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Opened 10 months ago
Closed 10 months ago
#16623 closed defect (duplicate)
MemoryError opening mmCIF file
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
[deleted to fit within ticket limits]
> 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
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError opening mmCIF file |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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