 6577 hydrogens added > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonate.cxs > hide #16.1 models > show #16.1 models > tug #16.2:352 toAtoms #16.1:351 > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1.cxs ——— End of log from Wed Mar 13 08:51:37 2024 ——— opened ChimeraX session > hide #16.1 models > show #16.1 models > hide #16.2 models > show #16.2 models > select #17/A:574 7 atoms, 7 bonds, 1 residue, 1 model selected > select #17/A:574-796 1776 atoms, 1813 bonds, 223 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #16.1/A Alignment identifier is 16.1/A > sequence chain #16.2/A Alignment identifier is 16.2/A > select #16.1/A:217-248 516 atoms, 527 bonds, 32 residues, 1 model selected > select #16.1/A 2136 atoms, 2170 bonds, 135 residues, 1 model selected > select #16.2/A:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select #16.2/A:1-722 9027 atoms, 9114 bonds, 587 residues, 1 model selected > select #16.2/A:1-722 9027 atoms, 9114 bonds, 587 residues, 1 model selected > select #16.2/A:1-722 9027 atoms, 9114 bonds, 587 residues, 1 model selected > select #16.2/A 11164 atoms, 11276 bonds, 718 residues, 1 model selected > select clear > hide #!16 models > show #!16 models > combine #16.1 #16.2 modelId 19 name DNMT3B16_1and2recombined Remapping chain ID 'A' in AF-Q9UBC3-F1-model_v4.pdb 2 #16.2 to 'B' > hide #16.2 models > show #16.2 models > hide #!16 models > hide #19 models > show #19 models > select #19/B:352 14 atoms, 13 bonds, 1 residue, 1 model selected > select #19/A:351 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #19/B:352 28 atoms, 26 bonds, 2 residues, 1 model selected > ui tool show ""Build Structure"" > bond sel Created 21 bonds > show #!15 models > hide #19 models > show #19 models > select #15/B:216 9 atoms, 8 bonds, 1 residue, 1 model selected > select #19/B:216 15 atoms, 14 bonds, 1 residue, 1 model selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1CombineAddBond.cxs > tug #19:216 toAtoms #15/B:216 For 15 tugged atoms expected 15 destination atoms, got 9 > select #15/B:216 9 atoms, 8 bonds, 1 residue, 1 model selected > select #19/B:216 15 atoms, 14 bonds, 1 residue, 1 model selected > select #19/A:217 23 atoms, 23 bonds, 1 residue, 1 model selected > select #19/A:217 23 atoms, 23 bonds, 1 residue, 1 model selected > hide sel target a > select clear > select #15/B:216 9 atoms, 8 bonds, 1 residue, 1 model selected > show (#!15 & sel) target ab > style (#!15 & sel) ball Changed 9 atom styles > color (#!15 & sel) byelement > select clear > select #15/B:216 9 atoms, 8 bonds, 1 residue, 1 model selected > select #19/B:216 15 atoms, 14 bonds, 1 residue, 1 model selected > select #15/B:217 12 atoms, 12 bonds, 1 residue, 1 model selected > select #19/B:215 11 atoms, 10 bonds, 1 residue, 1 model selected > select #19/B:214 11 atoms, 10 bonds, 1 residue, 1 model selected > select #15/B:218 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show ""Add Hydrogens"" [Repeated 1 time(s)] > addh #!15 Summary of feedback from adding hydrogens to 5ciu #15 --- notes | Termini for 5ciu (#15) chain B determined from SEQRES records Termini for 5ciu (#15) chain C determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: 5ciu #15/B GLU 216, 5ciu #15/B PHE 292, 5ciu #15/B LEU 329, 5ciu #15/C THR 32 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 5ciu #15/B LEU 289, 5ciu #15/B LYS 315, 5ciu #15/B ASN 351, 5ciu #15/C PRO 38 206 hydrogen bonds Adding 'H' to 5ciu #15/B GLU 216 Adding 'H' to 5ciu #15/B PHE 292 Adding 'H' to 5ciu #15/B LEU 329 Adding 'H' to 5ciu #15/C THR 32 5ciu #15/B ASN 351 is not terminus, removing H atom from 'C' 5ciu #15/C PRO 38 is not terminus, removing H atom from 'C' 1146 hydrogens added > select #19/B:216 15 atoms, 14 bonds, 1 residue, 1 model selected > color sel byelement > select #15/B:216 15 atoms, 14 bonds, 1 residue, 1 model selected > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1CombineAddBondProtonate5ciu.cxs [Errno 2] No such file or directory: 'D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1CombineAddBondProtonate5ciu.cxs.1840.tmp' > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1CombineAddBondProtonate5ciu.cxs [Errno 2] No such file or directory: 'D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcAdd2x6s01Align6s01H3TailAdd5ciu_Add2xDNMT3BAlphaFoldColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1CombineAddBondProtonate5ciu.cxs.1840.tmp' > save > D:/Users/mdivjak/Documents/maya/projects/EpigeneticsDNAMethylationProject/ChimeraX/DNMT3A_6PA7ModelEtcColourMatchDNMT3B_PWWPto5ciuRETRY_SplitPWWPMatchTo5ciuAtomsProtonateTug1CombineAddBondProtonate5ciu.cxs ——— End of log from Wed Mar 13 11:37:21 2024 ——— opened ChimeraX session > tug #19/B:216 toAtoms #15/B:216 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\tug\tugatoms.py"", line 353, in _simulate simulation.step(sim_steps) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\openmm\app\simulation.py"", line 141, in step self._simulate(endStep=self.currentStep+steps) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\openmm\app\simulation.py"", line 210, in _simulate self.integrator.step(stepsToGo) File ""C:\Program Files\ChimeraX\bin\Lib\site-packages\openmm\openmm.py"", line 18533, in step return _openmm.VariableLangevinIntegrator_step(self, steps) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ openmm.OpenMMException: Particle coordinate is NaN. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\motion.py"", line 49, in __call__ self.func(self.session, f) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\tug\tugcommand.py"", line 74, in simulation_frame tugger.tug_to_positions(points) File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\tug\tugatoms.py"", line 330, in tug_to_positions self._simulate() File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\tug\tugatoms.py"", line 360, in _simulate max_force=self._max_force() ^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\tug\tugatoms.py"", line 313, in _max_force self._sim_forces = c.getState(getForces = True).getForces(asNumpy = True)/(kilojoule_per_mole/nanometer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX\bin\Lib\site-packages\openmm\openmm.py"", line 4524, in getState state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ openmm.OpenMMException: Particle coordinate is NaN. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan Error processing trigger ""new frame"": openmm.OpenMMException: Particle coordinate is NaN. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan File ""C:\Program Files\ChimeraX\bin\Lib\site-packages\openmm\openmm.py"", line 4524, in getState state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 537.70 OpenGL renderer: Quadro RTX 6000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Dell Inc. Model: Precision 7920 Rack OS: Microsoft Windows 10 Pro for Workstations (Build 19045) Memory: 410,695,991,296 MaxProcessMemory: 137,438,953,344 CPU: 48 Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 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: 2023.11.17 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 comtypes: 1.1.14 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: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 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 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 pywin32: 305 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 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 WMI: 1.5.1 }}} " defect assigned normal Structure Editing all ChimeraX