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Opened 20 months ago
Last modified 20 months ago
#14755 assigned defect
tug after session restore: openmm.OpenMMException: Particle coordinate is NaN
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Change History (2)
comment:1 by , 20 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → tug after session restore: openmm.OpenMMException: Particle coordinate is NaN |
comment:2 by , 20 months ago
During the tug the OpenMM molecular dynamics produced a NaN (not-a-number) xyz coordinate. Probably some very close atoms caused the simulations to explode. ChimeraX tries to catch this and minimize the structure (which is less likely to explode) by looking for when forces get exceptionally large. I'll try to add some code so ChimeraX also catches this NaN error and have it minimize the energy. But in general if the structure has clashing atoms it may be that OpenMM cannot simulate or minimize it.
Sorry for the slow reply to your report. I have been on vacation the last 3 weeks and returned to work today.
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Reported by Maja Divjak