![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Last modified 11 months ago
#16623 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Mon Jul 10 18:33:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jul 10 15:59:37 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jul 6 13:25:11 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jul 5 13:38:28 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jul 5 13:32:58 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jul 4 14:24:08 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jul 4 13:42:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jul 3 22:05:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jul 3 21:54:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jun 29 18:48:25 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jun 29 15:37:27 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 28 18:20:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 28 17:55:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 28 16:04:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 27 13:05:48 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 27 12:45:33 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Updating list of available bundles failed: Internal Server Error
Log from Mon Jun 26 10:11:19 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Fri Jun 23 14:27:32 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jun 22 13:48:19 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 21 13:00:17 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 14:01:06 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 13:59:27 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 13:41:59 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 13:33:55 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 13:21:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jun 19 14:50:40 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Updating list of available bundles failed: Internal Server Error
Log from Sat Jun 17 16:13:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Fri Jun 16 15:07:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jun 15 13:33:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 14 15:40:04 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 13 12:23:11 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 13 11:14:29 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jun 12 13:04:04 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Mon Jun 12 10:47:51 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Fri Jun 9 15:09:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Fri Jun 9 12:21:12 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Thu Jun 8 16:20:57 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología\Alpha fold\overlap of CP structures.cxs" format session
Log from Thu Jun 8 14:55:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Thu Jun 8 12:29:59 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Thu Jun 8 09:54:20 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Wed Jun 7 16:42:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Wed Jun 7 14:34:33 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Tue Jun 6 14:34:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Tue Jun 6 14:16:52 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Fri May 26 15:30:48 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs" format session
Log from Thu May 25 17:54:54 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs" format session
Log from Thu May 25 12:52:10 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/structures.cxs" format session
Log from Wed May 24 12:56:46 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs" format session
Log from Wed Mar 29 11:43:44 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> format session
Log from Thu Mar 23 12:13:26 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> format session
Log from Fri Mar 17 10:55:50 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
Log from Wed Mar 15 16:42:48 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
Log from Tue Mar 14 17:14:03 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp vs Barmah Forrest 2yew.cxs"
Log from Fri Mar 10 16:26:58 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu.cxs" format session
Log from Thu Mar 9 14:24:14 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga.cxs" format session
Log from Thu Mar 9 12:12:18 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mauriciocomas/Downloads/7vga.pdb
7vga.pdb title:
Cryo-em structure of alphavirus, getah virus [more info...]
Chain information for 7vga.pdb #1
---
Chain | Description
A D G J | E1 envelope glycoprotein
B E H K | E2 envelope glycoprotein
C F I L | capsid protein
> select /A/D/G/J
812 atoms, 808 bonds, 116 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /B/E/H/K
1464 atoms, 1492 bonds, 208 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /C/F/I/L
4884 atoms, 5000 bonds, 632 residues, 1 model selected
> hide sel atoms
> select /C
1221 atoms, 1250 bonds, 158 residues, 1 model selected
> show sel cartoons
> open /Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/3j2w.pdb
> format pdb
3j2w.pdb title:
Electron cryo-microscopy of chikungunya virus [more info...]
Chain information for 3j2w.pdb #2
---
Chain | Description
A B C D | glycoprotein E1
E F G H | glycoprotein E1
I J K L | capsid protein
M N O | glycoprotein E2
P | glycoprotein E2
Q R S T | glycoprotein E2
> select #1/A#1/D#1/G#1/J
812 atoms, 808 bonds, 116 residues, 1 model selected
> hide sel atoms
> select #1/B#1/E#1/H#1/K
1464 atoms, 1492 bonds, 208 residues, 1 model selected
> hide sel atoms
> select #1/C#1/F#1/I#1/L#2/I#2/J#2/K#2/L
9448 atoms, 9676 bonds, 1228 residues, 2 models selected
> hide sel atoms
> select #2/A#2/B#2/C#2/D#2/E#2/F#2/G#2/H
13312 atoms, 13667 bonds, 1756 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> select #2/M#2/N#2/O#2/P#2/Q#2/R#2/S#2/T
13052 atoms, 13416 bonds, 1668 residues, 1 model selected
> hide sel atoms
> select #1/C
1221 atoms, 1250 bonds, 158 residues, 1 model selected
> select #1/F
1221 atoms, 1250 bonds, 158 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #2/I
1141 atoms, 1169 bonds, 149 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #2 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 7vga.pdb, chain A (#1) with 3j2w.pdb, chain A (#2), sequence
alignment score = 1009.4
Fewer than 3 residues aligned; cannot match 7vga.pdb, chain A with 3j2w.pdb,
chain A
> ui tool show Matchmaker
> matchmaker #2 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 7vga.pdb, chain A (#1) with 3j2w.pdb, chain A (#2), sequence
alignment score = 1009.4
Fewer than 3 residues aligned; cannot match 7vga.pdb, chain A with 3j2w.pdb,
chain A
> ui tool show Matchmaker
> select #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> matchmaker #2 & sel to #1 & sel
No 'to' model specified
> ~select #2
Nothing selected
> select #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> select #1
7160 atoms, 7300 bonds, 956 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
7160 atoms, 7300 bonds, 956 residues, 1 model selected
> select #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 & sel to #1/C & sel pairing bs
No 'to' chains specified
> ~select #2
Nothing selected
> select #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 & sel to #1/C & sel pairing bs
No 'to' chains specified
> ui tool show Matchmaker
> matchmaker #2 & sel to #1/I & sel pairing bs
No 'to' chains specified
> matchmaker #2/I#1/C & sel to #1/C#2/I & sel pairing ss
Different number of reference/match chains (0 ref, 1 match)
> ui tool show Matchmaker
> matchmaker #2/I to #1/C 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 7vga.pdb, chain C (#1) with 3j2w.pdb, chain I (#2), sequence
alignment score = 590.7
RMSD between 145 pruned atom pairs is 0.988 angstroms; (across all 149 pairs:
1.054)
> set bgColor white
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C #1/F #1/I #1/L
Alignment identifier is 1
> sequence chain #2/I #2/J #2/K #2/L
Alignment identifier is 2
> select #1/C,F,I,L:166-167
84 atoms, 84 bonds, 8 residues, 1 model selected
> select #1/C,F,I,L:166
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/C,F,I,L:166
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/C,F,I,L:166
36 atoms, 32 bonds, 4 residues, 1 model selected
> style sel stick
Changed 36 atom styles
> show sel atoms
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #2/I
Alignment identifier is 2/I
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #2/I:241
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/I:240-241
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:240-241
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:240-241
13 atoms, 12 bonds, 2 residues, 1 model selected
> select
> #2/I:120-125,128-134,139-140,149-150,161-163,168-172,191-195,198-203,206-210,222-224,230-239,243-251,256-259,265-266
546 atoms, 546 bonds, 69 residues, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240-241
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #1/C:171
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:171-173
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #1/C:222-223
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/C:222-226
45 atoms, 46 bonds, 5 residues, 1 model selected
> select #1/C:231
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:231-235
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #1/C:263
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:263-265
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #1/C:242
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:242
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:241-242
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select
> #1/C:123-125,130-133,150-151,184-185,193-194,201-203,208-211,223-225,230-234,239-240,244-246,249-252,257-260
346 atoms, 345 bonds, 41 residues, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:148-149
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/C:148-149
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #2/I:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:139
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:139
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/C:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga.cxs"
——— End of log from Thu Mar 9 12:12:18 2023 ———
opened ChimeraX session
> open /Users/mauriciocomas/Downloads/1kxf.pdb
1kxf.pdb title:
Sindbis virus capsid, (wild-type) residues 1-264, tetragonal crystal form
(form II) [more info...]
Chain information for 1kxf.pdb #3
---
Chain | Description
A | sindbis virus CORE protein
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker #3/A to #2/I 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 3j2w.pdb, chain I (#2) with 1kxf.pdb, chain A (#3), sequence
alignment score = 511.3
RMSD between 145 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
0.818)
> hide #1 models
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:112-220
840 atoms, 861 bonds, 109 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> show #1 models
> hide #1 models
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #3/A:136
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:136
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #3/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:159
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:159-163
37 atoms, 37 bonds, 5 residues, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:159
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:159-160
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:160
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:160-162
23 atoms, 23 bonds, 3 residues, 1 model selected
> show #1 models
> hide #1 models
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf.cxs"
> save /Users/mauriciocomas/Desktop/image1.png supersample 3
> select #3/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:109
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:109
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:156
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:156-157
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> color sel dim gray
> select clear
> save /Users/mauriciocomas/Desktop/image1.png supersample 3
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163-167
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #1 models
> hide #3 models
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf.cxs"
> open /Users/mauriciocomas/Downloads/7sfu.pdb
7sfu.pdb title:
Cryoem structure of venezuelan equine encephalitis virus (veev) Tc-83 strain
VLP [more info...]
Chain information for 7sfu.pdb #4
---
Chain | Description
A D G J | E1 envelope glycoprotein
B E H K | E2 envelope glycoprotein
C F I L | capsid protein
Non-standard residues in 7sfu.pdb #4
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> ui tool show Matchmaker
> matchmaker #4/L to #1/C 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 7vga.pdb, chain C (#1) with 7sfu.pdb, chain L (#4), sequence
alignment score = 442
RMSD between 141 pruned atom pairs is 1.006 angstroms; (across all 158 pairs:
1.916)
> hide #2 models
> hide #1 models
> show #1 models
> hide #1 models
> select #4/A#4/D#4/G#4/J
13536 atoms, 13928 bonds, 1772 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4/B#4/E#4/H#4/K
13328 atoms, 13724 bonds, 1700 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> select #1/C#2/I#4/C#4/F#4/I#4/L
7470 atoms, 7639 bonds, 955 residues, 3 models selected
> hide sel & #4 atoms
> select #4/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> select #1/C#2/I#4/C#4/F#4/I#4/L
7470 atoms, 7639 bonds, 955 residues, 3 models selected
> show sel & #4 cartoons
> show #3 models
> hide #3 models
> select #1/C#2/I#4/C#4/F#4/I#4/L
7470 atoms, 7639 bonds, 955 residues, 3 models selected
> hide sel & #4 cartoons
> select #4/L
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> show #3 models
> show #2 models
> show #1 models
> select clear
> hide #1 models
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:124
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/L:124-275
1188 atoms, 1216 bonds, 152 residues, 1 model selected
> select #4/L:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:123-127
39 atoms, 38 bonds, 5 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:133-134
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #4/L:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu.cxs"
——— End of log from Thu Mar 9 14:24:14 2023 ———
opened ChimeraX session
> hide #2 models
> open /Users/mauriciocomas/Downloads/6xo4.pdb
6xo4.pdb title:
Cryoem structure of eastern equine encephalitis (eeev) VLP [more info...]
Chain information for 6xo4.pdb #5
---
Chain | Description
A D G J | togavirin
B E H K | togavirin
C F I L | togavirin
> select #5/A#5/B#5/C#5/D#5/E#5/F#5/G#5/H#5/I#5/J#5/K#5/L
30900 atoms, 31776 bonds, 4 pseudobonds, 3992 residues, 2 models selected
> hide sel atoms
> select #5/A
3307 atoms, 3401 bonds, 1 pseudobond, 433 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #5/C
1165 atoms, 1192 bonds, 151 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker #5/C to #4/L 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 7sfu.pdb, chain L (#4) with 6xo4.pdb, chain C (#5), sequence
alignment score = 559.6
RMSD between 98 pruned atom pairs is 1.141 angstroms; (across all 151 pairs:
2.080)
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> ui tool show Matchmaker
> matchmaker #5/F to #2/I 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 3j2w.pdb, chain I (#2) with 6xo4.pdb, chain F (#5), sequence
alignment score = 429.9
RMSD between 107 pruned atom pairs is 1.240 angstroms; (across all 149 pairs:
1.932)
> show #!5 models
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> show #!5 models
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> select #5
30900 atoms, 31776 bonds, 4 pseudobonds, 3992 residues, 2 models selected
> show #!5 models
> hide #5.1 models
> ~select #5.1
30900 atoms, 31776 bonds, 3992 residues, 1 model selected
> hide #!5 models
> ui tool show Matchmaker
> matchmaker #5/C to #2/I 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 3j2w.pdb, chain I (#2) with 6xo4.pdb, chain C (#5), sequence
alignment score = 429.9
RMSD between 107 pruned atom pairs is 1.240 angstroms; (across all 149 pairs:
1.932)
> show #!5 models
> hide #4 models
> show #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/C
Alignment identifier is 5/C
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel dim gray
> ui mousemode right select
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #5/C:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/C:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:154-156
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #5/C:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/C:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/C:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/C:158-159
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/C:158-159
20 atoms, 20 bonds, 2 residues, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color sel dim gray
> hide sel atoms
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right rotate
> ui mousemode right select
> select #5/C:234
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:233-234
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
Drag select of 2 residues
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> color sel red
> color sel blue
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right rotate
> ui mousemode right select
> select #5/C:233@CB
1 atom, 1 residue, 1 model selected
> color sel red
Drag select of 3 residues
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right rotate
> ui mousemode right translate
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8.cxs"
> save /Users/mauriciocomas/Desktop/image11.png supersample 3
> ui mousemode right select
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!5 models
> open /Users/mauriciocomas/Downloads/4agk.pdb
4agk.pdb title:
Crystal structure of capsid protein (110-267) from aura virus [more info...]
Chain information for 4agk.pdb #6
---
Chain | Description
A | capsid protein
> ui tool show Matchmaker
> matchmaker #6/A to #2/I 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 3j2w.pdb, chain I (#2) with 4agk.pdb, chain A (#6), sequence
alignment score = 513.6
RMSD between 146 pruned atom pairs is 0.668 angstroms; (across all 149 pairs:
0.815)
> ui mousemode right select
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select clear
> select #6/A:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:165
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:163
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel atoms
> color sel dim gray
> select #6/A:240
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk.cxs"
> save /Users/mauriciocomas/Desktop/image12.png supersample 3
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #6 models
> open /Users/mauriciocomas/Downloads/1vcp.pdb
1vcp.pdb title:
Semliki forest virus capsid protein (crystal form I) [more info...]
Chain information for 1vcp.pdb #7
---
Chain | Description
A B C | semliki forest virus capsid protein
Non-standard residues in 1vcp.pdb #7
---
HG — mercury (II) ion
> select #7/A#7/B#7/C
3429 atoms, 3510 bonds, 9 pseudobonds, 450 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #7/A
1143 atoms, 1170 bonds, 2 pseudobonds, 150 residues, 2 models selected
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #7/A to #2/I 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 3j2w.pdb, chain I (#2) with 1vcp.pdb, chain A (#7), sequence
alignment score = 759.4
RMSD between 149 pruned atom pairs is 0.484 angstroms; (across all 149 pairs:
0.484)
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #7/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #7/A:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 9 atom styles
> show sel atoms
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp.cxs"
> save /Users/mauriciocomas/Desktop/image13.png supersample 3
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:146
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:147-148
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #7/A:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!7 models
> open /Users/mauriciocomas/Downloads/2yew.pdb
2yew.pdb title:
Modeling barmah forest virus structural proteins [more info...]
Chain information for 2yew.pdb #8
---
Chain | Description
A D G J | COAT protein
B E H K | spike glycoprotein E1
C F I L | spike glycoprotein E2
> select #8/A#8/D#8/G#8/J
5264 atoms, 5384 bonds, 684 residues, 1 model selected
> hide sel atoms
> select #8/B#8/E#8/H#8/K
12900 atoms, 13216 bonds, 4 pseudobonds, 1704 residues, 2 models selected
> hide sel atoms
> select #8/C#8/F#8/I#8/L
12956 atoms, 13316 bonds, 1684 residues, 1 model selected
> hide sel atoms
> select #8/A
1316 atoms, 1346 bonds, 171 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker #8/A to #2/I 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 3j2w.pdb, chain I (#2) with 2yew.pdb, chain A (#8), sequence
alignment score = 572.6
RMSD between 66 pruned atom pairs is 1.154 angstroms; (across all 149 pairs:
3.464)
> ui mousemode right rotate
> ui mousemode right select
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select #8/A:134
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:135
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:134
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:135
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide #!8 models
> select #8/D
1316 atoms, 1346 bonds, 171 residues, 1 model selected
> show #2 cartoons
> hide #2 cartoons
> hide #2 models
> show #2 models
> select #2/I
1141 atoms, 1169 bonds, 149 residues, 1 model selected
> show sel cartoons
> select #8/D
1316 atoms, 1346 bonds, 171 residues, 1 model selected
> show #2 cartoons
> hide #2 cartoons
> select #2/I
1141 atoms, 1169 bonds, 149 residues, 1 model selected
> show sel cartoons
> select clear
> select #8/G
1316 atoms, 1346 bonds, 171 residues, 1 model selected
> show #2 cartoons
> hide #2 cartoons
> select #2/I
1141 atoms, 1169 bonds, 149 residues, 1 model selected
> show sel cartoons
> select clear
> show #!8 models
Drag select of 9 residues
Drag select of 5 residues
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right rotate
> ui mousemode right select
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> ui mousemode right rotate
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp vs Barmah Forrest 2yew.cxs"
> save /Users/mauriciocomas/Desktop/image14.png supersample 3
> ui mousemode right select
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp vs Barmah Forrest 2yew.cxs"
——— End of log from Fri Mar 10 16:26:58 2023 ———
opened ChimeraX session
> open /Users/mauriciocomas/Downloads/7ko8.pdb
7ko8.pdb title:
Cryo-em structure of the mature and infective mayaro virus [more info...]
Chain information for 7ko8.pdb #9
---
Chain | Description
A D G J | capsid protein
B E H L | E1 glycoprotein
C F I M | E2 glycoprotein
Non-standard residues in 7ko8.pdb #9
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide #!8 models
> select #9/A
1170 atoms, 1200 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/D
1170 atoms, 1199 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/G
1170 atoms, 1199 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/G
1170 atoms, 1199 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/J
1170 atoms, 1199 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/B#9/E#9/H#9/L
13160 atoms, 13517 bonds, 1732 residues, 1 model selected
> hide sel atoms
> select #9/C#9/F#9/I#9/M
12924 atoms, 13269 bonds, 1664 residues, 1 model selected
> hide sel atoms
> select #9/A
1170 atoms, 1200 bonds, 152 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
> ui mousemode right translate
> ui mousemode right select
> matchmaker #9/A to #2/I 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 3j2w.pdb, chain I (#2) with 7ko8.pdb, chain A (#9), sequence
alignment score = 566.3
RMSD between 131 pruned atom pairs is 1.142 angstroms; (across all 149 pairs:
1.442)
> ui mousemode right zoom
> select ligand
557 atoms, 581 bonds, 43 residues, 2 models selected
> hide sel & #9 atoms
> ui mousemode right translate
> save /Users/mauriciocomas/Desktop/mayaro format fasta alignment 8/A
> ui mousemode right select
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:108
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:108-253
1112 atoms, 1139 bonds, 146 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select clear
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/mayaro format fasta alignment 9/A
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> hide #9 models
> show #9 models
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:117-118
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #9/A:138
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel dim gray
> select #9/A:138
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:138
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #9/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> show #!8 models
> hide #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> save /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/BFV format
> fasta alignment 8/A
> save /Users/mauriciocomas/Desktop/BFV format fasta alignment 8/A
> select clear
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select clear
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:133@CA
1 atom, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!8 models
> show #3 models
> hide #3 models
> show #!7 models
> select #7/A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/SINV format fasta alignment 7/A
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #3 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> save /Users/mauriciocomas/Desktop/SINV format fasta alignment 3/A
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> select #3/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #6 models
> hide #3 models
Drag select of 4 residues
> ui mousemode right rotate
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> save /Users/mauriciocomas/Desktop/Aura format fasta alignment 6/A
> ui mousemode right select
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #4 models
> hide #6 models
> select #2/I:195
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #4/L:254
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> save /Users/mauriciocomas/Desktop/VEEV format fasta alignment 6/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/VEEV format fasta alignment 4/L
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #4/L:247@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #4/L:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
——— End of log from Tue Mar 14 17:14:03 2023 ———
opened ChimeraX session
> hide #4 models
> ui mousemode right rotate
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> show #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> select clear
> save /Users/mauriciocomas/Desktop/image31.png supersample 3
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:182
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/I:182-183
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190-191
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183-184
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:166
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/I:166-181
125 atoms, 127 bonds, 16 residues, 1 model selected
> select #2/I:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183-184
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 4 residues
> ui mousemode right rotate
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183-184
21 atoms, 21 bonds, 2 residues, 1 model selected
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #!7 models
> show #1 models
> hide #1 models
> show #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image32.png supersample 3
> ui mousemode right select
> select #9/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #9 models
> show #1 models
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> save /Users/mauriciocomas/Desktop/image33.png supersample 3
> select #1/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> save /Users/mauriciocomas/Desktop/image34.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #2 models
> show #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image35.png supersample 3
> select #8/A:133@CB
1 atom, 1 residue, 1 model selected
> show #2 models
> hide #1 models
> hide sel atoms
> undo
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/image36.png supersample 3
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!8 models
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel dark gray
> select #3/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> select #3/A:161-162
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/A:161-162
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:162-163
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:178
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:178
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:179-180
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel dim gray
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/image37.png supersample 3
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image38.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #3 models
> show #6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:181
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/A:181
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> show sel atoms
> show sel atoms
> show sel cartoons
> select #6/A:131
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:131-267
1036 atoms, 1064 bonds, 137 residues, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> show sel atoms
> style sel sphere
Changed 4 atom styles
> color sel dim gray
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image39.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #6 models
> show #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:203
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/L:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:196-197
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/L:196-197
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/L:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select clear
> save /Users/mauriciocomas/Desktop/image40.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> show #!5 models
> hide #!5 models
> hide #4 models
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/C
Alignment identifier is 5/C
> select #5/C:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:175
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dark gray
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel dim gray
> ui mousemode right select
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:183-184
11 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/C:184
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:184
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel dim gray
> select clear
> save /Users/mauriciocomas/Desktop/image41.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #!5 models
> select clear
> save /Users/mauriciocomas/Desktop/image42.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
——— End of log from Wed Mar 15 16:42:48 2023 ———
opened ChimeraX session
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:126-184
448 atoms, 455 bonds, 59 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> ui tool show "Show Sequence Viewer"
> sequence chain #2/I
Alignment identifier is 2/I
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126-133
58 atoms, 58 bonds, 8 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 8 atom styles
> show sel atoms
> save /Users/mauriciocomas/Desktop/image9.png supersample 3
> show #3 models
> hide #3 models
> show #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #7/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> save /Users/mauriciocomas/Desktop/image10.png supersample 3
> hide #!7 models
> show #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #9/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image11.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> ui mousemode right select
> select #2/I:154@CG
1 atom, 1 residue, 1 model selected
> hide #9 models
> show #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123-128
45 atoms, 44 bonds, 6 residues, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #1/C:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> save /Users/mauriciocomas/Desktop/image12.png supersample 3
> hide #1 models
> show #!8 models
> hide #!8 models
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right translate
> show #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:112-113
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:114
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:114
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide sel cartoons
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right select
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image13.png supersample 3
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #6 models
> hide #6 models
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:137
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:137-186
390 atoms, 399 bonds, 50 residues, 1 model selected
> show #6 models
> hide #6 models
> select #6
1279 atoms, 1181 bonds, 279 residues, 1 model selected
> ~select #6
Nothing selected
> select #6
1279 atoms, 1181 bonds, 279 residues, 1 model selected
> ~select #6
Nothing selected
> select #3
1240 atoms, 1252 bonds, 175 residues, 1 model selected
> ~select #3
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> show sel atoms
> show sel atoms
> style sel stick
Changed 4 atom styles
> show sel atoms
> hide sel atoms
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123-129
46 atoms, 46 bonds, 7 residues, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123-124
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:123-124
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:124-125
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/A:124-125
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide sel atoms
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel gray
> select clear
> save /Users/mauriciocomas/Desktop/image14.png supersample 3
> hide #3 models
> show #9 models
> hide #9 models
> show #6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:157
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> save /Users/mauriciocomas/Desktop/image15.png supersample 3
> hide #6 models
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/C
Alignment identifier is 5/C
> select clear
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> color sel dim gray
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:119-120
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/C:119-120
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> show sel atoms
> hide sel atoms
> select #5/C:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:117-123
52 atoms, 51 bonds, 7 residues, 1 model selected
> select #5/C:115
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:115-118
31 atoms, 31 bonds, 4 residues, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:148-149
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:145-146
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/C:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> select #5/C:146-147
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #5/C:146-147
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #5/C:147-148
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/C:147-148
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel dim gray
> save /Users/mauriciocomas/Desktop/image16.png supersample 3
> hide #!5 models
> show #4 models
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:135-136
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/L:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #4/L:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/L:165
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:165-166
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/L:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/L:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel dim gray
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
——— End of log from Fri Mar 17 10:55:50 2023 ———
opened ChimeraX session
> show #1 models
> hide #4 models
> ui mousemode right select
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select clear
> save /Users/mauriciocomas/Desktop/image1.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
——— End of log from Thu Mar 23 12:13:26 2023 ———
opened ChimeraX session
> hide #1 models
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/mauriciocomas/Desktop/3j2w monomer" format fasta alignment 2/I
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "move label"
> ui mousemode right label
> label #2/I:128
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui tool show "Color Actions"
> color sel bychain
> color sel cyan
> select clear
> select #2/I:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:139
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:139
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel cyan
> select #2/I:190@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!7 models
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel hot pink
> ui tool show "Color Actions"
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right label
> label #7/A:128
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> color sel blue
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> ui mousemode right select
> select #7/A:154@CB
1 atom, 1 residue, 1 model selected
> select #7/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:178
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:154@CB
1 atom, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:178
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel blue
> select #7/A:183@CB
1 atom, 1 residue, 1 model selected
> color sel blue
> select #7/A:190@CB
1 atom, 1 residue, 1 model selected
> color sel red
> select #7/A:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> select clear
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> select #7/A:183@CA
1 atom, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #!7 models
> hide #2 models
> show #2 models
> show #9 models
> select #9/A:138
7 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> hide sel atoms
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #9/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #9/A:145@CB
1 atom, 1 residue, 1 model selected
> select #9/A:148
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:148
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:170
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #9/A:174@CD
1 atom, 1 residue, 1 model selected
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #9/A:231@CA
1 atom, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #9 models
> show #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> hide #1-2 atoms
> undo
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:157-158
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:157-158
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #1/C:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #1 models
> show #!8 models
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:114
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #8/A:133@N
1 atom, 1 residue, 1 model selected
> select #8/A:133@CA
1 atom, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #8/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #8/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> select #8/A:242
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178-179
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> show #3 models
> hide #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #3/A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #3/A:150@CB
1 atom, 1 residue, 1 model selected
> select #3/A:150@CB
1 atom, 1 residue, 1 model selected
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:154@CB
1 atom, 1 residue, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:153-154
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel blue
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:176-177
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:179@CA
1 atom, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:180
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:180
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240@OE2
1 atom, 1 residue, 1 model selected
> select #2/I:240@CB
1 atom, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> show #6 models
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:146@CA
1 atom, 1 residue, 1 model selected
> select #6/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #6/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:156@CA
1 atom, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:152
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:152-156
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #6/A:160
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/A:160-162
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #6/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/A:148-157
75 atoms, 76 bonds, 10 residues, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:152
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:152
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> color sel dim gray
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:156-157
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/A:156-157
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:183
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:183
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:183
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> show sel atoms
> color sel dim gray
> select clear
> select #6/A:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #6/A:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #6 models
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/C
Alignment identifier is 5/C
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:121@CA
1 atom, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:157@CB
1 atom, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150-151
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:155-156
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/C:154-156
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152-153
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:159-160
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/I:159-160
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/I:160
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:160
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel cartoons
> show sel atoms
> color sel blue
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/C:175
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:190@CG
1 atom, 1 residue, 1 model selected
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #5/C:233-234
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:233-234
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #!5 models
> show #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #4/L:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #4/L:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/L:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #4/L:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> color sel dim gray
> select #4/L:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/L:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel blue
> select clear
> select #4/L:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #4/L:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
——— End of log from Wed Mar 29 11:43:44 2023 ———
opened ChimeraX session
> hide #4 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphFold
> Colaboratory Ross River.pdb"
Chain information for AlphFold Colaboratory Ross River.pdb #10
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #10 to #2
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 3j2w.pdb, chain I (#2) with AlphFold Colaboratory Ross River.pdb,
chain A (#10), sequence alignment score = 670.2
RMSD between 146 pruned atom pairs is 0.751 angstroms; (across all 149 pairs:
0.841)
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A
Alignment identifier is 10/A
> ui mousemode right select
> select #10/A:129
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #10/A:131
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #10/A:160
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #10/A:157
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel blue
> select #10/A:181
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #10/A:186
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #10/A:193
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #10/A:243
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image3.png supersample 3
> select #10/A:157
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image4.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> open "/Users/mauriciocomas/Downloads/YP_009020571.1 and 20 other
> sequences.aln"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 31, in open_file
seqs, file_attrs, file_markups = ns['read'](session, stream)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/io/readALN.py", line 33, in read
raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
with 'CLUSTAL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event
_open_dropped_file(self.session, event.file())
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 421, in collated_open
return func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/__init__.py", line 61, in open
return open_file(session, data, file_name,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
OSError: Syntax error in ALN file 'YP_009020571.1 and 20 other sequences.aln':
First non-blank line does not start with 'CLUSTAL'
OSError: Syntax error in ALN file 'YP_009020571.1 and 20 other sequences.aln':
First non-blank line does not start with 'CLUSTAL'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
See log for complete Python traceback.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Alphavirus
> sequences/Madaragia YP_009020571.1 and 20 other sequences.aln"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 31, in open_file
seqs, file_attrs, file_markups = ns['read'](session, stream)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/io/readALN.py", line 33, in read
raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
with 'CLUSTAL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event
_open_dropped_file(self.session, event.file())
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 421, in collated_open
return func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/__init__.py", line 61, in open
return open_file(session, data, file_name,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
OSError: Syntax error in ALN file 'Madaragia YP_009020571.1 and 20 other
sequences.aln': First non-blank line does not start with 'CLUSTAL'
OSError: Syntax error in ALN file 'Madaragia YP_009020571.1 and 20 other
sequences.aln': First non-blank line does not start with 'CLUSTAL'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
See log for complete Python traceback.
> hide #10 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
> 2/AlphaFold Colaboratory Middelburg virus.pdb"
Chain information for AlphaFold Colaboratory Middelburg virus.pdb #11
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #11 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 7vga.pdb, chain C (#1) with AlphaFold Colaboratory Middelburg
virus.pdb, chain A (#11), sequence alignment score = 810.9
RMSD between 151 pruned atom pairs is 0.862 angstroms; (across all 158 pairs:
1.359)
> show #10 models
> hide #10 models
> ui tool show "Show Sequence Viewer"
> sequence chain #11/A
Alignment identifier is 11/A
> select #11/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #11/A:132
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #11/A:158
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #11/A:161
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #11/A:182
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #11/A:187
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel dim gray
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:184-185
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:194
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #11/A:244
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image1.png supersample 3
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/structures.cxs"
——— End of log from Wed May 24 12:56:46 2023 ———
opened ChimeraX session
> hide #11 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
> 2/AlphaFold Colaboratory Everglades virus.pdb"
Chain information for AlphaFold Colaboratory Everglades virus.pdb #12
---
Chain | Description
A | No description available
> 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 7vga.pdb, chain C (#1) with AlphaFold Colaboratory Everglades
virus.pdb, chain A (#12), sequence alignment score = 512.4
RMSD between 151 pruned atom pairs is 0.937 angstroms; (across all 158 pairs:
1.296)
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> ui mousemode right select
> select #12/A:132
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #12/A:134
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #12/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #12/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #12/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel dim gray
> select #12/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel dim gray
> select #12/A:159-160
28 atoms, 27 bonds, 2 residues, 1 model selected
> select #12/A:159-160
28 atoms, 27 bonds, 2 residues, 1 model selected
> style sel stick
Changed 28 atom styles
> show sel atoms
> select #12/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #12/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui tool show "Color Actions"
> color sel bychain
> select #12/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #2/I:152
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #12/A:165
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #12/A:165
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #12/A:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #12/A:189
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel medium blue
> select #12/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel dim gray
> select #12/A:247
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/A:246
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #12/A:246
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/structures.cxs"
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs"
——— End of log from Thu May 25 12:52:10 2023 ———
opened ChimeraX session
> hide #12 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
> 2/Alpha Fold Collaboratory Salmon Pancrease Disease.pdb"
Chain information for Alpha Fold Collaboratory Salmon Pancrease Disease.pdb
#13
---
Chain | Description
A | No description available
> 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 7vga.pdb, chain C (#1) with Alpha Fold Collaboratory Salmon
Pancrease Disease.pdb, chain A (#13), sequence alignment score = 305.8
RMSD between 123 pruned atom pairs is 1.087 angstroms; (across all 157 pairs:
2.548)
> ui mousemode right rotate
> ui tool show "Show Sequence Viewer"
> sequence chain #13/A
Alignment identifier is 13/A
> ui mousemode right select
> select #13/A:141
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #13/A:144
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel dim gray
> select #13/A:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #13/A:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #13/A:172
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:169
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #13/A:172
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:174-175
42 atoms, 42 bonds, 2 residues, 1 model selected
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
Drag select of 5 residues
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:169
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 15 atom styles
> show sel atoms
> select #13/A:192
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #13/A:193
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:193
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel blue
> style sel stick
Changed 24 atom styles
> show sel atoms
> select #13/A:129
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:198
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 15 atom styles
> show sel atoms
> select #13/A:204
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #13/A:254
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> select clear
> ui mousemode right rotate
> save /Users/mauriciocomas/Desktop/image9.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs"
——— End of log from Thu May 25 17:54:54 2023 ———
opened ChimeraX session
> hide #13 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
> 2/Alpha Fold Collaboratory Fort Morgan virus.pdb"
Chain information for Alpha Fold Collaboratory Fort Morgan virus.pdb #14
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #14 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 7vga.pdb, chain C (#1) with Alpha Fold Collaboratory Fort Morgan
virus.pdb, chain A (#14), sequence alignment score = 506.1
RMSD between 152 pruned atom pairs is 0.926 angstroms; (across all 158 pairs:
1.271)
> ui tool show "Show Sequence Viewer"
> sequence chain #14/A
Alignment identifier is 14/A
> ui mousemode right select
> select #14/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #14/A:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #14/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #14/A:118
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #14/A:118
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #14/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #14/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #14/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #14/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #14/A:146
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #14/A:146
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #14/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #14/A:151-152
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #14/A:151-152
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #14/A:152
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #14/A:152
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #14/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #14/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel medium blue
> style sel stick
Changed 22 atom styles
> show sel atoms
> select #14/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #14/A:184
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:184
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #14/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:234
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #14/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image11.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs"
——— End of log from Fri May 26 15:30:48 2023 ———
opened ChimeraX session
> hide #14 models
> open "C:/Users/Carolina/Downloads/Ndumu virus Alphafold.pdb"
Chain information for Ndumu virus Alphafold.pdb #15
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #15 to #2
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 3j2w.pdb, chain I (#2) with Ndumu virus Alphafold.pdb, chain A
(#15), sequence alignment score = 653.9
RMSD between 144 pruned atom pairs is 0.776 angstroms; (across all 149 pairs:
1.015)
> matchmaker #15 to #2
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 3j2w.pdb, chain I (#2) with Ndumu virus Alphafold.pdb, chain A
(#15), sequence alignment score = 653.9
RMSD between 144 pruned atom pairs is 0.776 angstroms; (across all 149 pairs:
1.015)
> save "C:/Users/Carolina/Downloads/overlap of CP structures.cxs"
> ui mousemode right translate
> show #10 models
> hide #10 models
> color #15 #ff5500ff
> color #15 #ffaa00ff
> color #15 #ffaa7fff
> color #15 #ffa470ff
> color #15 #ff9c6bff
> color #15 #ff9a67ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Tue Jun 6 14:16:52 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #15/A
Alignment identifier is 15/A
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #15/A:128
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> show sel atoms
> style sel stick
Changed 15 atom styles
> style sel stick
Changed 15 atom styles
> show sel cartoons
> style sel stick
Changed 15 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel red
> ui mousemode right select
> select #15/A:242
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #15/A:159
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:156
15 atoms, 14 bonds, 1 residue, 1 model selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Tue Jun 6 14:34:43 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #15/A:127
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:128
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:242
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:192
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #15/A:193
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #15/A:192
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
Drag select of 1 residues
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:185
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:180
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:180
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/A:156
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:159
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Wed Jun 7 14:34:33 2023 ———
opened ChimeraX session
> show target m
> hide target m
> show #15 models
> show #2 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Everglades virus Alphafold.pdb"
Chain information for Everglades virus Alphafold.pdb #16
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-15#!5,7-8 to #16
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 Everglades virus Alphafold.pdb, chain A (#16) with 3j2w.pdb, chain
I (#2), sequence alignment score = 536
RMSD between 147 pruned atom pairs is 0.728 angstroms; (across all 149 pairs:
0.822)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 1kxf.pdb, chain
A (#3), sequence alignment score = 570.4
RMSD between 149 pruned atom pairs is 0.682 angstroms; (across all 158 pairs:
2.151)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 7sfu.pdb, chain
F (#4), sequence alignment score = 808
RMSD between 147 pruned atom pairs is 0.721 angstroms; (across all 162 pairs:
2.067)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 4agk.pdb, chain
A (#6), sequence alignment score = 550.5
RMSD between 149 pruned atom pairs is 0.715 angstroms; (across all 151 pairs:
0.781)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 7ko8.pdb, chain
G (#9), sequence alignment score = 563
RMSD between 134 pruned atom pairs is 1.120 angstroms; (across all 152 pairs:
1.600)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797
RMSD between 150 pruned atom pairs is 0.554 angstroms; (across all 260 pairs:
18.148)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
788.3
RMSD between 152 pruned atom pairs is 0.630 angstroms; (across all 262 pairs:
22.549)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1435.7
RMSD between 274 pruned atom pairs is 0.060 angstroms; (across all 274 pairs:
0.060)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 549.1
RMSD between 134 pruned atom pairs is 0.953 angstroms; (across all 266 pairs:
27.039)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
1003.7
RMSD between 162 pruned atom pairs is 0.329 angstroms; (across all 254 pairs:
31.074)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 814.3
RMSD between 142 pruned atom pairs is 0.555 angstroms; (across all 266 pairs:
35.306)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 6xo4.pdb, chain
C (#5), sequence alignment score = 677.5
RMSD between 106 pruned atom pairs is 1.220 angstroms; (across all 151 pairs:
2.045)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 1vcp.pdb, chain
C (#7), sequence alignment score = 569.9
RMSD between 147 pruned atom pairs is 0.619 angstroms; (across all 149 pairs:
0.761)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 2yew.pdb, chain
G (#8), sequence alignment score = 512.3
RMSD between 55 pruned atom pairs is 1.276 angstroms; (across all 171 pairs:
11.421)
> hide #15 models
> color #16 #0055ffff
> color #16 #ff55ffff
> color #16 magenta
> hide #16 models
> show #16 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Wed Jun 7 16:42:56 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:132
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:134
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:246
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> view clip false
[Repeated 1 time(s)]Drag select of 4 atoms, 9 residues, 2 bonds
> ui mousemode right translate
> ui mousemode right select
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:195
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
Alignment identifier is 16/A
Drag select of 3 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:189
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #16/A:183
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> select clear
> ui mousemode right translate
> ui mousemode right select
Drag select of 1 residues
> select #16/A:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Thu Jun 8 09:54:20 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Bebaru virus Alphafold.pdb"
Chain information for Bebaru virus Alphafold.pdb #17
---
Chain | Description
A | No description available
> color #17 #00aa7fff
> ui tool show Matchmaker
> matchmaker #2-4,6,9-16#!5,7-8 to #17
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 Bebaru virus Alphafold.pdb, chain A (#17) with 3j2w.pdb, chain I
(#2), sequence alignment score = 675.4
RMSD between 148 pruned atom pairs is 0.764 angstroms; (across all 149 pairs:
0.786)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 1kxf.pdb, chain A
(#3), sequence alignment score = 566.3
RMSD between 148 pruned atom pairs is 0.837 angstroms; (across all 157 pairs:
1.897)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 7sfu.pdb, chain I
(#4), sequence alignment score = 593
RMSD between 143 pruned atom pairs is 0.808 angstroms; (across all 161 pairs:
2.693)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 4agk.pdb, chain A
(#6), sequence alignment score = 561
RMSD between 148 pruned atom pairs is 0.729 angstroms; (across all 150 pairs:
0.808)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 7ko8.pdb, chain D
(#9), sequence alignment score = 805.5
RMSD between 138 pruned atom pairs is 1.056 angstroms; (across all 152 pairs:
1.688)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 1142
RMSD between 163 pruned atom pairs is 0.340 angstroms; (across all 262 pairs:
25.400)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
1126.9
RMSD between 166 pruned atom pairs is 0.337 angstroms; (across all 260 pairs:
13.918)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
814.6
RMSD between 147 pruned atom pairs is 0.553 angstroms; (across all 256 pairs:
26.037)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 509.8
RMSD between 129 pruned atom pairs is 0.766 angstroms; (across all 258 pairs:
33.546)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
810.1
RMSD between 148 pruned atom pairs is 0.467 angstroms; (across all 255 pairs:
22.095)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 946.6
RMSD between 150 pruned atom pairs is 0.331 angstroms; (across all 257 pairs:
26.554)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 814.6
RMSD between 147 pruned atom pairs is 0.553 angstroms; (across all 256 pairs:
26.039)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 6xo4.pdb, chain C
(#5), sequence alignment score = 520.4
RMSD between 100 pruned atom pairs is 1.207 angstroms; (across all 150 pairs:
2.057)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 1vcp.pdb, chain C
(#7), sequence alignment score = 729.6
RMSD between 149 pruned atom pairs is 0.572 angstroms; (across all 149 pairs:
0.572)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 2yew.pdb, chain G
(#8), sequence alignment score = 724.2
RMSD between 49 pruned atom pairs is 1.194 angstroms; (across all 171 pairs:
9.614)
> hide #16 models
> color #17 #007d5cff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 17/A
> select #17/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
Drag select of 1 atoms, 1 bonds
Drag select of 4 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #17/A:187
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #17/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #17/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #17/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #17/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #17/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #17/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/A:150
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> select clear
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Thu Jun 8 12:29:59 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Caaingua virus AlphaFold.pdb"
Chain information for Caaingua virus AlphaFold.pdb #18
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-17#!5,7-8 to #18
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 Caaingua virus AlphaFold.pdb, chain A (#18) with 3j2w.pdb, chain I
(#2), sequence alignment score = 458.4
RMSD between 130 pruned atom pairs is 0.780 angstroms; (across all 149 pairs:
2.000)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 1kxf.pdb, chain A
(#3), sequence alignment score = 475.4
RMSD between 137 pruned atom pairs is 0.844 angstroms; (across all 158 pairs:
2.636)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 7sfu.pdb, chain I
(#4), sequence alignment score = 487.6
RMSD between 132 pruned atom pairs is 0.852 angstroms; (across all 162 pairs:
2.515)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 4agk.pdb, chain A
(#6), sequence alignment score = 508.1
RMSD between 138 pruned atom pairs is 0.816 angstroms; (across all 151 pairs:
1.682)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 7ko8.pdb, chain D
(#9), sequence alignment score = 485.3
RMSD between 124 pruned atom pairs is 1.036 angstroms; (across all 152 pairs:
2.096)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 707.3
RMSD between 138 pruned atom pairs is 0.591 angstroms; (across all 252 pairs:
19.368)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
732
RMSD between 133 pruned atom pairs is 0.547 angstroms; (across all 249 pairs:
27.925)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
681.8
RMSD between 151 pruned atom pairs is 0.608 angstroms; (across all 265 pairs:
18.650)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 529
RMSD between 121 pruned atom pairs is 0.853 angstroms; (across all 258 pairs:
27.133)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
675.6
RMSD between 139 pruned atom pairs is 0.598 angstroms; (across all 247 pairs:
34.105)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 669.2
RMSD between 135 pruned atom pairs is 0.619 angstroms; (across all 259 pairs:
38.678)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 681.8
RMSD between 151 pruned atom pairs is 0.608 angstroms; (across all 265 pairs:
18.649)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 705
RMSD between 117 pruned atom pairs is 0.563 angstroms; (across all 250 pairs:
34.618)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 6xo4.pdb, chain C
(#5), sequence alignment score = 413.1
RMSD between 95 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
2.833)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 1vcp.pdb, chain C
(#7), sequence alignment score = 489.6
RMSD between 136 pruned atom pairs is 0.711 angstroms; (across all 149 pairs:
1.711)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 2yew.pdb, chain G
(#8), sequence alignment score = 446.9
RMSD between 52 pruned atom pairs is 1.300 angstroms; (across all 171 pairs:
9.079)
> hide #17 models
> color #18 #ff5500ff
> color #18 #c54200ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Thu Jun 8 14:55:45 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:123
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 18/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #18/A:125
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:125
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:242
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:242
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> color #18 #f35100ff
> color #18 #eb4e00ff
> color sel red
> color #18 #ffaa00ff
> color #18 #ff9b0eff
> color #18 #ff790cff
> color #18 #ff850aff
> show #15 models
> hide #15 models
> color #18 #ee7c09ff
> color sel red
> ui mousemode right select
Drag select of 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #18/A:123
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #18/A:125
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #18/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel gray
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:182
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #18/A:181
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #18/A:182
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #18/A:174
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #18/A:151
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 3 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #18/A:182
14 atoms, 13 bonds, 1 residue, 1 model selected
Drag select of 11 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide #18 models
> show #16 models
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:196@CA
1 atom, 1 residue, 1 model selected
Alignment identifier is 16/A
> color sel orange
> style sel stick
Changed 1 atom style
> show sel atoms
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel red
> color sel orange
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel gray
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Thu Jun 8 16:20:57 2023 ———
opened ChimeraX session
> hide #16 models
> show #18 models
> ui mousemode right select
Drag select of 1 residues
> select clear
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Cabassou virus Alphafold.pdb"
Chain information for Cabassou virus Alphafold.pdb #19
---
Chain | Description
A | No description available
> hide #18 models
> select add #18
4336 atoms, 4396 bonds, 269 residues, 1 model selected
> select subtract #18
Nothing selected
> ui tool show Matchmaker
> matchmaker #2-4,6,9-18#!5,7-8 to #19
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 Cabassou virus Alphafold.pdb, chain A (#19) with 3j2w.pdb, chain I
(#2), sequence alignment score = 523.2
RMSD between 146 pruned atom pairs is 0.713 angstroms; (across all 149 pairs:
0.884)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 1kxf.pdb, chain A
(#3), sequence alignment score = 557.2
RMSD between 150 pruned atom pairs is 0.659 angstroms; (across all 158 pairs:
2.145)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 7sfu.pdb, chain F
(#4), sequence alignment score = 796.5
RMSD between 148 pruned atom pairs is 0.761 angstroms; (across all 162 pairs:
2.057)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 4agk.pdb, chain A
(#6), sequence alignment score = 555.1
RMSD between 150 pruned atom pairs is 0.694 angstroms; (across all 151 pairs:
0.721)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 7ko8.pdb, chain G
(#9), sequence alignment score = 565
RMSD between 133 pruned atom pairs is 1.092 angstroms; (across all 152 pairs:
1.625)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 820.3
RMSD between 151 pruned atom pairs is 0.605 angstroms; (across all 258 pairs:
27.418)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
783.7
RMSD between 8 pruned atom pairs is 1.343 angstroms; (across all 261 pairs:
33.012)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1238.2
RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 273 pairs:
36.940)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 567.2
RMSD between 5 pruned atom pairs is 1.242 angstroms; (across all 269 pairs:
26.754)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
992.6
RMSD between 162 pruned atom pairs is 0.383 angstroms; (across all 255 pairs:
42.412)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 812.5
RMSD between 147 pruned atom pairs is 0.649 angstroms; (across all 265 pairs:
39.998)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1238.2
RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 273 pairs:
36.940)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 803.3
RMSD between 13 pruned atom pairs is 1.246 angstroms; (across all 257 pairs:
34.843)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 703.7
RMSD between 149 pruned atom pairs is 0.682 angstroms; (across all 261 pairs:
25.890)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 6xo4.pdb, chain C
(#5), sequence alignment score = 693.4
RMSD between 104 pruned atom pairs is 1.218 angstroms; (across all 151 pairs:
2.050)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 1vcp.pdb, chain C
(#7), sequence alignment score = 557.1
RMSD between 147 pruned atom pairs is 0.589 angstroms; (across all 149 pairs:
0.717)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 2yew.pdb, chain G
(#8), sequence alignment score = 512.3
RMSD between 54 pruned atom pairs is 1.264 angstroms; (across all 171 pairs:
9.925)
> show #18 models
> hide #18 models
> color #19 #aaff7fff
> color #19 #92d96cff
> color #19 #90d56aff
> color #19 #88ca65ff
> color #19 #8fd46aff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Fri Jun 9 12:21:12 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Eilat virus Alphafold.pdb"
Chain information for Eilat virus Alphafold.pdb #20
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-19#!5,7-8 to #20
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 Eilat virus Alphafold.pdb, chain A (#20) with 3j2w.pdb, chain I
(#2), sequence alignment score = 459.1
RMSD between 145 pruned atom pairs is 0.743 angstroms; (across all 149 pairs:
0.843)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 1kxf.pdb, chain A
(#3), sequence alignment score = 618.2
RMSD between 148 pruned atom pairs is 0.717 angstroms; (across all 159 pairs:
1.840)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 7sfu.pdb, chain I
(#4), sequence alignment score = 520.6
RMSD between 138 pruned atom pairs is 0.873 angstroms; (across all 162 pairs:
2.526)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 4agk.pdb, chain A
(#6), sequence alignment score = 660.7
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 152 pairs:
0.685)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 7ko8.pdb, chain G
(#9), sequence alignment score = 491.3
RMSD between 125 pruned atom pairs is 1.096 angstroms; (across all 152 pairs:
1.726)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphFold Colaboratory
Ross River.pdb, chain A (#10), sequence alignment score = 688.4
RMSD between 151 pruned atom pairs is 0.721 angstroms; (across all 251 pairs:
32.337)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
705.8
RMSD between 7 pruned atom pairs is 1.275 angstroms; (across all 248 pairs:
30.093)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
706.4
RMSD between 10 pruned atom pairs is 1.510 angstroms; (across all 254 pairs:
29.648)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 512.7
RMSD between 5 pruned atom pairs is 1.118 angstroms; (across all 251 pairs:
27.761)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
719.5
RMSD between 151 pruned atom pairs is 0.659 angstroms; (across all 245 pairs:
31.518)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 640.6
RMSD between 149 pruned atom pairs is 0.662 angstroms; (across all 252 pairs:
29.525)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 706.4
RMSD between 10 pruned atom pairs is 1.511 angstroms; (across all 254 pairs:
29.647)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 702.4
RMSD between 127 pruned atom pairs is 0.613 angstroms; (across all 251 pairs:
36.013)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 647.9
RMSD between 142 pruned atom pairs is 0.759 angstroms; (across all 242 pairs:
33.358)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 707.1
RMSD between 148 pruned atom pairs is 0.716 angstroms; (across all 253 pairs:
23.904)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 6xo4.pdb, chain C
(#5), sequence alignment score = 441.5
RMSD between 91 pruned atom pairs is 1.178 angstroms; (across all 150 pairs:
2.235)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 1vcp.pdb, chain C
(#7), sequence alignment score = 506.2
RMSD between 144 pruned atom pairs is 0.683 angstroms; (across all 149 pairs:
0.855)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 2yew.pdb, chain G
(#8), sequence alignment score = 461.4
RMSD between 55 pruned atom pairs is 1.242 angstroms; (across all 171 pairs:
7.961)
> color #20 #55aa00ff
> color #20 #00aa7fff
> color #20 #00b182ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> hide #20 models
> show #20 models
> hide #20 models
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 19/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select clear
Drag select of 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #19/A:45
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #19/A:198
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> ui mousemode right select
> select #19/A:198
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right select
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:190
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #19/A:189
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:184
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #19/A:191
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #19/A:190
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #19/A:184
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
Drag select of 2 residues
> select #19/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> show #18 models
> hide #18 models
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:190
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide #19 models
> show #20 models
Drag select of 1 atoms, 5 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #20/A:112
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
Alignment identifier is 20/A
> style sel stick
Changed 22 atom styles
> show sel atoms
Drag select of 1 bonds
> ui mousemode right translate
> ui mousemode right select
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:115
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:115
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #20/A:227
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:227
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:177
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:170
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
Drag select of 4 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:165
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #20/A:164
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #20/A:165
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
Drag select of 12 atoms, 40 residues, 8 bonds
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:144
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel orange
> style sel stick
Changed 11 atom styles
> show sel atoms
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:141
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel gray
> style sel stick
Changed 19 atom styles
> show sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Fri Jun 9 15:09:21 2023 ———
opened ChimeraX session
> hide #20 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Highlands J. virus Alphafold.pdb"
Chain information for Highlands J. virus Alphafold.pdb #21
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-20#!5,7-8 to #21
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 Highlands J. virus Alphafold.pdb, chain A (#21) with 3j2w.pdb,
chain I (#2), sequence alignment score = 534.6
RMSD between 147 pruned atom pairs is 0.672 angstroms; (across all 149 pairs:
0.755)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 1kxf.pdb,
chain A (#3), sequence alignment score = 584.9
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 158 pairs:
2.143)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 7sfu.pdb,
chain F (#4), sequence alignment score = 704.2
RMSD between 148 pruned atom pairs is 0.808 angstroms; (across all 162 pairs:
2.057)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 4agk.pdb,
chain A (#6), sequence alignment score = 563.1
RMSD between 150 pruned atom pairs is 0.643 angstroms; (across all 151 pairs:
0.671)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 7ko8.pdb,
chain G (#9), sequence alignment score = 593.5
RMSD between 134 pruned atom pairs is 1.109 angstroms; (across all 152 pairs:
1.587)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 804.8
RMSD between 148 pruned atom pairs is 0.558 angstroms; (across all 257 pairs:
26.440)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
818.8
RMSD between 151 pruned atom pairs is 0.625 angstroms; (across all 258 pairs:
21.384)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
996.4
RMSD between 163 pruned atom pairs is 0.346 angstroms; (across all 254 pairs:
15.033)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 539.8
RMSD between 132 pruned atom pairs is 0.906 angstroms; (across all 256 pairs:
30.694)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
1232.6
RMSD between 164 pruned atom pairs is 0.338 angstroms; (across all 259 pairs:
25.527)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 774.7
RMSD between 147 pruned atom pairs is 0.592 angstroms; (across all 251 pairs:
32.099)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Everglades
virus Alphafold.pdb, chain A (#16), sequence alignment score = 996.4
RMSD between 163 pruned atom pairs is 0.346 angstroms; (across all 254 pairs:
15.031)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 830.6
RMSD between 151 pruned atom pairs is 0.547 angstroms; (across all 256 pairs:
26.017)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 698.7
RMSD between 151 pruned atom pairs is 0.680 angstroms; (across all 248 pairs:
24.738)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1000.3
RMSD between 159 pruned atom pairs is 0.253 angstroms; (across all 255 pairs:
39.413)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 734.7
RMSD between 151 pruned atom pairs is 0.665 angstroms; (across all 244 pairs:
36.300)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 6xo4.pdb,
chain C (#5), sequence alignment score = 922.1
RMSD between 103 pruned atom pairs is 1.185 angstroms; (across all 151 pairs:
2.034)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 1vcp.pdb,
chain C (#7), sequence alignment score = 566.4
RMSD between 147 pruned atom pairs is 0.527 angstroms; (across all 149 pairs:
0.665)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 2yew.pdb,
chain G (#8), sequence alignment score = 540.8
RMSD between 53 pruned atom pairs is 1.232 angstroms; (across all 169 pairs:
7.986)
> color #21 #00aaffff
> color #21 #007cbaff
> select add #20
3966 atoms, 4011 bonds, 255 residues, 1 model selected
> select subtract #20
Nothing selected
> show #20 models
> hide #20 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Mon Jun 12 10:47:51 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel red
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 2/I
Alignment identifier is 2/I
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 21/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel orange
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #21/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> style sel stick
Changed 17 atom styles
> show sel atoms
Drag select of 8 atoms, 6 bonds
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #21/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel magenta
Drag select of 1 atoms, 9 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #21/A:175
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #21/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
Drag select of 2 residues
> select clear
[Repeated 3 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select clear
> select #21/A:148
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
Drag select of 6 residues
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select clear
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Mon Jun 12 13:04:04 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/prediction Madariaga virus.zip"
Unrecognized file suffix '.zip'
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Madariaga virus Alpha Fold.pdb"
Chain information for Madariaga virus Alpha Fold.pdb #22
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-21#!5,7-8 to #22
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 Madariaga virus Alpha Fold.pdb, chain A (#22) with 3j2w.pdb, chain
I (#2), sequence alignment score = 522
RMSD between 147 pruned atom pairs is 0.696 angstroms; (across all 149 pairs:
0.789)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 1kxf.pdb, chain
A (#3), sequence alignment score = 569.7
RMSD between 150 pruned atom pairs is 0.715 angstroms; (across all 158 pairs:
2.187)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 7sfu.pdb, chain
F (#4), sequence alignment score = 693.9
RMSD between 145 pruned atom pairs is 0.763 angstroms; (across all 162 pairs:
2.000)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 4agk.pdb, chain
A (#6), sequence alignment score = 550.5
RMSD between 150 pruned atom pairs is 0.691 angstroms; (across all 151 pairs:
0.721)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 7ko8.pdb, chain
G (#9), sequence alignment score = 589.5
RMSD between 133 pruned atom pairs is 1.135 angstroms; (across all 152 pairs:
1.607)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 785.6
RMSD between 150 pruned atom pairs is 0.551 angstroms; (across all 253 pairs:
30.619)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
784.8
RMSD between 149 pruned atom pairs is 0.602 angstroms; (across all 253 pairs:
31.010)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
991.5
RMSD between 147 pruned atom pairs is 0.277 angstroms; (across all 256 pairs:
36.174)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 557.2
RMSD between 107 pruned atom pairs is 0.830 angstroms; (across all 260 pairs:
49.521)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
1201.4
RMSD between 171 pruned atom pairs is 0.328 angstroms; (across all 259 pairs:
11.288)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 767.1
RMSD between 148 pruned atom pairs is 0.604 angstroms; (across all 253 pairs:
21.396)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 991.5
RMSD between 147 pruned atom pairs is 0.278 angstroms; (across all 256 pairs:
36.175)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 810.1
RMSD between 150 pruned atom pairs is 0.536 angstroms; (across all 249 pairs:
25.607)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 679.6
RMSD between 84 pruned atom pairs is 0.443 angstroms; (across all 250 pairs:
38.023)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 996.6
RMSD between 158 pruned atom pairs is 0.330 angstroms; (across all 257 pairs:
38.933)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 719.3
RMSD between 148 pruned atom pairs is 0.691 angstroms; (across all 243 pairs:
28.968)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Highlands J.
virus Alphafold.pdb, chain A (#21), sequence alignment score = 1253.2
RMSD between 119 pruned atom pairs is 0.235 angstroms; (across all 259 pairs:
32.666)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 6xo4.pdb, chain
C (#5), sequence alignment score = 1014.1
RMSD between 100 pruned atom pairs is 1.163 angstroms; (across all 151 pairs:
2.109)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 1vcp.pdb, chain
C (#7), sequence alignment score = 555.2
RMSD between 147 pruned atom pairs is 0.560 angstroms; (across all 149 pairs:
0.708)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 2yew.pdb, chain
G (#8), sequence alignment score = 534.1
RMSD between 54 pruned atom pairs is 1.237 angstroms; (across all 171 pairs:
10.062)
> hide #21 models
> show #21 models
> hide #22 models
> show #22 models
> hide #21 models
> color #22 #ff5500ff
> color #22 #eb4e00ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:118
19 atoms, 18 bonds, 1 residue, 1 model selected
Alignment identifier is 22/A
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> style sel stick
Changed 17 atom styles
> show sel atoms
> hide sel atoms
> style sel stick
Changed 17 atom styles
> show sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> hide sel atoms
> show sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel magenta
> ui mousemode right translate
> color #22 #ffaa7fff
> color #22 #ee9e77ff
> color #22 #ffaa00ff
> color #22 #cc8800ff
> color #22 #b37700ff
> color #22 #b57900ff
> color #22 #ce8900ff
> color #22 #ff5500ff
> ui mousemode right select
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 13 11:14:29 2023 ———
opened ChimeraX session
> select #22/A:1-30
505 atoms, 519 bonds, 30 residues, 1 model selected
> select #22/A:1-30
505 atoms, 519 bonds, 30 residues, 1 model selected
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #22/A:170
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #22/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 5 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> style sel stick
Changed 17 atom styles
> show sel atoms
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #22/A:149
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #22/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
Drag select of 3 residues, 2 atoms, 4 bonds
> select #22/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 13 12:23:11 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Mosso das Pedras virus AlphaFold.pdb"
Chain information for Mosso das Pedras virus AlphaFold.pdb #23
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-22#!5,7-8 to #23
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 Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 3j2w.pdb,
chain I (#2), sequence alignment score = 525
RMSD between 147 pruned atom pairs is 0.747 angstroms; (across all 149 pairs:
0.843)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 1kxf.pdb,
chain A (#3), sequence alignment score = 555.1
RMSD between 150 pruned atom pairs is 0.697 angstroms; (across all 158 pairs:
2.182)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 7sfu.pdb,
chain F (#4), sequence alignment score = 774.4
RMSD between 146 pruned atom pairs is 0.748 angstroms; (across all 162 pairs:
2.048)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 4agk.pdb,
chain A (#6), sequence alignment score = 564
RMSD between 151 pruned atom pairs is 0.736 angstroms; (across all 151 pairs:
0.736)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 7ko8.pdb,
chain G (#9), sequence alignment score = 530.6
RMSD between 138 pruned atom pairs is 1.162 angstroms; (across all 152 pairs:
1.566)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 796.6
RMSD between 151 pruned atom pairs is 0.563 angstroms; (across all 261 pairs:
34.344)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
791.9
RMSD between 135 pruned atom pairs is 0.567 angstroms; (across all 263 pairs:
37.641)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1181.5
RMSD between 13 pruned atom pairs is 1.031 angstroms; (across all 272 pairs:
39.100)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 560.8
RMSD between 25 pruned atom pairs is 0.636 angstroms; (across all 270 pairs:
41.007)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
979.8
RMSD between 164 pruned atom pairs is 0.325 angstroms; (across all 255 pairs:
31.044)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Ndumu
virus Alphafold.pdb, chain A (#15), sequence alignment score = 808.2
RMSD between 149 pruned atom pairs is 0.627 angstroms; (across all 267 pairs:
30.210)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Everglades
virus Alphafold.pdb, chain A (#16), sequence alignment score = 1181.5
RMSD between 13 pruned atom pairs is 1.030 angstroms; (across all 272 pairs:
39.103)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Bebaru
virus Alphafold.pdb, chain A (#17), sequence alignment score = 796.3
RMSD between 147 pruned atom pairs is 0.540 angstroms; (across all 258 pairs:
32.949)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Caaingua
virus AlphaFold.pdb, chain A (#18), sequence alignment score = 669.3
RMSD between 143 pruned atom pairs is 0.659 angstroms; (across all 254 pairs:
36.135)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Cabassou
virus Alphafold.pdb, chain A (#19), sequence alignment score = 1176
RMSD between 165 pruned atom pairs is 0.262 angstroms; (across all 274 pairs:
29.984)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Eilat
virus Alphafold.pdb, chain A (#20), sequence alignment score = 704.1
RMSD between 148 pruned atom pairs is 0.693 angstroms; (across all 253 pairs:
13.728)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Highlands
J. virus Alphafold.pdb, chain A (#21), sequence alignment score = 962.3
RMSD between 12 pruned atom pairs is 1.277 angstroms; (across all 255 pairs:
27.902)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Madariaga
virus Alpha Fold.pdb, chain A (#22), sequence alignment score = 976.4
RMSD between 163 pruned atom pairs is 0.314 angstroms; (across all 257 pairs:
25.593)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 6xo4.pdb,
chain C (#5), sequence alignment score = 680.4
RMSD between 103 pruned atom pairs is 1.187 angstroms; (across all 151 pairs:
2.065)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 1vcp.pdb,
chain C (#7), sequence alignment score = 558.9
RMSD between 147 pruned atom pairs is 0.584 angstroms; (across all 149 pairs:
0.736)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 2yew.pdb,
chain G (#8), sequence alignment score = 499.1
RMSD between 55 pruned atom pairs is 1.261 angstroms; (across all 170 pairs:
9.233)
> hide #22 models
> select add #22
4167 atoms, 4228 bonds, 261 residues, 1 model selected
> select subtract #22
Nothing selected
> color #23 #aaaa7fff
> color #23 #999972ff
> color #23 #94946eff
> color #23 #9e9e76ff
> color #23 #a3a379ff
> color #23 #a5a57bff
> color #23 #a1a178ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:137
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
Alignment identifier is 23/A
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:139
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:251
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:189
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:168
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #23/A:165
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #23/A:168
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #23/A:165
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
[Repeated 1 time(s)]
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:137
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #23/A:139
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #23/A:251
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:189
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #23/A:168@CA
1 atom, 1 residue, 1 model selected
> select #23/A:165
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 14 15:40:04 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Southern Elephant Seal virus AlphaFold.pdb"
Chain information for Southern Elephant Seal virus AlphaFold.pdb #24
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-23#!5,7-8 to #24
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 Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
3j2w.pdb, chain I (#2), sequence alignment score = 595.1
RMSD between 149 pruned atom pairs is 0.700 angstroms; (across all 149 pairs:
0.700)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
1kxf.pdb, chain A (#3), sequence alignment score = 543.6
RMSD between 147 pruned atom pairs is 0.771 angstroms; (across all 157 pairs:
1.959)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
7sfu.pdb, chain I (#4), sequence alignment score = 577.8
RMSD between 143 pruned atom pairs is 0.786 angstroms; (across all 161 pairs:
2.477)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
4agk.pdb, chain A (#6), sequence alignment score = 575.4
RMSD between 147 pruned atom pairs is 0.663 angstroms; (across all 150 pairs:
0.772)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
7ko8.pdb, chain D (#9), sequence alignment score = 657.3
RMSD between 133 pruned atom pairs is 1.065 angstroms; (across all 152 pairs:
1.706)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
AlphFold Colaboratory Ross River.pdb, chain A (#10), sequence alignment score
= 914
RMSD between 154 pruned atom pairs is 0.396 angstroms; (across all 251 pairs:
23.072)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
AlphaFold Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment
score = 910.1
RMSD between 156 pruned atom pairs is 0.463 angstroms; (across all 251 pairs:
24.684)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
AlphaFold Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment
score = 745.1
RMSD between 147 pruned atom pairs is 0.547 angstroms; (across all 258 pairs:
29.865)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Alpha Fold Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence
alignment score = 561.1
RMSD between 132 pruned atom pairs is 0.772 angstroms; (across all 265 pairs:
33.702)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Alpha Fold Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence
alignment score = 747.2
RMSD between 150 pruned atom pairs is 0.471 angstroms; (across all 258 pairs:
22.727)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Ndumu virus Alphafold.pdb, chain A (#15), sequence alignment score = 876.2
RMSD between 153 pruned atom pairs is 0.454 angstroms; (across all 260 pairs:
16.995)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Everglades virus Alphafold.pdb, chain A (#16), sequence alignment score =
745.1
RMSD between 147 pruned atom pairs is 0.547 angstroms; (across all 258 pairs:
29.865)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Bebaru virus Alphafold.pdb, chain A (#17), sequence alignment score = 885.6
RMSD between 154 pruned atom pairs is 0.323 angstroms; (across all 250 pairs:
25.775)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Caaingua virus AlphaFold.pdb, chain A (#18), sequence alignment score = 686.5
RMSD between 101 pruned atom pairs is 0.541 angstroms; (across all 257 pairs:
34.122)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Cabassou virus Alphafold.pdb, chain A (#19), sequence alignment score = 746.3
RMSD between 5 pruned atom pairs is 0.781 angstroms; (across all 261 pairs:
39.736)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Eilat virus Alphafold.pdb, chain A (#20), sequence alignment score = 688.6
RMSD between 154 pruned atom pairs is 0.690 angstroms; (across all 238 pairs:
27.995)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Highlands J. virus Alphafold.pdb, chain A (#21), sequence alignment score =
761.8
RMSD between 150 pruned atom pairs is 0.515 angstroms; (across all 252 pairs:
24.621)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Madariaga virus Alpha Fold.pdb, chain A (#22), sequence alignment score =
744.9
RMSD between 150 pruned atom pairs is 0.532 angstroms; (across all 254 pairs:
26.232)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Mosso das Pedras virus AlphaFold.pdb, chain A (#23), sequence alignment score
= 761.8
RMSD between 150 pruned atom pairs is 0.559 angstroms; (across all 260 pairs:
36.762)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
6xo4.pdb, chain C (#5), sequence alignment score = 496.9
RMSD between 101 pruned atom pairs is 1.204 angstroms; (across all 150 pairs:
2.038)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
1vcp.pdb, chain C (#7), sequence alignment score = 628.6
RMSD between 149 pruned atom pairs is 0.536 angstroms; (across all 149 pairs:
0.536)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
2yew.pdb, chain G (#8), sequence alignment score = 628.5
RMSD between 56 pruned atom pairs is 1.258 angstroms; (across all 171 pairs:
5.304)
> hide #23 models
> select add #23
4449 atoms, 4504 bonds, 279 residues, 1 model selected
> select subtract #23
Nothing selected
> show #23 models
> hide #23 models
> color #24 #555500ff
> color #24 black
> color #24 #550000ff
> color #24 #aaaa7fff
> color #24 #aaaa00ff
> color #24 #555500ff
> color #24 #6c6c00ff
> color #24 #7f7f00ff
> color #24 #666600ff
> color #24 #aaaa7fff
> color #24 #757557ff
> color #24 #707053ff
> color #24 #68684dff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 24/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:129
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:191
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:184
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:179
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> set bgColor black
> set bgColor white
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:158
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:155
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:129
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:129
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:184
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:179
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:158
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:155
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jun 15 13:33:00 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Mucambo virus AlphaFold.pdb"
Chain information for Mucambo virus AlphaFold.pdb #25
---
Chain | Description
A | No description available
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #2-4,6,9-24#!5,7-8 to #25
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 Mucambo virus AlphaFold.pdb, chain A (#25) with 3j2w.pdb, chain I
(#2), sequence alignment score = 529.5
RMSD between 148 pruned atom pairs is 0.719 angstroms; (across all 149 pairs:
0.763)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1kxf.pdb, chain A
(#3), sequence alignment score = 561.4
RMSD between 150 pruned atom pairs is 0.671 angstroms; (across all 158 pairs:
1.955)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7sfu.pdb, chain F
(#4), sequence alignment score = 791.4
RMSD between 148 pruned atom pairs is 0.732 angstroms; (across all 162 pairs:
2.042)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 4agk.pdb, chain A
(#6), sequence alignment score = 559.3
RMSD between 150 pruned atom pairs is 0.713 angstroms; (across all 151 pairs:
0.739)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7ko8.pdb, chain G
(#9), sequence alignment score = 568.5
RMSD between 129 pruned atom pairs is 1.055 angstroms; (across all 152 pairs:
1.523)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797.8
RMSD between 148 pruned atom pairs is 0.605 angstroms; (across all 261 pairs:
27.742)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
775.8
RMSD between 151 pruned atom pairs is 0.653 angstroms; (across all 262 pairs:
24.551)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1240.9
RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
24.227)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 569.6
RMSD between 132 pruned atom pairs is 0.920 angstroms; (across all 267 pairs:
15.674)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
974.5
RMSD between 155 pruned atom pairs is 0.353 angstroms; (across all 255 pairs:
37.484)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 830.2
RMSD between 137 pruned atom pairs is 0.550 angstroms; (across all 267 pairs:
41.448)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1240.9
RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
24.231)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 795.9
RMSD between 146 pruned atom pairs is 0.593 angstroms; (across all 258 pairs:
29.444)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 680.9
RMSD between 130 pruned atom pairs is 0.713 angstroms; (across all 261 pairs:
27.031)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1287
RMSD between 13 pruned atom pairs is 0.146 angstroms; (across all 274 pairs:
25.862)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 686.9
RMSD between 11 pruned atom pairs is 1.306 angstroms; (across all 254 pairs:
32.777)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 984.3
RMSD between 156 pruned atom pairs is 0.293 angstroms; (across all 255 pairs:
25.661)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 988.9
RMSD between 135 pruned atom pairs is 0.294 angstroms; (across all 257 pairs:
42.924)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1167.1
RMSD between 20 pruned atom pairs is 1.361 angstroms; (across all 274 pairs:
38.794)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 764.6
RMSD between 147 pruned atom pairs is 0.552 angstroms; (across all 262 pairs:
31.695)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 6xo4.pdb, chain C
(#5), sequence alignment score = 701.7
RMSD between 104 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
2.018)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1vcp.pdb, chain C
(#7), sequence alignment score = 563.4
RMSD between 147 pruned atom pairs is 0.576 angstroms; (across all 149 pairs:
0.688)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 2yew.pdb, chain G
(#8), sequence alignment score = 508.8
RMSD between 54 pruned atom pairs is 1.257 angstroms; (across all 171 pairs:
5.382)
> hide #24 models
> color #25 #ff557fff
> color #25 #f4517aff
> color #25 #e64d73ff
> color #25 #da496dff
> color #25 #e34c72ff
> color #25 #f8537cff
> color #25 #ff007fff
> color #25 #ff557fff
> color #25 #be3f5fff
> color #25 #e14b71ff
> color #25 #ef5078ff
> color #25 #ffaaffff
> color #25 #ff557fff
> color #25 #ff679cff
> color #25 #ff82baff
> color #25 #ff97dbff
> color #25 #ff86c7ff
> color #25 #ff81d9ff
> color #25 #ff7bcaff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 25/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
Alignment identifier is 2/I
> select #25/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> style sel stick
Changed 15 atom styles
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #25/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:164
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #25/A:164
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> hide sel atoms
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel orange
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Fri Jun 16 15:07:56 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Onyong-nyong virus AlphaFold.pdb"
Chain information for Onyong-nyong virus AlphaFold.pdb #26
---
Chain | Description
A | No description available
> select add #25
4421 atoms, 4479 bonds, 275 residues, 1 model selected
> hide #25 models
> select subtract #25
Nothing selected
> ui tool show Matchmaker
> matchmaker #2-4,6,9-25#!5,7-8 to #26
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 Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 3j2w.pdb,
chain I (#2), sequence alignment score = 693.1
RMSD between 145 pruned atom pairs is 0.692 angstroms; (across all 149 pairs:
0.928)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 1kxf.pdb,
chain A (#3), sequence alignment score = 550.8
RMSD between 145 pruned atom pairs is 0.764 angstroms; (across all 157 pairs:
1.974)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 7sfu.pdb,
chain I (#4), sequence alignment score = 571.5
RMSD between 141 pruned atom pairs is 0.808 angstroms; (across all 161 pairs:
2.633)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 4agk.pdb,
chain A (#6), sequence alignment score = 554.2
RMSD between 145 pruned atom pairs is 0.645 angstroms; (across all 150 pairs:
0.967)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 7ko8.pdb,
chain D (#9), sequence alignment score = 789.3
RMSD between 135 pruned atom pairs is 1.096 angstroms; (across all 152 pairs:
1.761)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 1011.1
RMSD between 161 pruned atom pairs is 0.532 angstroms; (across all 259 pairs:
26.498)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
990.1
RMSD between 166 pruned atom pairs is 0.493 angstroms; (across all 260 pairs:
12.774)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
745.5
RMSD between 148 pruned atom pairs is 0.549 angstroms; (across all 253 pairs:
25.234)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 521
RMSD between 129 pruned atom pairs is 0.751 angstroms; (across all 253 pairs:
34.504)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
761.6
RMSD between 148 pruned atom pairs is 0.466 angstroms; (across all 257 pairs:
22.771)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 883
RMSD between 153 pruned atom pairs is 0.307 angstroms; (across all 255 pairs:
28.508)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Everglades
virus Alphafold.pdb, chain A (#16), sequence alignment score = 745.5
RMSD between 148 pruned atom pairs is 0.549 angstroms; (across all 253 pairs:
25.235)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 1010.1
RMSD between 168 pruned atom pairs is 0.393 angstroms; (across all 256 pairs:
13.447)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 714.7
RMSD between 131 pruned atom pairs is 0.592 angstroms; (across all 248 pairs:
30.461)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 737.3
RMSD between 12 pruned atom pairs is 0.503 angstroms; (across all 255 pairs:
37.820)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 665.2
RMSD between 146 pruned atom pairs is 0.659 angstroms; (across all 248 pairs:
33.950)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Highlands J.
virus Alphafold.pdb, chain A (#21), sequence alignment score = 778.5
RMSD between 148 pruned atom pairs is 0.516 angstroms; (across all 257 pairs:
23.355)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Madariaga
virus Alpha Fold.pdb, chain A (#22), sequence alignment score = 752.9
RMSD between 148 pruned atom pairs is 0.535 angstroms; (across all 255 pairs:
24.725)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Mosso das
Pedras virus AlphaFold.pdb, chain A (#23), sequence alignment score = 734.5
RMSD between 148 pruned atom pairs is 0.559 angstroms; (across all 255 pairs:
31.406)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Southern
Elephant Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score =
881.1
RMSD between 151 pruned atom pairs is 0.324 angstroms; (across all 248 pairs:
23.757)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 737.4
RMSD between 147 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
32.618)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 6xo4.pdb,
chain C (#5), sequence alignment score = 495.9
RMSD between 99 pruned atom pairs is 1.202 angstroms; (across all 150 pairs:
2.096)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 1vcp.pdb,
chain C (#7), sequence alignment score = 720.3
RMSD between 145 pruned atom pairs is 0.504 angstroms; (across all 149 pairs:
0.805)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 2yew.pdb,
chain G (#8), sequence alignment score = 682.7
RMSD between 54 pruned atom pairs is 1.188 angstroms; (across all 171 pairs:
9.494)
> color #26 #55557fff
> color #26 #67679aff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Sat Jun 17 16:13:53 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:119
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 26/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #26/A:119
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:119
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:121
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #26/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #26/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #26/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:150
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:150
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #26/A:147
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
Drag select of 9 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:237
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Pixuna virus AlphaFold.pdb"
Chain information for Pixuna virus AlphaFold.pdb #27
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-26#!5,7-8 to #27
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 Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
(#2), sequence alignment score = 521
RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
0.820)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
(#3), sequence alignment score = 570.9
RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
1.897)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
(#4), sequence alignment score = 784.4
RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
2.028)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
(#6), sequence alignment score = 557.4
RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
0.770)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
(#9), sequence alignment score = 555.5
RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
1.573)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
31.415)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
757.5
RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
32.104)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 600.2
RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
45.726)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
931.2
RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
24.821)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
16.320)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
26.677)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
31.729)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
39.936)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
22.031)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
36.964)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
20.809)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
22.847)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
24.355)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
36.851)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
28.486)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
(#5), sequence alignment score = 676.1
RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
2.057)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
(#7), sequence alignment score = 554.2
RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
0.747)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
(#8), sequence alignment score = 518.2
RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
6.032)
> hide #26 models
> color #27 #ff5500ff
> color #27 #aa007fff
> color #27 #a7007dff
> color #27 #a10079ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:133
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 27/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:135
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:135
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #27/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #27/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel cartoons
> style sel stick
Changed 15 atom styles
> show sel cartoons
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #27/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #27/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #27/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #27/A:161
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> ui mousemode right translate
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jun 19 14:50:40 2023 ———
opened ChimeraX session
> hide #27 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/RioNegro virus AlphaFold.pdb"
Chain information for RioNegro virus AlphaFold.pdb #28
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-27#!5,7-8 to #28
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 RioNegro virus AlphaFold.pdb, chain A (#28) with 3j2w.pdb, chain I
(#2), sequence alignment score = 527.8
RMSD between 147 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
0.789)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1kxf.pdb, chain A
(#3), sequence alignment score = 566.3
RMSD between 150 pruned atom pairs is 0.681 angstroms; (across all 158 pairs:
1.969)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7sfu.pdb, chain F
(#4), sequence alignment score = 787.7
RMSD between 147 pruned atom pairs is 0.760 angstroms; (across all 162 pairs:
2.092)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 4agk.pdb, chain A
(#6), sequence alignment score = 560.5
RMSD between 150 pruned atom pairs is 0.690 angstroms; (across all 151 pairs:
0.725)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7ko8.pdb, chain G
(#9), sequence alignment score = 543.1
RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 152 pairs:
1.558)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 810.7
RMSD between 149 pruned atom pairs is 0.612 angstroms; (across all 260 pairs:
26.607)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
814.9
RMSD between 150 pruned atom pairs is 0.655 angstroms; (across all 262 pairs:
19.991)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1186.9
RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
22.699)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 570
RMSD between 129 pruned atom pairs is 0.916 angstroms; (across all 274 pairs:
14.045)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
971.5
RMSD between 153 pruned atom pairs is 0.346 angstroms; (across all 255 pairs:
34.468)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 805.7
RMSD between 110 pruned atom pairs is 0.481 angstroms; (across all 266 pairs:
39.937)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1186.9
RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
22.702)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 803.1
RMSD between 150 pruned atom pairs is 0.602 angstroms; (across all 255 pairs:
27.125)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 690.7
RMSD between 142 pruned atom pairs is 0.666 angstroms; (across all 260 pairs:
24.522)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1172
RMSD between 14 pruned atom pairs is 1.444 angstroms; (across all 275 pairs:
24.262)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 686
RMSD between 13 pruned atom pairs is 1.555 angstroms; (across all 251 pairs:
32.745)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 974.3
RMSD between 154 pruned atom pairs is 0.271 angstroms; (across all 255 pairs:
21.224)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 972.7
RMSD between 133 pruned atom pairs is 0.245 angstroms; (across all 257 pairs:
43.677)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1260.3
RMSD between 23 pruned atom pairs is 1.168 angstroms; (across all 278 pairs:
34.771)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 777
RMSD between 148 pruned atom pairs is 0.570 angstroms; (across all 265 pairs:
31.463)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1175.9
RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
6.018)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 731.4
RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 255 pairs:
29.382)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Pixuna virus
AlphaFold.pdb, chain A (#27), sequence alignment score = 1160.6
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
35.129)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 6xo4.pdb, chain C
(#5), sequence alignment score = 670.2
RMSD between 100 pruned atom pairs is 1.164 angstroms; (across all 151 pairs:
2.092)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1vcp.pdb, chain C
(#7), sequence alignment score = 561.7
RMSD between 146 pruned atom pairs is 0.547 angstroms; (across all 149 pairs:
0.720)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 2yew.pdb, chain G
(#8), sequence alignment score = 489.8
RMSD between 57 pruned atom pairs is 1.297 angstroms; (across all 171 pairs:
6.267)
> color #28 #55557fff
> color #28 #55007fff
> color #28 black
> color #28 #545454ff
> color #28 #868686ff
> color #28 #212121ff
> color #28 #414141ff
> color #28 #4c4c4cff
> color #28 #55557fff
> color #28 #4e4e75ff
> color #28 #414161ff
> color #28 black
> color #28 #2c2c2cff
> color #28 #474747ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 13:21:24 2023 ———
opened ChimeraX session
Alignment identifier is 27/A
> select add #27
4429 atoms, 4485 bonds, 275 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #28
4421 atoms, 4477 bonds, 278 residues, 1 model selected
Alignment identifier is 28/A
> select subtract #28
Nothing selected
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:136
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> hide sel atoms
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:138
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:250
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:200
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:193
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:193
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:188
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:167
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #28/A:164
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> hide #28 models
> show #28 models
> hide #28 models
> show #27 models
> select add #28
4421 atoms, 4477 bonds, 278 residues, 1 model selected
> select subtract #28
Nothing selected
> show #26 models
> hide #26 models
> hide #27 models
> show #27 models
> ui tool show Matchmaker
> matchmaker #2-4,6,9-26,28#!5,7-8 to #27
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 Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
(#2), sequence alignment score = 521
RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
0.820)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
(#3), sequence alignment score = 570.9
RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
1.897)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
(#4), sequence alignment score = 784.4
RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
2.028)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
(#6), sequence alignment score = 557.4
RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
0.770)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
(#9), sequence alignment score = 555.5
RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
1.573)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
31.415)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
757.5
RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
32.104)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 600.2
RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
45.726)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
931.2
RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
24.821)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
16.320)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
26.677)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
31.729)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
39.936)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
22.031)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
36.964)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
20.809)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
22.847)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
24.355)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
36.851)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
28.486)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with RioNegro virus
AlphaFold.pdb, chain A (#28), sequence alignment score = 1160.6
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
35.129)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
(#5), sequence alignment score = 676.1
RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
2.057)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
(#7), sequence alignment score = 554.2
RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
0.747)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
(#8), sequence alignment score = 518.2
RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
6.032)
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 13:33:55 2023 ———
opened ChimeraX session
> hide #27 models
> show #28 models
> show #26 models
> hide #26 models
> ui tool show Matchmaker
> matchmaker #2-4,6,9-27#!5,7-8 to #28
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 RioNegro virus AlphaFold.pdb, chain A (#28) with 3j2w.pdb, chain I
(#2), sequence alignment score = 527.8
RMSD between 147 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
0.789)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1kxf.pdb, chain A
(#3), sequence alignment score = 566.3
RMSD between 150 pruned atom pairs is 0.681 angstroms; (across all 158 pairs:
1.969)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7sfu.pdb, chain F
(#4), sequence alignment score = 787.7
RMSD between 147 pruned atom pairs is 0.760 angstroms; (across all 162 pairs:
2.092)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 4agk.pdb, chain A
(#6), sequence alignment score = 560.5
RMSD between 150 pruned atom pairs is 0.690 angstroms; (across all 151 pairs:
0.725)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7ko8.pdb, chain G
(#9), sequence alignment score = 543.1
RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 152 pairs:
1.558)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 810.7
RMSD between 149 pruned atom pairs is 0.612 angstroms; (across all 260 pairs:
26.607)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
814.9
RMSD between 150 pruned atom pairs is 0.655 angstroms; (across all 262 pairs:
19.991)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1186.9
RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
22.699)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 570
RMSD between 129 pruned atom pairs is 0.916 angstroms; (across all 274 pairs:
14.045)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
971.5
RMSD between 153 pruned atom pairs is 0.346 angstroms; (across all 255 pairs:
34.468)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 805.7
RMSD between 110 pruned atom pairs is 0.481 angstroms; (across all 266 pairs:
39.937)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1186.9
RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
22.702)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 803.1
RMSD between 150 pruned atom pairs is 0.602 angstroms; (across all 255 pairs:
27.125)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 690.7
RMSD between 142 pruned atom pairs is 0.666 angstroms; (across all 260 pairs:
24.522)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1172
RMSD between 14 pruned atom pairs is 1.444 angstroms; (across all 275 pairs:
24.262)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 686
RMSD between 13 pruned atom pairs is 1.555 angstroms; (across all 251 pairs:
32.745)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 974.3
RMSD between 154 pruned atom pairs is 0.271 angstroms; (across all 255 pairs:
21.224)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 972.7
RMSD between 133 pruned atom pairs is 0.245 angstroms; (across all 257 pairs:
43.677)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1260.3
RMSD between 23 pruned atom pairs is 1.168 angstroms; (across all 278 pairs:
34.771)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 777
RMSD between 148 pruned atom pairs is 0.570 angstroms; (across all 265 pairs:
31.463)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1175.9
RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
6.018)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 731.4
RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 255 pairs:
29.382)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Pixuna virus
AlphaFold.pdb, chain A (#27), sequence alignment score = 1160.6
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
35.129)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 6xo4.pdb, chain C
(#5), sequence alignment score = 670.2
RMSD between 100 pruned atom pairs is 1.164 angstroms; (across all 151 pairs:
2.092)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1vcp.pdb, chain C
(#7), sequence alignment score = 561.7
RMSD between 146 pruned atom pairs is 0.547 angstroms; (across all 149 pairs:
0.720)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 2yew.pdb, chain G
(#8), sequence alignment score = 489.8
RMSD between 57 pruned atom pairs is 1.297 angstroms; (across all 171 pairs:
6.267)
> show #26 models
> hide #26 models
> hide #28 models
> show #27 models
> ui tool show Matchmaker
> matchmaker #2-4,6,9-26,28#!5,7-8 to #27
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 Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
(#2), sequence alignment score = 521
RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
0.820)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
(#3), sequence alignment score = 570.9
RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
1.897)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
(#4), sequence alignment score = 784.4
RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
2.028)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
(#6), sequence alignment score = 557.4
RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
0.770)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
(#9), sequence alignment score = 555.5
RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
1.573)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
31.415)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
757.5
RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
32.104)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 600.2
RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
45.726)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
931.2
RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
24.821)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
16.320)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
26.677)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
31.729)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
39.936)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
22.031)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
36.964)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
20.809)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
22.847)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
24.355)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
36.851)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
28.486)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with RioNegro virus
AlphaFold.pdb, chain A (#28), sequence alignment score = 1160.6
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
35.129)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
(#5), sequence alignment score = 676.1
RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
2.057)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
(#7), sequence alignment score = 554.2
RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
0.747)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
(#8), sequence alignment score = 518.2
RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
6.032)
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> hide #27 models
> show #26 models
> hide #26 models
> show #26 models
> hide #26 models
> show #25 models
> show #24 models
> hide #24 models
> show #23 models
> hide #23 models
> ui tool show Matchmaker
> matchmaker #2-4,6,9-24,26-28#!5,7-8 to #25
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 Mucambo virus AlphaFold.pdb, chain A (#25) with 3j2w.pdb, chain I
(#2), sequence alignment score = 529.5
RMSD between 148 pruned atom pairs is 0.719 angstroms; (across all 149 pairs:
0.763)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1kxf.pdb, chain A
(#3), sequence alignment score = 561.4
RMSD between 150 pruned atom pairs is 0.671 angstroms; (across all 158 pairs:
1.955)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7sfu.pdb, chain F
(#4), sequence alignment score = 791.4
RMSD between 148 pruned atom pairs is 0.732 angstroms; (across all 162 pairs:
2.042)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 4agk.pdb, chain A
(#6), sequence alignment score = 559.3
RMSD between 150 pruned atom pairs is 0.713 angstroms; (across all 151 pairs:
0.739)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7ko8.pdb, chain G
(#9), sequence alignment score = 568.5
RMSD between 129 pruned atom pairs is 1.055 angstroms; (across all 152 pairs:
1.523)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797.8
RMSD between 148 pruned atom pairs is 0.605 angstroms; (across all 261 pairs:
27.742)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
775.8
RMSD between 151 pruned atom pairs is 0.653 angstroms; (across all 262 pairs:
24.551)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1240.9
RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
24.227)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 569.6
RMSD between 132 pruned atom pairs is 0.920 angstroms; (across all 267 pairs:
15.674)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
974.5
RMSD between 155 pruned atom pairs is 0.353 angstroms; (across all 255 pairs:
37.484)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 830.2
RMSD between 137 pruned atom pairs is 0.550 angstroms; (across all 267 pairs:
41.448)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1240.9
RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
24.231)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 795.9
RMSD between 146 pruned atom pairs is 0.593 angstroms; (across all 258 pairs:
29.444)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 680.9
RMSD between 130 pruned atom pairs is 0.713 angstroms; (across all 261 pairs:
27.031)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1287
RMSD between 13 pruned atom pairs is 0.146 angstroms; (across all 274 pairs:
25.862)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 686.9
RMSD between 11 pruned atom pairs is 1.306 angstroms; (across all 254 pairs:
32.777)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 984.3
RMSD between 156 pruned atom pairs is 0.293 angstroms; (across all 255 pairs:
25.661)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 988.9
RMSD between 135 pruned atom pairs is 0.294 angstroms; (across all 257 pairs:
42.924)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1167.1
RMSD between 20 pruned atom pairs is 1.361 angstroms; (across all 274 pairs:
38.794)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 764.6
RMSD between 147 pruned atom pairs is 0.552 angstroms; (across all 262 pairs:
31.695)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 737.4
RMSD between 147 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
32.618)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Pixuna virus
AlphaFold.pdb, chain A (#27), sequence alignment score = 1188.8
RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
36.851)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with RioNegro virus
AlphaFold.pdb, chain A (#28), sequence alignment score = 1175.9
RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
6.018)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 6xo4.pdb, chain C
(#5), sequence alignment score = 701.7
RMSD between 104 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
2.018)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1vcp.pdb, chain C
(#7), sequence alignment score = 563.4
RMSD between 147 pruned atom pairs is 0.576 angstroms; (across all 149 pairs:
0.688)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 2yew.pdb, chain G
(#8), sequence alignment score = 508.8
RMSD between 54 pruned atom pairs is 1.257 angstroms; (across all 171 pairs:
5.382)
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 13:41:59 2023 ———
opened ChimeraX session
> hide #25 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #27 models
> show #26 models
> hide #26 models
> show #25 models
> hide #25 models
> hide #27 models
> show #28 models
> show #26 models
> hide #26 models
> show #27 models
> hide #28 models
> ui tool show Matchmaker
> matchmaker #27 to #2
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 3j2w.pdb, chain I (#2) with Pixuna virus AlphaFold.pdb, chain A
(#27), sequence alignment score = 521
RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
0.820)
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #28 models
> show #26 models
> hide #28 models
> hide #26 models
> show #26 models
> hide #27 models
> show #25 models
> hide #26 models
> show #24 models
> hide #25 models
> show #13 models
> hide #24 models
> show #25 models
> show #26 models
> hide #26 models
> hide #25 models
> show #27 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> hide #27 models
> hide #13 models
> show #28 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 13:59:27 2023 ———
opened ChimeraX session
> show #27 models
> hide #27 models
> hide #28 models
> show #28 models
> hide #28 models
> show #27 models
> hide #27 models
> show #28 models
> show #26 models
> show #25 models
> hide #25 models
> hide #26 models
> hide #28 models
> show #28 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 14:01:06 2023 ———
opened ChimeraX session
> show #27 models
> hide #27 models
> show #26 models
> hide #26 models
> show #25 models
> hide #25 models
> hide #28 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Tonate virus AlphaFold.pdb"
Chain information for Tonate virus AlphaFold.pdb #29
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #29 to #2
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 3j2w.pdb, chain I (#2) with Tonate virus AlphaFold.pdb, chain A
(#29), sequence alignment score = 516.2
RMSD between 147 pruned atom pairs is 0.812 angstroms; (across all 149 pairs:
0.929)
> color #29 #555500ff
> color #29 #550000ff
> color #29 #0055ffff
> color #29 #0042c7ff
> color #29 #00007fff
> color #29 #0000a6ff
> color #29 #0000ecff
> color #29 #00007cff
> color #29 #200e7cff
> color #29 #27167cff
> color #29 #2e1e7cff
> color #29 #36287cff
> color #29 #40237cff
> color #29 #3b2e7cff
> color #29 #5240adff
> color #29 #3638adff
> color #29 #585cadff
> color #29 #4b54adff
> color #29 #333a76ff
> color #29 #404894ff
> color #29 #616ee1ff
> color #29 #434c9cff
> color #29 #3d458dff
> color #29 #394084ff
> color #29 #363d7dff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
Alignment identifier is 29/A
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #29/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #29/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #29/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #29/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> select #29/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> show #27 models
> hide #2 models
> show #2 models
> hide #27 models
> select add #29
4432 atoms, 4487 bonds, 275 residues, 1 model selected
> select subtract #29
Nothing selected
> hide #29 models
> show #17 models
> ui tool show Matchmaker
> matchmaker #17 to #2
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 3j2w.pdb, chain I (#2) with Bebaru virus Alphafold.pdb, chain A
(#17), sequence alignment score = 675.4
RMSD between 148 pruned atom pairs is 0.764 angstroms; (across all 149 pairs:
0.786)
> show #29 models
> hide #29 models
> show #14 models
> hide #17 models
> hide #14 models
> show #29 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 21 13:00:17 2023 ———
opened ChimeraX session
> ui tool show Registration
> hide #29 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Trocara virus AlphaFold.pdb"
Chain information for Trocara virus AlphaFold.pdb #30
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #30 to #2
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 3j2w.pdb, chain I (#2) with Trocara virus AlphaFold.pdb, chain A
(#30), sequence alignment score = 500.7
RMSD between 144 pruned atom pairs is 0.680 angstroms; (across all 149 pairs:
0.933)
> color #30 #550000ff
> color #30 #670000ff
> color #30 #740000ff
> color #30 #940000ff
> color #30 #750000ff
> color #30 #750b0bff
> color #30 #752616ff
> color #30 #752620ff
> color #30 #751414ff
> color #30 #750b0bff
> color #30 #b51212ff
> color #30 #620a0aff
> color #30 #810d0dff
> color #30 #8f0e0eff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 30/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 1 bonds
> select #30/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #30/A:236
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:236
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190@CA
1 atom, 1 residue, 1 model selected
> select #30/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #30/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> show #28 models
> hide #28 models
> show #28 models
> show #27 models
> hide #27 models
> hide #28 models
> select add #30
4192 atoms, 4243 bonds, 264 residues, 1 model selected
> select subtract #30
Nothing selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jun 22 13:48:19 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Una virus AlphaFold.pdb"
Chain information for Una virus AlphaFold.pdb #31
---
Chain | Description
A | No description available
> hide #30 models
> ui tool show Matchmaker
> matchmaker #31 to #2
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 3j2w.pdb, chain I (#2) with Una virus AlphaFold.pdb, chain A (#31),
sequence alignment score = 668.1
RMSD between 144 pruned atom pairs is 0.726 angstroms; (across all 149 pairs:
0.900)
> color #31 #ff557fff
> color #31 #ff007fff
> color #31 #55557fff
> color #31 #ff557fff
> color #31 #ff5580ff
> color #31 #ffaaffff
> color #31 #ff557fff
> color #31 #ff5a99ff
> color #31 #ff5ea4ff
> color #31 #ff67abff
> color #31 #ff69a2ff
> color #31 #ff5496ff
> color #31 #ff557fff
> color #31 #ff5892ff
> color #31 #ff4f8dff
> color #31 #ff52a6ff
> color #31 #ff54a1ff
> ui mousemode right select
Drag select of 2 atoms, 1 bonds
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 31/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 6 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 19 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #31/A:150
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> show #30 models
> hide #31 models
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:236
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide #30 models
> show #31 models
> ui mousemode right translate
> show #30 models
> show #29 models
> hide #29 models
> hide #30 models
> hide #31 models
> show #31 models
> select add #30
4192 atoms, 4243 bonds, 264 residues, 1 model selected
> select subtract #30
Nothing selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Fri Jun 23 14:27:32 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Whataroa virus AlphaFold.pdb"
Chain information for Whataroa virus AlphaFold.pdb #32
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #32 to #2
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 3j2w.pdb, chain I (#2) with Whataroa virus AlphaFold.pdb, chain A
(#32), sequence alignment score = 516.5
RMSD between 146 pruned atom pairs is 0.667 angstroms; (across all 149 pairs:
0.786)
> hide #31 models
> color #32 #ffaa7fff
> color #32 #ffaa00ff
> color #32 #ffff7fff
> color #32 yellow
> color #32 #ffcb0eff
> color #32 #ffcd07ff
> color #32 #ffca0cff
> color #32 #ffd711ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:123
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 32/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:126
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 2 atoms, 2 residues, 3 bonds
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:181
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> color #32 #ffec20ff
> color #32 #ffd70cff
> color #32 #ffff7fff
> color #32 #ffaa00ff
> color #32 #ffff7fff
> color #32 #ffff5cff
> color #32 #fcff4aff
> color #32 #ddff43ff
> color #32 #ffff38ff
> color #32 #ff9cd9ff
> color #32 #ffa7d2ff
> color #32 #ffa4d3ff
> color #32 #fcff39ff
> color #32 #ffef3aff
> style sel stick
Changed 14 atom styles
> hide sel atoms
> show sel atoms
> color sel orange
> ui mousemode right select
> select #32/A:123
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> select #32/A:126
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #32/A:123
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #32/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #32/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:152
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:152
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> hide sel atoms
> show sel atoms
> color sel gray
> select #32/A:155
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:155
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/AguaSalud alphavirus AlphaFold.pdb"
Chain information for AguaSalud alphavirus AlphaFold.pdb #33
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #33 to #2
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 3j2w.pdb, chain I (#2) with AguaSalud alphavirus AlphaFold.pdb,
chain A (#33), sequence alignment score = 497.5
RMSD between 147 pruned atom pairs is 0.696 angstroms; (across all 149 pairs:
0.798)
> hide #32 models
> select add #32
4214 atoms, 4273 bonds, 266 residues, 1 model selected
> select subtract #32
Nothing selected
> color #33 #56344dff
> color #33 #4e3256ff
> color #33 #562651ff
> color #33 #561b3cff
> color #33 #ffaaffff
> color #33 #f78affff
> color #33 #ff66f0ff
> color #33 #f352ffff
> color #33 #55ffffff
> color #33 #ffaaffff
> color #33 #ffb3feff
> color #33 #fcb0ffff
> color #33 #ffa1efff
> color #33 #ffb9e9ff
> color #33 #ffb2e7ff
> color #33 #ffaed8ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:123
11 atoms, 10 bonds, 1 residue, 1 model selected
Alignment identifier is 33/A
> select #33/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #33/A:123
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #33/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> set bgColor black
[Repeated 1 time(s)]
> set bgColor white
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:126
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #33/A:127
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #33/A:126
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> show #32 models
> select #32/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide #32 models
> select add #32
4214 atoms, 4273 bonds, 266 residues, 1 model selected
> select subtract #32
Nothing selected
> select #33/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190@CA
1 atom, 1 residue, 1 model selected
> select #33/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:181
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> style sel stick
Changed 24 atom styles
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:155
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #33/A:152
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> show #32 models
> hide #33 models
> show #33 models
> hide #32 models
> select add #33
4198 atoms, 4258 bonds, 266 residues, 1 model selected
> select subtract #33
Nothing selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
[Repeated 1 time(s)]
——— End of log from Mon Jun 26 10:11:19 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Comber alphavirus AlphaFold.pdb"
Chain information for Comber alphavirus AlphaFold.pdb #34
---
Chain | Description
A | No description available
> hide #33 models
> ui tool show Matchmaker
> matchmaker #34 to #2
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 3j2w.pdb, chain I (#2) with Comber alphavirus AlphaFold.pdb, chain
A (#34), sequence alignment score = 336.5
RMSD between 118 pruned atom pairs is 0.991 angstroms; (across all 144 pairs:
3.924)
> color #34 #cd7248ff
> color #34 #cd4a33ff
> color #34 #cd5647ff
> color #34 #cd7d44ff
> color #34 #bd733fff
> color #34 #b36d3cff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Harbor porpoise alphavirus AlphaFold.pdb"
Chain information for Harbor porpoise alphavirus AlphaFold.pdb #35
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #35 to #2
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 3j2w.pdb, chain I (#2) with Harbor porpoise alphavirus
AlphaFold.pdb, chain A (#35), sequence alignment score = 612.2
RMSD between 146 pruned atom pairs is 0.708 angstroms; (across all 149 pairs:
0.922)
> hide #34 models
> color #35 #ff557fff
> color #35 #ffff7fff
> color #35 yellow
> color #35 #ffff7fff
> color #35 #fff049ff
> color #35 #f6ff42ff
> color #35 #e0ff6eff
> color #35 #d3ff73ff
> color #35 #ddff61ff
> color #35 #cbea59ff
> color #35 #bcd953ff
> color #35 #bad94aff
> color #35 #c9d93cff
> color #35 #bdd92fff
> color #35 #c0d941ff
> color #35 #cad946ff
> color #35 #d1d93cff
> color #35 #bad931ff
> color #35 #d9d93fff
> color #35 #bfd93cff
> color #35 #d1d93cff
> color #35 #b7d93cff
> color #35 #bfd93cff
> color #35 #bed938ff
> color #35 #cae63cff
> color #35 #c2e640ff
> color #35 #cae63eff
> color #35 #c9e53eff
> show #34 models
> hide #35 models
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:161
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 34/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel blue
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #34/A:274
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 1 atoms, 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #34/A:274
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:224
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:224
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:224
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:224
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> style sel stick
Changed 7 atom styles
> hide sel atoms
> show sel atoms
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:190@CA
1 atom, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> show sel cartoons
> show sel atoms
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:218
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> style sel stick
Changed 7 atom styles
> show sel atoms
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:213
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157@CA
1 atom, 1 residue, 1 model selected
> select #34/A:192
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:192
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 27 12:45:33 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> hide #34 models
> select add #34
4798 atoms, 4847 bonds, 303 residues, 1 model selected
> select subtract #34
Nothing selected
> show #35 models
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #35/A:95
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:95
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:95
12 atoms, 11 bonds, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Alignment identifier is 35/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:97
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:209
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #35/A:152
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> hide sel atoms
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:147
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:126
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 1 residues
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #35/A:123
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #35/A:123
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 27 13:05:48 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Mwinilunga alphavirus AlphaFold.pdb"
Chain information for Mwinilunga alphavirus AlphaFold.pdb #36
---
Chain | Description
A | No description available
> hide #35 models
> select add #35
3771 atoms, 3815 bonds, 236 residues, 1 model selected
> select subtract #35
Nothing selected
> color #36 #cd4e7aff
> color #36 #cd4355ff
> color #36 #8d81cdff
> color #36 #7867cdff
> color #36 #574fcdff
> color #36 #7272cdff
> color #36 #8383ebff
> color #36 #888debff
> ui tool show Angles/Torsions
> ui tool show Matchmaker
> matchmaker #36 to #2
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 3j2w.pdb, chain I (#2) with Mwinilunga alphavirus AlphaFold.pdb,
chain A (#36), sequence alignment score = 461.6
RMSD between 143 pruned atom pairs is 0.699 angstroms; (across all 149 pairs:
0.975)
> color #36 #8086dcff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:113
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 36/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:113
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:116
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:228
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #36/A:178
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #36/A:172
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #36/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 28 16:04:54 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #36/A:178
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> ui mousemode right translate
> color sel orange
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:166
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> style sel stick
Changed 24 atom styles
> ui mousemode right translate
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:145
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #36/A:145
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:142
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> set bgColor white
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/selected_prediction Pirahy virus.pdb"
Chain information for selected_prediction Pirahy virus.pdb #37
---
Chain | Description
A | No description available
> hide #36 models
> select add #36
3980 atoms, 4027 bonds, 256 residues, 1 model selected
> select subtract #36
Nothing selected
> ui tool show Matchmaker
> matchmaker #37 to #2
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 3j2w.pdb, chain I (#2) with selected_prediction Pirahy virus.pdb,
chain A (#37), sequence alignment score = 544.4
RMSD between 147 pruned atom pairs is 0.769 angstroms; (across all 149 pairs:
0.873)
> color #37 #55557fff
> color #37 #550000ff
> color #37 #0055ffff
> color #37 #aaff7fff
> color #37 #55ff00ff
> color #37 #4ade00ff
> color #37 #4cde0dff
> color #37 #47de1dff
> color #37 #65de39ff
> color #37 #6bde41ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:134
12 atoms, 11 bonds, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Alignment identifier is 37/A
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:136
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:136
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:248
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:248
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:198
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
[Repeated 1 time(s)]
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #37/A:191
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:186
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #37/A:185
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #37/A:186
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:186
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:165
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #37/A:162
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> hide #37 models
> select add #37
4402 atoms, 4459 bonds, 276 residues, 1 model selected
> show #37 models
> select subtract #37
Nothing selected
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/selected_prediction tai forest alphavirus
> .pdb"
Chain information for selected_prediction tai forest alphavirus .pdb #38
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #38 to #2
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 3j2w.pdb, chain I (#2) with selected_prediction tai forest
alphavirus .pdb, chain A (#38), sequence alignment score = 454.7
RMSD between 140 pruned atom pairs is 0.831 angstroms; (across all 149 pairs:
1.170)
> hide #37 models
> color #38 #348d22ff
> color #38 #aaaa00ff
> color #38 #aaaa7fff
> color #38 #93936eff
> color #38 #939362ff
> color #38 #939360ff
> color #38 #938f54ff
> color #38 #93934bff
> color #38 #a6a655ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:115
17 atoms, 16 bonds, 1 residue, 1 model selected
Alignment identifier is 38/A
> select #38/A:114
12 atoms, 11 bonds, 1 residue, 1 model selected
Drag select of 12 residues
> select clear
> select #38/A:114
12 atoms, 11 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 38/A
Alignment identifier is 38/A
> ui mousemode right zoom
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:117
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> ui mousemode right translate
> color sel gray
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:229
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:179
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:172
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
Drag select of 1 atoms, 6 residues
> select clear
> select #38/A:146
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> select #38/A:147
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:143
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 28 17:55:43 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/selected_prediction Weglinng hagfish
> alphavirus consensus.pdb"
Chain information for selected_prediction Weglinng hagfish alphavirus
consensus.pdb #39
---
Chain | Description
A | No description available
> hide #38 models
> select add #38
4010 atoms, 4055 bonds, 257 residues, 1 model selected
> select subtract #38
Nothing selected
> color #39 #550000ff
> color #39 #aa5500ff
> color #39 #550000ff
> color #39 #6b0000ff
> color #39 #810000ff
> color #39 #814a3dff
> ui tool show Matchmaker
> matchmaker #39 to #2
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 3j2w.pdb, chain I (#2) with selected_prediction Weglinng hagfish
alphavirus consensus.pdb, chain A (#39), sequence alignment score = 364.7
RMSD between 66 pruned atom pairs is 0.877 angstroms; (across all 134 pairs:
4.771)
> set bgColor white
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 39/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #39/A:188
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel magenta
> show sel atoms
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #39/A:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #39/A:299
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #39/A:250
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #39/A:263
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #39/A:299
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #39/A:243
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #39/A:238
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:238
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:217
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:214
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> color #39 #965647ff
> color #39 #ba6a58ff
> color #39 #7f483cff
> color #39 #8f5043ff
> color #39 #8c4e42ff
> color #39 #8c5444ff
> color #39 #8c4545ff
> color #39 #8c4b49ff
> color #39 #9d5452ff
> color #39 #96514eff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:188
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #39/A:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #39/A:299
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> set bgColor black
> set bgColor white
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #39/A:243
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color sel blue
> ui mousemode right select
> select #39/A:238
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel blue
Drag select of 4 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:214
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> color sel red
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:217
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel orange
[Repeated 1 time(s)]
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
Drag select of 44 residues
> select #39/A:187
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 28 18:20:41 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Norwegian salmonid alphavirus AlphaFold.pdb"
Chain information for Norwegian salmonid alphavirus AlphaFold.pdb #40
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #40 to #2
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 3j2w.pdb, chain I (#2) with Norwegian salmonid alphavirus
AlphaFold.pdb, chain A (#40), sequence alignment score = 379.7
RMSD between 128 pruned atom pairs is 0.984 angstroms; (across all 148 pairs:
1.791)
> hide #39 models
> select add #39
4950 atoms, 4999 bonds, 312 residues, 1 model selected
> select subtract #39
Nothing selected
> color #40 #cd8444ff
> color #40 #cd6c58ff
> color #40 #cd8b4aff
> color #40 #966636ff
> color #40 #ba7f43ff
> color #40 #b57b41ff
> color #40 #b58a34ff
> color #40 #9e782dff
> color #40 #ba8e35ff
> color #40 #b08632ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40/A:140
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 40/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:142
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:253
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:204
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #40/A:204
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> set bgColor white
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:192
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #40/A:140
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #40/A:142
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #40/A:253
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #40/A:192
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:171
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #40/A:167
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #40/A:168
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #40/A:168
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #40/A:171
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #40/A:167
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #40/A:168
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #40/A:192
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/selected_prediction Wenling fish
> alphavirus.pdb"
Chain information for selected_prediction Wenling fish alphavirus.pdb #41
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #41 to #2
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 3j2w.pdb, chain I (#2) with selected_prediction Wenling fish
alphavirus.pdb, chain A (#41), sequence alignment score = 320.8
RMSD between 130 pruned atom pairs is 0.918 angstroms; (across all 148 pairs:
1.592)
> hide #40 models
> select add #40
4420 atoms, 4461 bonds, 281 residues, 1 model selected
> select subtract #40
Nothing selected
> color #41 #286b1aff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:155
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #41/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:155
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #41/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
Alignment identifier is 41/A
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:158
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide #41 models
> select add #41
4748 atoms, 4801 bonds, 296 residues, 1 model selected
> select subtract #41
Nothing selected
> show #26 models
> hide #26 models
> show #39 models
> show #40 models
> hide #39 models
> show #38 models
> hide #40 models
> hide #38 models
> show #41 models
> ui mousemode right select
> select #41/A:158
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:158
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:269
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 1 residues
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #41/A:219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:219
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jun 29 15:37:27 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:138
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:213
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:208
17 atoms, 17 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:187
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:187
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 15 atom styles
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 3 atoms, 6 residues, 2 bonds
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:184
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Yada yada virus AlphaFold.pdb"
Chain information for Yada yada virus AlphaFold.pdb #42
---
Chain | Description
A | No description available
> color #42 #5555ffff
> color #42 #5500ffff
> color #42 #ff007fff
> color #42 #ca0065ff
> color #42 #5dcac6ff
> color #42 #6647caff
> color #42 #ca6d89ff
> color #42 #ca758cff
> color #42 #ca7585ff
> color #42 #77ca53ff
> color #42 #ca78c3ff
> color #42 #ca7894ff
> color #42 #ca6d83ff
> color #42 magenta
> color #42 #ff2ad8ff
> color #42 #ff1ebbff
> color #42 #b623ffff
> color #42 #da23ffff
> color #42 #e837ffff
> color #42 #ff4c91ff
> color #42 #ff3acaff
> color #42 #ff2fd2ff
> color #42 #ff11b4ff
> color #42 #c30d89ff
> color #42 #c340abff
> color #42 #5d6fc3ff
> color #42 #7a73c3ff
> color #42 #c35344ff
> color #42 #a8473bff
> color #42 #a84e37ff
> color #42 #a8412fff
> color #42 #a83931ff
> color #42 #b63d35ff
> color #42 #b6877bff
> color #42 #b67d6fff
> color #42 #b65b5bff
> color #42 #a65353ff
> color #42 #b15959ff
> color #42 #b13e3aff
> color #42 #b13227ff
> color #42 #89b19eff
> ui tool show Matchmaker
> matchmaker #42 to #2
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 3j2w.pdb, chain I (#2) with Yada yada virus AlphaFold.pdb, chain A
(#42), sequence alignment score = 480
RMSD between 140 pruned atom pairs is 0.706 angstroms; (across all 149 pairs:
0.975)
> hide #41 models
> select add #41
4748 atoms, 4801 bonds, 296 residues, 1 model selected
> select subtract #41
Nothing selected
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:125
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 42/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
Drag select of 1 atoms, 1 bonds
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:190
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:183
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> color #42 #a5d6beff
> color #42 #9eccb6ff
> color sel gray
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel red
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #42/A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:125
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> select #42/A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color sel blue
> ui mousemode right select
> select #42/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color sel red
> ui mousemode right select
> select #42/A:190
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #42/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:157
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #42/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #42/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jun 29 18:48:25 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Aura virus AlphaFold.pdb"
Chain information for Aura virus AlphaFold.pdb #43
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #43 to #2
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 3j2w.pdb, chain I (#2) with Aura virus AlphaFold.pdb, chain A
(#43), sequence alignment score = 493.2
RMSD between 143 pruned atom pairs is 0.738 angstroms; (across all 149 pairs:
1.063)
> color #43 #55007fff
> color #43 #8d00d3ff
> hide #42 models
> select add #42
4151 atoms, 4199 bonds, 268 residues, 1 model selected
> select subtract #42
Nothing selected
> ui mousemode right select
> select #43/A:124
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 43/A
> select #43/A:125
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #43/A:124
15 atoms, 14 bonds, 1 residue, 1 model selected
Drag select of 15 residues
> select clear
Drag select of 31 residues
> ui mousemode right translate
> ui mousemode right select
> select #43/A:125
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right select
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel light sea green
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:239
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #43/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #43/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel magenta
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
[Repeated 3 time(s)]
> hide sel atoms
> show sel atoms
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:177
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> color #43 #ff55ffff
> color #43 #aaaaffff
> color #43 #8d8dd3ff
> color #43 #9696e1ff
> color #43 #a391e1ff
> color #43 #b58ae1ff
> color #43 #bb8ee8ff
> color sel blue
> ui mousemode right select
> select #43/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> hide sel atoms
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel magenta
> ui mousemode right translate
> color #43 #c797f7ff
> color sel magenta
> color sel blue
> color sel magenta
> ui mousemode right select
> select #43/A:177
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:189@CA
1 atom, 1 residue, 1 model selected
> select #43/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #43/A:239
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> select #43/A:125
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #43/A:239
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #43/A:153
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jul 3 21:54:16 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/BFV AlphaFold.pdb"
Chain information for BFV AlphaFold.pdb #44
---
Chain | Description
A | No description available
> hide #43 models
> select add #43
4223 atoms, 4279 bonds, 267 residues, 1 model selected
> select subtract #43
Nothing selected
> color #44 #ffaa7fff
> color #44 #ffb375ff
> color #44 #ffa77bff
> color #44 #ffae6cff
> color #44 #c78854ff
> color #44 #d18f59ff
> color #44 #dc965dff
> color #44 #cf8d58ff
> color #44 #d18f59ff
> ui tool show Matchmaker
> matchmaker #44 to #2
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 3j2w.pdb, chain I (#2) with BFV AlphaFold.pdb, chain A (#44),
sequence alignment score = 630.2
RMSD between 144 pruned atom pairs is 0.775 angstroms; (across all 149 pairs:
1.027)
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:112
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 44/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #44/A:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #44/A:226
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> set bgColor black
> set bgColor white
> ui mousemode right select
Drag select of 1 residues
> select #44/A:176
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 3 residues
> select clear
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:164
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:143
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #44/A:140
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #44/A:140
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #44/A:140
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jul 3 22:05:56 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/WEEV AlphaFold.pdb"
Chain information for WEEV AlphaFold.pdb #45
---
Chain | Description
A | No description available
> color #45 #00aaffff
> color #45 blue
> color #45 #00007fff
> color #45 #5500ffff
> color #45 #00aaffff
> color #45 #0093ddff
> color #45 #0083c5ff
> color #45 #0079b6ff
> hide #44 models
> color #45 #0084c6ff
> color #45 #2f78c6ff
> color #45 #4075c6ff
> color #45 #5581c6ff
> color #45 #6a92c6ff
> show #36 models
> hide #36 models
> select add #44
4047 atoms, 4099 bonds, 253 residues, 1 model selected
> select subtract #44
Nothing selected
> ui tool show Matchmaker
> matchmaker #45 to #2
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 3j2w.pdb, chain I (#2) with WEEV AlphaFold.pdb, chain A (#45),
sequence alignment score = 514.5
RMSD between 148 pruned atom pairs is 0.714 angstroms; (across all 149 pairs:
0.757)
> ui mousemode right select
> select #45/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 45/A
> ui mousemode right translate
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #45/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #45/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select #2/I:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #45/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 15 atom styles
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #45/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel magenta
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jul 4 13:42:21 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #45/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:148
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 10 atom styles
> show sel atoms
[Repeated 1 time(s)]
> color sel gray
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #45/A:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jul 4 14:24:08 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/EEEV AlphaFold.pdb"
Chain information for EEEV AlphaFold.pdb #46
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #46 to #2
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 3j2w.pdb, chain I (#2) with EEEV AlphaFold.pdb, chain A (#46),
sequence alignment score = 506.1
RMSD between 148 pruned atom pairs is 0.711 angstroms; (across all 149 pairs:
0.764)
> hide #45 models
> select add #45
4153 atoms, 4213 bonds, 259 residues, 1 model selected
> select subtract #45
Nothing selected
> color #46 black
> color #46 #444444ff
> color #46 #646464ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 46/A
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> set bgColor black
> set bgColor white
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #46/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel magenta
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #46/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> style sel stick
Changed 17 atom styles
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
Drag select of 2 residues
> select #2/I:156
5 atoms, 4 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #46/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jul 5 13:32:58 2023 ———
opened ChimeraX session
> color #46 #424242ff
> color #46 #323232ff
> color #46 #3a3a3aff
> ui mousemode right select
> select #46/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #46/A:171@CA
1 atom, 1 residue, 1 model selected
> color #46 #28293aff
> color #46 #aaaa7fff
> color #46 #55007fff
> color #46 magenta
> color #46 #550000ff
> color #46 #660000ff
> color #46 #710000ff
> color #46 #6f0000ff
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> show #30 models
> hide #30 models
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #46/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel orange
> select #46/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #46/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
Drag select of 2 residues
> select #46/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #46/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #46/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #46/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #46/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jul 5 13:38:28 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Getah virus AlphaFold.pdb"
Chain information for Getah virus AlphaFold.pdb #47
---
Chain | Description
A | No description available
> color #47 #aaaa7fff
> color #47 #aa5500ff
> color #47 #a15100ff
> color #47 #8c4600ff
> color #47 #8c4b0aff
> color #47 #8c5512ff
> color #47 #8c5d0cff
> color #47 #9c680dff
> color #47 #8c5d0cff
> color #47 #aa5500ff
> color #47 #a35200ff
> color #47 #ad5700ff
> hide #46 models
> select add #46
4167 atoms, 4228 bonds, 261 residues, 1 model selected
> select subtract #46
Nothing selected
> ui tool show Matchmaker
> matchmaker #47 to #2
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 3j2w.pdb, chain I (#2) with Getah virus AlphaFold.pdb, chain A
(#47), sequence alignment score = 673.5
RMSD between 145 pruned atom pairs is 0.778 angstroms; (across all 149 pairs:
0.993)
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 47/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #47/A:129
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:191
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:184
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:158
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #47/A:155
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Mayaro virus AlphaFold.pdb"
Chain information for Mayaro virus AlphaFold.pdb #48
---
Chain | Description
A | No description available
> hide #47 models
> select add #47
4298 atoms, 4353 bonds, 268 residues, 1 model selected
> select subtract #47
Nothing selected
> color #48 #ffaa00ff
> color #48 #55aa00ff
> color #48 #51a200ff
> ui tool show Matchmaker
> matchmaker #48 to #2
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 3j2w.pdb, chain I (#2) with Mayaro virus AlphaFold.pdb, chain A
(#48), sequence alignment score = 674.3
RMSD between 147 pruned atom pairs is 0.759 angstroms; (across all 149 pairs:
0.801)
> color #48 #59b100ff
> color #48 #5bb600ff
[Repeated 1 time(s)]
> color #48 #5bb500ff
> color #48 #5ab300ff
> color #48 #60ba00ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:117
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 48/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:119
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel orange red
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:181
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jul 6 13:25:11 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #48/A:117
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #48/A:119
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #48/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #48/A:181
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel red
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:148
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel red
> color sel blue
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #48/A:145
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #48/A:145
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #48/A:145
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/SFV AlphaFold.pdb"
Chain information for SFV AlphaFold.pdb #49
---
Chain | Description
A | No description available
> color #49 #cd965eff
> color #49 #ffaaffff
> color #49 #ff007fff
> color #49 #ff257cff
> color #49 #ff478eff
> color #49 #ff66b5ff
> color #49 #ff8abfff
> color #49 #ff74b3ff
> color #49 #ff576dff
> select add #48
4180 atoms, 4234 bonds, 258 residues, 1 model selected
> select subtract #48
Nothing selected
> ui tool show Matchmaker
> matchmaker #49 to #2
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 3j2w.pdb, chain I (#2) with SFV AlphaFold.pdb, chain A (#49),
sequence alignment score = 688.6
RMSD between 147 pruned atom pairs is 0.722 angstroms; (across all 149 pairs:
0.761)
> hide #48 models
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 49/A
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #49/A:128
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #49/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> color #49 #ff6b75ff
> color #49 #ff8c98ff
> color #49 #ff878fff
> color #49 #ff7d7fff
> ui mousemode right rotate
> ui mousemode right select
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> select #49/A:128
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #49/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:190
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color sel red
> style sel stick
Changed 15 atom styles
> show sel atoms
> ui mousemode right select
Drag select of 1 residues
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #49/A:183
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jul 10 15:59:37 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:157
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #49/A:154
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel blue
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Sindbis virus AlphaFold.pdb"
Chain information for Sindbis virus AlphaFold.pdb #50
---
Chain | Description
A | No description available
> color #50 white
> color #50 #ccccccff
> color #50 #c5c5c5ff
> color #50 #b0b0b0ff
> color #50 #b8b8b8ff
> hide #49 models
> select add #49
4263 atoms, 4315 bonds, 267 residues, 1 model selected
> select subtract #49
Nothing selected
> ui tool show Matchmaker
> matchmaker #50 to #2
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 3j2w.pdb, chain I (#2) with Sindbis virus AlphaFold.pdb, chain A
(#50), sequence alignment score = 517.9
RMSD between 146 pruned atom pairs is 0.676 angstroms; (across all 149 pairs:
0.789)
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 50/A
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> show #49 models
Drag select of 2 residues
> select clear
> hide #50 models
> ui mousemode right translate
> ui mousemode right select
> select #49/A:183
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
Alignment identifier is 49/A
> show #50 models
> select add #49
4263 atoms, 4315 bonds, 267 residues, 1 model selected
> select subtract #49
Nothing selected
Drag select of 2 residues
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
Alignment identifier is 49/A
Drag select of 3 residues
> select #50/A:110
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide #50 models
> select add #50
4183 atoms, 4237 bonds, 264 residues, 1 model selected
> select subtract #50
Nothing selected
> ui mousemode right select
> select #49/A:183
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #49/A:157
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #49/A:157
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide #49 models
> select add #49
4263 atoms, 4315 bonds, 267 residues, 1 model selected
> select subtract #49
Nothing selected
> show #50 models
> ui mousemode right select
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
Drag select of 8 residues
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
Drag select of 2 residues
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel orange red
> ui mousemode right translate
> ui mousemode right select
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel light gray
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> color sel byhetero
> color sel byelement
> color #50 #bcbcbcff
Drag select of 5 residues
> select clear
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:236
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:179
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #50/A:179
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #50/A:150
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jul 10 18:33:01 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/fold_sec1_full_data_0.json"
fold_sec1_full_data_0.json does not look like Mole Online json file, does not
contain Channels.
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/fold_sec1_full_data_1.json"
fold_sec1_full_data_1.json does not look like Mole Online json file, does not
contain Channels.
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/fold_sec1_model_3.cif"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/fold_sec1_model_3.cif"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open
return mmcif.open_mmcif(session, data, file_name, **kw)
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
MemoryError: not enough memory
MemoryError: not enough memory
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) UHD Graphics 600
OpenGL vendor: Intel
Python: 3.9.11
Locale: es_MX.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: ASUSTeK COMPUTER INC.
Model: VivoBook_ASUSLaptop E410MAB_R429MA
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 4,109,217,792
MaxProcessMemory: 137,438,953,344
CPU: 2 Intel(R) Celeron(R) N4020 CPU @ 1.10GHz
OSLanguage: es-MX
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Note:
See TracTickets
for help on using tickets.
