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Opened 5 months ago
Last modified 5 months ago
#17903 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.10.dev202501160116 (2025-01-16 01:16:53 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.dev202501160116 (2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología\AlphaFold3\CHIKVaaint.cxs" format session
Log from Mon Jun 2 19:21:36 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Thu May 22 13:36:48 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
Log from Thu May 22 13:21:18 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología\AlphaFold3\CHIKVaaint.cxs" format session
Log from Tue Feb 25 17:51:14 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología\AlphaFold3\CHIKVaaint.cxs" format session
Log from Mon Feb 24 09:50:56 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología\AlphaFold3\CHIKVaaint.cxs" format session
Log from Fri Feb 21 21:14:08 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología\AlphaFold3\CHIKVaaint.cxs" format session
Log from Tue Feb 11 09:48:29 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología\AlphaFold3\CHIKVaaint.cxs" format session
Log from Sun Feb 2 22:29:43 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
Log from Wed Jan 29 14:59:10 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open C:/Users/Carolina/Documents/CHIKVaaint.cxs
Log from Wed Jan 29 09:08:51 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\Documents\Prueba Chimera.cxs" format session
Log from Tue Jan 21 18:31:41 2025UCSF ChimeraX version: 1.10.dev202501160116
(2025-01-16)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología CHIKV Assembly\Sindbis\overlap of CP structures comp.
> Sindbis.cxs" format session
Log from Wed Aug 9 11:27:54 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Wed Aug 2 13:12:02 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Wed Aug 2 11:55:29 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Wed Aug 2 11:23:08 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Tue Aug 1 14:51:39 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Tue Aug 1 09:36:23 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Mon Jul 31 12:55:07 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Mon Jul 31 10:36:12 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Wed Jul 19 11:49:32 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Tue Jul 18 21:16:37 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\\\overlap of CP structures comp. Sindbis.cxs"
Log from Tue Jul 18 20:54:16 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\\\overlap of CP structures.cxs"
Log from Mon Jul 10 18:33:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jul 10 15:59:37 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jul 6 13:25:11 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jul 5 13:38:28 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jul 5 13:32:58 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jul 4 14:24:08 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jul 4 13:42:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jul 3 22:05:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jul 3 21:54:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jun 29 18:48:25 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jun 29 15:37:27 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 28 18:20:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 28 17:55:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 28 16:04:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 27 13:05:48 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 27 12:45:33 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Updating list of available bundles failed: Internal Server Error
Log from Mon Jun 26 10:11:19 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Fri Jun 23 14:27:32 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jun 22 13:48:19 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 21 13:00:17 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 14:01:06 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 13:59:27 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 13:41:59 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 13:33:55 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 20 13:21:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jun 19 14:50:40 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Updating list of available bundles failed: Internal Server Error
Log from Sat Jun 17 16:13:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Fri Jun 16 15:07:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Thu Jun 15 13:33:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Wed Jun 14 15:40:04 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 13 12:23:11 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Tue Jun 13 11:14:29 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\AlphaFold\\\overlap of CP structures.cxs"
Log from Mon Jun 12 13:04:04 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Mon Jun 12 10:47:51 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Fri Jun 9 15:09:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Fri Jun 9 12:21:12 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Thu Jun 8 16:20:57 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\Carolina\OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP\Lab Virología\Alpha fold\overlap of CP structures.cxs" format session
Log from Thu Jun 8 14:55:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Thu Jun 8 12:29:59 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Thu Jun 8 09:54:20 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Wed Jun 7 16:42:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Wed Jun 7 14:34:33 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Tue Jun 6 14:34:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Carolina\\\OneDrive - Universidad Autonoma de San Luis
> Potosi - UASLP\\\Lab Virología\\\Alpha fold\\\overlap of CP structures.cxs"
Log from Tue Jun 6 14:16:52 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Fri May 26 15:30:48 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs" format session
Log from Thu May 25 17:54:54 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs" format session
Log from Thu May 25 12:52:10 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/structures.cxs" format session
Log from Wed May 24 12:56:46 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs" format session
Log from Wed Mar 29 11:43:44 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> format session
Log from Thu Mar 23 12:13:26 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> format session
Log from Fri Mar 17 10:55:50 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
Log from Wed Mar 15 16:42:48 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
Log from Tue Mar 14 17:14:03 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp vs Barmah Forrest 2yew.cxs"
Log from Fri Mar 10 16:26:58 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu.cxs" format session
Log from Thu Mar 9 14:24:14 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga.cxs" format session
Log from Thu Mar 9 12:12:18 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mauriciocomas/Downloads/7vga.pdb
7vga.pdb title:
Cryo-em structure of alphavirus, getah virus [more info...]
Chain information for 7vga.pdb #1
---
Chain | Description
A D G J | E1 envelope glycoprotein
B E H K | E2 envelope glycoprotein
C F I L | capsid protein
> select /A/D/G/J
812 atoms, 808 bonds, 116 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /B/E/H/K
1464 atoms, 1492 bonds, 208 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /C/F/I/L
4884 atoms, 5000 bonds, 632 residues, 1 model selected
> hide sel atoms
> select /C
1221 atoms, 1250 bonds, 158 residues, 1 model selected
> show sel cartoons
> open /Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/3j2w.pdb
> format pdb
3j2w.pdb title:
Electron cryo-microscopy of chikungunya virus [more info...]
Chain information for 3j2w.pdb #2
---
Chain | Description
A B C D | glycoprotein E1
E F G H | glycoprotein E1
I J K L | capsid protein
M N O | glycoprotein E2
P | glycoprotein E2
Q R S T | glycoprotein E2
> select #1/A#1/D#1/G#1/J
812 atoms, 808 bonds, 116 residues, 1 model selected
> hide sel atoms
> select #1/B#1/E#1/H#1/K
1464 atoms, 1492 bonds, 208 residues, 1 model selected
> hide sel atoms
> select #1/C#1/F#1/I#1/L#2/I#2/J#2/K#2/L
9448 atoms, 9676 bonds, 1228 residues, 2 models selected
> hide sel atoms
> select #2/A#2/B#2/C#2/D#2/E#2/F#2/G#2/H
13312 atoms, 13667 bonds, 1756 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> select #2/M#2/N#2/O#2/P#2/Q#2/R#2/S#2/T
13052 atoms, 13416 bonds, 1668 residues, 1 model selected
> hide sel atoms
> select #1/C
1221 atoms, 1250 bonds, 158 residues, 1 model selected
> select #1/F
1221 atoms, 1250 bonds, 158 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #2/I
1141 atoms, 1169 bonds, 149 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain A (#1) with 3j2w.pdb, chain A (#2), sequence
alignment score = 1009.4
Fewer than 3 residues aligned; cannot match 7vga.pdb, chain A with 3j2w.pdb,
chain A
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain A (#1) with 3j2w.pdb, chain A (#2), sequence
alignment score = 1009.4
Fewer than 3 residues aligned; cannot match 7vga.pdb, chain A with 3j2w.pdb,
chain A
> ui tool show Matchmaker
> select #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> matchmaker #2 & sel to #1 & sel
No 'to' model specified
> ~select #2
Nothing selected
> select #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> select #1
7160 atoms, 7300 bonds, 956 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
7160 atoms, 7300 bonds, 956 residues, 1 model selected
> select #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 & sel to #1/C & sel pairing bs
No 'to' chains specified
> ~select #2
Nothing selected
> select #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 & sel to #1/C & sel pairing bs
No 'to' chains specified
> ui tool show Matchmaker
> matchmaker #2 & sel to #1/I & sel pairing bs
No 'to' chains specified
> matchmaker #2/I#1/C & sel to #1/C#2/I & sel pairing ss
Different number of reference/match chains (0 ref, 1 match)
> ui tool show Matchmaker
> matchmaker #2/I to #1/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain C (#1) with 3j2w.pdb, chain I (#2), sequence
alignment score = 590.7
RMSD between 145 pruned atom pairs is 0.988 angstroms; (across all 149 pairs:
1.054)
> set bgColor white
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C #1/F #1/I #1/L
Alignment identifier is 1
> sequence chain #2/I #2/J #2/K #2/L
Alignment identifier is 2
> select #1/C,F,I,L:166-167
84 atoms, 84 bonds, 8 residues, 1 model selected
> select #1/C,F,I,L:166
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/C,F,I,L:166
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #1/C,F,I,L:166
36 atoms, 32 bonds, 4 residues, 1 model selected
> style sel stick
Changed 36 atom styles
> show sel atoms
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #2/I
Alignment identifier is 2/I
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #2/I:241
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/I:240-241
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:240-241
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:240-241
13 atoms, 12 bonds, 2 residues, 1 model selected
> select
> #2/I:120-125,128-134,139-140,149-150,161-163,168-172,191-195,198-203,206-210,222-224,230-239,243-251,256-259,265-266
546 atoms, 546 bonds, 69 residues, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240-241
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #1/C:171
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:171-173
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #1/C:222-223
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/C:222-226
45 atoms, 46 bonds, 5 residues, 1 model selected
> select #1/C:231
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:231-235
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #1/C:263
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:263-265
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #1/C:242
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:242
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:241-242
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select
> #1/C:123-125,130-133,150-151,184-185,193-194,201-203,208-211,223-225,230-234,239-240,244-246,249-252,257-260
346 atoms, 345 bonds, 41 residues, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:148-149
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/C:148-149
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #2/I:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:139
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:139
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:139
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/C:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga.cxs"
——— End of log from Thu Mar 9 12:12:18 2023 ———
opened ChimeraX session
> open /Users/mauriciocomas/Downloads/1kxf.pdb
1kxf.pdb title:
Sindbis virus capsid, (wild-type) residues 1-264, tetragonal crystal form
(form II) [more info...]
Chain information for 1kxf.pdb #3
---
Chain | Description
A | sindbis virus CORE protein
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker #3/A to #2/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with 1kxf.pdb, chain A (#3), sequence
alignment score = 511.3
RMSD between 145 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
0.818)
> hide #1 models
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:112-220
840 atoms, 861 bonds, 109 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> show #1 models
> hide #1 models
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #3/A:136
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:136
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #3/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:159
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:159-163
37 atoms, 37 bonds, 5 residues, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:159
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:159-160
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:160
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:160-162
23 atoms, 23 bonds, 3 residues, 1 model selected
> show #1 models
> hide #1 models
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf.cxs"
> save /Users/mauriciocomas/Desktop/image1.png supersample 3
> select #3/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:109
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:109
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:122
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:156
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:156-157
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> color sel dim gray
> select clear
> save /Users/mauriciocomas/Desktop/image1.png supersample 3
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163-167
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #1 models
> hide #3 models
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf.cxs"
> open /Users/mauriciocomas/Downloads/7sfu.pdb
7sfu.pdb title:
Cryoem structure of venezuelan equine encephalitis virus (veev) Tc-83 strain
VLP [more info...]
Chain information for 7sfu.pdb #4
---
Chain | Description
A D G J | E1 envelope glycoprotein
B E H K | E2 envelope glycoprotein
C F I L | capsid protein
Non-standard residues in 7sfu.pdb #4
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> ui tool show Matchmaker
> matchmaker #4/L to #1/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain C (#1) with 7sfu.pdb, chain L (#4), sequence
alignment score = 442
RMSD between 141 pruned atom pairs is 1.006 angstroms; (across all 158 pairs:
1.916)
> hide #2 models
> hide #1 models
> show #1 models
> hide #1 models
> select #4/A#4/D#4/G#4/J
13536 atoms, 13928 bonds, 1772 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4/B#4/E#4/H#4/K
13328 atoms, 13724 bonds, 1700 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> select #1/C#2/I#4/C#4/F#4/I#4/L
7470 atoms, 7639 bonds, 955 residues, 3 models selected
> hide sel & #4 atoms
> select #4/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> select #1/C#2/I#4/C#4/F#4/I#4/L
7470 atoms, 7639 bonds, 955 residues, 3 models selected
> show sel & #4 cartoons
> show #3 models
> hide #3 models
> select #1/C#2/I#4/C#4/F#4/I#4/L
7470 atoms, 7639 bonds, 955 residues, 3 models selected
> hide sel & #4 cartoons
> select #4/L
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> show #3 models
> show #2 models
> show #1 models
> select clear
> hide #1 models
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:124
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/L:124-275
1188 atoms, 1216 bonds, 152 residues, 1 model selected
> select #4/L:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:123-127
39 atoms, 38 bonds, 5 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:133-134
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #4/L:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu.cxs"
——— End of log from Thu Mar 9 14:24:14 2023 ———
opened ChimeraX session
> hide #2 models
> open /Users/mauriciocomas/Downloads/6xo4.pdb
6xo4.pdb title:
Cryoem structure of eastern equine encephalitis (eeev) VLP [more info...]
Chain information for 6xo4.pdb #5
---
Chain | Description
A D G J | togavirin
B E H K | togavirin
C F I L | togavirin
> select #5/A#5/B#5/C#5/D#5/E#5/F#5/G#5/H#5/I#5/J#5/K#5/L
30900 atoms, 31776 bonds, 4 pseudobonds, 3992 residues, 2 models selected
> hide sel atoms
> select #5/A
3307 atoms, 3401 bonds, 1 pseudobond, 433 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #5/C
1165 atoms, 1192 bonds, 151 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker #5/C to #4/L pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7sfu.pdb, chain L (#4) with 6xo4.pdb, chain C (#5), sequence
alignment score = 559.6
RMSD between 98 pruned atom pairs is 1.141 angstroms; (across all 151 pairs:
2.080)
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> ui tool show Matchmaker
> matchmaker #5/F to #2/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with 6xo4.pdb, chain F (#5), sequence
alignment score = 429.9
RMSD between 107 pruned atom pairs is 1.240 angstroms; (across all 149 pairs:
1.932)
> show #!5 models
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> show #!5 models
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> select #5
30900 atoms, 31776 bonds, 4 pseudobonds, 3992 residues, 2 models selected
> show #!5 models
> hide #5.1 models
> ~select #5.1
30900 atoms, 31776 bonds, 3992 residues, 1 model selected
> hide #!5 models
> ui tool show Matchmaker
> matchmaker #5/C to #2/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with 6xo4.pdb, chain C (#5), sequence
alignment score = 429.9
RMSD between 107 pruned atom pairs is 1.240 angstroms; (across all 149 pairs:
1.932)
> show #!5 models
> hide #4 models
> show #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/C
Alignment identifier is 5/C
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel dim gray
> ui mousemode right select
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #5/C:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/C:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:154-156
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #5/C:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/C:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/C:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/C:158-159
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/C:158-159
20 atoms, 20 bonds, 2 residues, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> color sel dim gray
> hide sel atoms
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right rotate
> ui mousemode right select
> select #5/C:234
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:233-234
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
Drag select of 2 residues
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> color sel red
> color sel blue
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right rotate
> ui mousemode right select
> select #5/C:233@CB
1 atom, 1 residue, 1 model selected
> color sel red
Drag select of 3 residues
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right rotate
> ui mousemode right translate
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8.cxs"
> save /Users/mauriciocomas/Desktop/image11.png supersample 3
> ui mousemode right select
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!5 models
> open /Users/mauriciocomas/Downloads/4agk.pdb
4agk.pdb title:
Crystal structure of capsid protein (110-267) from aura virus [more info...]
Chain information for 4agk.pdb #6
---
Chain | Description
A | capsid protein
> ui tool show Matchmaker
> matchmaker #6/A to #2/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with 4agk.pdb, chain A (#6), sequence
alignment score = 513.6
RMSD between 146 pruned atom pairs is 0.668 angstroms; (across all 149 pairs:
0.815)
> ui mousemode right select
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select clear
> select #6/A:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:165
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:163
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel atoms
> color sel dim gray
> select #6/A:240
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk.cxs"
> save /Users/mauriciocomas/Desktop/image12.png supersample 3
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #6 models
> open /Users/mauriciocomas/Downloads/1vcp.pdb
1vcp.pdb title:
Semliki forest virus capsid protein (crystal form I) [more info...]
Chain information for 1vcp.pdb #7
---
Chain | Description
A B C | semliki forest virus capsid protein
Non-standard residues in 1vcp.pdb #7
---
HG — mercury (II) ion
> select #7/A#7/B#7/C
3429 atoms, 3510 bonds, 9 pseudobonds, 450 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #7/A
1143 atoms, 1170 bonds, 2 pseudobonds, 150 residues, 2 models selected
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #7/A to #2/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with 1vcp.pdb, chain A (#7), sequence
alignment score = 759.4
RMSD between 149 pruned atom pairs is 0.484 angstroms; (across all 149 pairs:
0.484)
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #7/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #7/A:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 9 atom styles
> show sel atoms
> select clear
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp.cxs"
> save /Users/mauriciocomas/Desktop/image13.png supersample 3
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:146
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:147-148
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #7/A:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!7 models
> open /Users/mauriciocomas/Downloads/2yew.pdb
2yew.pdb title:
Modeling barmah forest virus structural proteins [more info...]
Chain information for 2yew.pdb #8
---
Chain | Description
A D G J | COAT protein
B E H K | spike glycoprotein E1
C F I L | spike glycoprotein E2
> select #8/A#8/D#8/G#8/J
5264 atoms, 5384 bonds, 684 residues, 1 model selected
> hide sel atoms
> select #8/B#8/E#8/H#8/K
12900 atoms, 13216 bonds, 4 pseudobonds, 1704 residues, 2 models selected
> hide sel atoms
> select #8/C#8/F#8/I#8/L
12956 atoms, 13316 bonds, 1684 residues, 1 model selected
> hide sel atoms
> select #8/A
1316 atoms, 1346 bonds, 171 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker #8/A to #2/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with 2yew.pdb, chain A (#8), sequence
alignment score = 572.6
RMSD between 66 pruned atom pairs is 1.154 angstroms; (across all 149 pairs:
3.464)
> ui mousemode right rotate
> ui mousemode right select
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select #8/A:134
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:135
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/A:134
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:135
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide #!8 models
> select #8/D
1316 atoms, 1346 bonds, 171 residues, 1 model selected
> show #2 cartoons
> hide #2 cartoons
> hide #2 models
> show #2 models
> select #2/I
1141 atoms, 1169 bonds, 149 residues, 1 model selected
> show sel cartoons
> select #8/D
1316 atoms, 1346 bonds, 171 residues, 1 model selected
> show #2 cartoons
> hide #2 cartoons
> select #2/I
1141 atoms, 1169 bonds, 149 residues, 1 model selected
> show sel cartoons
> select clear
> select #8/G
1316 atoms, 1346 bonds, 171 residues, 1 model selected
> show #2 cartoons
> hide #2 cartoons
> select #2/I
1141 atoms, 1169 bonds, 149 residues, 1 model selected
> show sel cartoons
> select clear
> show #!8 models
Drag select of 9 residues
Drag select of 5 residues
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right rotate
> ui mousemode right select
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> ui mousemode right rotate
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp vs Barmah Forrest 2yew.cxs"
> save /Users/mauriciocomas/Desktop/image14.png supersample 3
> ui mousemode right select
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/CHIKV 3j2w
> vs Getah 7vga vs Sindbis 1kxf vs VEEV 7sfu vs Mayaro 7ko8 vs EEEV 7ko8 vs
> Aura 4agk vs SFV 1vcp vs Barmah Forrest 2yew.cxs"
——— End of log from Fri Mar 10 16:26:58 2023 ———
opened ChimeraX session
> open /Users/mauriciocomas/Downloads/7ko8.pdb
7ko8.pdb title:
Cryo-em structure of the mature and infective mayaro virus [more info...]
Chain information for 7ko8.pdb #9
---
Chain | Description
A D G J | capsid protein
B E H L | E1 glycoprotein
C F I M | E2 glycoprotein
Non-standard residues in 7ko8.pdb #9
---
BMA — β-D-mannopyranose (β-D-mannose; D-mannose; mannose)
MAN — α-D-mannopyranose (α-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide #!8 models
> select #9/A
1170 atoms, 1200 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/D
1170 atoms, 1199 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/G
1170 atoms, 1199 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/G
1170 atoms, 1199 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/J
1170 atoms, 1199 bonds, 152 residues, 1 model selected
> hide sel atoms
> select #9/B#9/E#9/H#9/L
13160 atoms, 13517 bonds, 1732 residues, 1 model selected
> hide sel atoms
> select #9/C#9/F#9/I#9/M
12924 atoms, 13269 bonds, 1664 residues, 1 model selected
> hide sel atoms
> select #9/A
1170 atoms, 1200 bonds, 152 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
> ui mousemode right translate
> ui mousemode right select
> matchmaker #9/A to #2/I pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with 7ko8.pdb, chain A (#9), sequence
alignment score = 566.3
RMSD between 131 pruned atom pairs is 1.142 angstroms; (across all 149 pairs:
1.442)
> ui mousemode right zoom
> select ligand
557 atoms, 581 bonds, 43 residues, 2 models selected
> hide sel & #9 atoms
> ui mousemode right translate
> save /Users/mauriciocomas/Desktop/mayaro format fasta alignment 8/A
> ui mousemode right select
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:108
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:108-253
1112 atoms, 1139 bonds, 146 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select clear
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/mayaro format fasta alignment 9/A
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> hide #9 models
> show #9 models
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:117-118
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #9/A:138
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel dim gray
> select #9/A:138
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:138
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #9/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> show #!8 models
> hide #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> save /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/BFV format
> fasta alignment 8/A
> save /Users/mauriciocomas/Desktop/BFV format fasta alignment 8/A
> select clear
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select clear
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:133@CA
1 atom, 1 residue, 1 model selected
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!8 models
> show #3 models
> hide #3 models
> show #!7 models
> select #7/A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/SINV format fasta alignment 7/A
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #3 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> save /Users/mauriciocomas/Desktop/SINV format fasta alignment 3/A
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> select #3/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #6 models
> hide #3 models
Drag select of 4 residues
> ui mousemode right rotate
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> save /Users/mauriciocomas/Desktop/Aura format fasta alignment 6/A
> ui mousemode right select
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #4 models
> hide #6 models
> select #2/I:195
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #4/L:254
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> save /Users/mauriciocomas/Desktop/VEEV format fasta alignment 6/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/VEEV format fasta alignment 4/L
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #4/L:247@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #4/L:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
——— End of log from Tue Mar 14 17:14:03 2023 ———
opened ChimeraX session
> hide #4 models
> ui mousemode right rotate
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> show #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> select clear
> save /Users/mauriciocomas/Desktop/image31.png supersample 3
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:182
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/I:182-183
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190-191
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183-184
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:166
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/I:166-181
125 atoms, 127 bonds, 16 residues, 1 model selected
> select #2/I:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183-184
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 4 residues
> ui mousemode right rotate
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:183-184
21 atoms, 21 bonds, 2 residues, 1 model selected
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #!7 models
> show #1 models
> hide #1 models
> show #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image32.png supersample 3
> ui mousemode right select
> select #9/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #9 models
> show #1 models
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> save /Users/mauriciocomas/Desktop/image33.png supersample 3
> select #1/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel red
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> save /Users/mauriciocomas/Desktop/image34.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #2 models
> show #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image35.png supersample 3
> select #8/A:133@CB
1 atom, 1 residue, 1 model selected
> show #2 models
> hide #1 models
> hide sel atoms
> undo
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/image36.png supersample 3
> select #8/A:151
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!8 models
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel dark gray
> select #3/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> select #3/A:161-162
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/A:161-162
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:162-163
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:162
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:178
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:178
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:179-180
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel dim gray
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> save /Users/mauriciocomas/Desktop/image37.png supersample 3
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image38.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #3 models
> show #6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:181
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/A:181
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> show sel atoms
> show sel atoms
> show sel cartoons
> select #6/A:131
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:131-267
1036 atoms, 1064 bonds, 137 residues, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> style sel stick
Changed 4 atom styles
> show sel atoms
> style sel sphere
Changed 4 atom styles
> color sel dim gray
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image39.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #6 models
> show #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:203
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/L:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:196-197
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/L:196-197
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/L:198
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select clear
> save /Users/mauriciocomas/Desktop/image40.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> show #!5 models
> hide #!5 models
> hide #4 models
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/C
Alignment identifier is 5/C
> select #5/C:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:175
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dark gray
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel dim gray
> ui mousemode right select
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:183-184
11 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/C:184
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:184
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel dim gray
> select clear
> save /Users/mauriciocomas/Desktop/image41.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> hide #!5 models
> select clear
> save /Users/mauriciocomas/Desktop/image42.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
——— End of log from Wed Mar 15 16:42:48 2023 ———
opened ChimeraX session
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:126-184
448 atoms, 455 bonds, 59 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> ui tool show "Show Sequence Viewer"
> sequence chain #2/I
Alignment identifier is 2/I
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126-133
58 atoms, 58 bonds, 8 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 8 atom styles
> show sel atoms
> save /Users/mauriciocomas/Desktop/image9.png supersample 3
> show #3 models
> hide #3 models
> show #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #7/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> save /Users/mauriciocomas/Desktop/image10.png supersample 3
> hide #!7 models
> show #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #9/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image11.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> ui mousemode right select
> select #2/I:154@CG
1 atom, 1 residue, 1 model selected
> hide #9 models
> show #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123-128
45 atoms, 44 bonds, 6 residues, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #1/C:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> save /Users/mauriciocomas/Desktop/image12.png supersample 3
> hide #1 models
> show #!8 models
> hide #!8 models
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right translate
> show #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:112-113
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:114
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:114
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide sel cartoons
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right select
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image13.png supersample 3
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #6 models
> hide #6 models
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:137
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:137-186
390 atoms, 399 bonds, 50 residues, 1 model selected
> show #6 models
> hide #6 models
> select #6
1279 atoms, 1181 bonds, 279 residues, 1 model selected
> ~select #6
Nothing selected
> select #6
1279 atoms, 1181 bonds, 279 residues, 1 model selected
> ~select #6
Nothing selected
> select #3
1240 atoms, 1252 bonds, 175 residues, 1 model selected
> ~select #3
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> show sel atoms
> show sel atoms
> style sel stick
Changed 4 atom styles
> show sel atoms
> hide sel atoms
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123-129
46 atoms, 46 bonds, 7 residues, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:123-124
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:123-124
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:124-125
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/A:124-125
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> color sel red
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:163
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide sel atoms
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel gray
> select clear
> save /Users/mauriciocomas/Desktop/image14.png supersample 3
> hide #3 models
> show #9 models
> hide #9 models
> show #6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:157
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> save /Users/mauriciocomas/Desktop/image15.png supersample 3
> hide #6 models
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/C
Alignment identifier is 5/C
> select clear
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> color sel dim gray
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:119-120
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/C:119-120
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/C:120
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> show sel atoms
> hide sel atoms
> select #5/C:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:117-123
52 atoms, 51 bonds, 7 residues, 1 model selected
> select #5/C:115
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:115-118
31 atoms, 31 bonds, 4 residues, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:148-149
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:145-146
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/C:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> select #5/C:146-147
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #5/C:146-147
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #5/C:147-148
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/C:147-148
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel dim gray
> save /Users/mauriciocomas/Desktop/image16.png supersample 3
> hide #!5 models
> show #4 models
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:135-136
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/L:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #4/L:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/L:165
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:165-166
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/L:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/L:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel dim gray
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
——— End of log from Fri Mar 17 10:55:50 2023 ———
opened ChimeraX session
> show #1 models
> hide #4 models
> ui mousemode right select
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select clear
> save /Users/mauriciocomas/Desktop/image1.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
——— End of log from Thu Mar 23 12:13:26 2023 ———
opened ChimeraX session
> hide #1 models
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/mauriciocomas/Desktop/3j2w monomer" format fasta alignment 2/I
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "move label"
> ui mousemode right label
> label #2/I:128
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126-127
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui tool show "Color Actions"
> color sel bychain
> color sel cyan
> select clear
> select #2/I:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:139
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:139
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:165
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel cyan
> select #2/I:190@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!7 models
> select #7/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel hot pink
> ui tool show "Color Actions"
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right label
> label #7/A:128
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> color sel blue
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> ui mousemode right select
> select #7/A:154@CB
1 atom, 1 residue, 1 model selected
> select #7/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:178
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/A:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:154@CB
1 atom, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:178
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel blue
> select #7/A:183@CB
1 atom, 1 residue, 1 model selected
> color sel blue
> select #7/A:190@CB
1 atom, 1 residue, 1 model selected
> color sel red
> select #7/A:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> select clear
> select #7/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> select #7/A:183@CA
1 atom, 1 residue, 1 model selected
> select #7/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #!7 models
> hide #2 models
> show #2 models
> show #9 models
> select #9/A:138
7 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> hide sel atoms
> select #9/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #9/A:119
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #9/A:145@CB
1 atom, 1 residue, 1 model selected
> select #9/A:148
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:148
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:179
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:170
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #9/A:174@CD
1 atom, 1 residue, 1 model selected
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:174
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #9/A:231@CA
1 atom, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:231
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #9 models
> show #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> hide #1-2 atoms
> undo
> select #1/C:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/C:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:157-158
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:157-158
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #1/C:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/C:241
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #1/C:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #1 models
> show #!8 models
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #8/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:114
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #8/A:133@N
1 atom, 1 residue, 1 model selected
> select #8/A:133@CA
1 atom, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #8/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #8/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:169
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> select #8/A:242
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178-179
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> show #3 models
> hide #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:161
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #3/A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #3/A:150@CB
1 atom, 1 residue, 1 model selected
> select #3/A:150@CB
1 atom, 1 residue, 1 model selected
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:154@CB
1 atom, 1 residue, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:153-154
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel blue
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:176
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:176-177
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:179@CA
1 atom, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:180
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:180
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> select #3/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240@OE2
1 atom, 1 residue, 1 model selected
> select #2/I:240@CB
1 atom, 1 residue, 1 model selected
> select #3/A:236
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> show #6 models
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:146@CA
1 atom, 1 residue, 1 model selected
> select #6/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #6/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #6/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:156@CA
1 atom, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:152
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:152-156
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #6/A:160
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/A:160-162
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #6/A:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/A:148-157
75 atoms, 76 bonds, 10 residues, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:152
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:152
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> color sel dim gray
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:156-157
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/A:156-157
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel blue
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:183
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:183
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:183
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:182
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel stick
Changed 4 atom styles
> show sel atoms
> color sel dim gray
> select clear
> select #6/A:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #6/A:239
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #6 models
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/C
Alignment identifier is 5/C
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:121@CA
1 atom, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #5/C:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:157@CB
1 atom, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150-151
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:155-156
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/C:154-156
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152-153
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:159-160
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/I:159-160
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/I:160
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:160
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C:150
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel cartoons
> show sel atoms
> color sel blue
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/C:175
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #2/I:190@CG
1 atom, 1 residue, 1 model selected
> select #5/C:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #5/C:233-234
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:233-234
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/C:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> hide #!5 models
> show #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/L:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/L:133
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select #4/L:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #4/L:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/L:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #4/L:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show sel atoms
> color sel dim gray
> select #4/L:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/L:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/L:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel blue
> select clear
> select #4/L:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #4/L:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel dim gray
> select #4/L:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Structures/overlap
> structures correct.cxs"
——— End of log from Wed Mar 29 11:43:44 2023 ———
opened ChimeraX session
> hide #4 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphFold
> Colaboratory Ross River.pdb"
Chain information for AlphFold Colaboratory Ross River.pdb #10
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #10 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with AlphFold Colaboratory Ross River.pdb,
chain A (#10), sequence alignment score = 670.2
RMSD between 146 pruned atom pairs is 0.751 angstroms; (across all 149 pairs:
0.841)
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A
Alignment identifier is 10/A
> ui mousemode right select
> select #10/A:129
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #10/A:131
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #10/A:160
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #10/A:157
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel blue
> select #10/A:181
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #10/A:186
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #10/A:193
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #10/A:243
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image3.png supersample 3
> select #10/A:157
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image4.png supersample 3
> save
> /Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/structures.cxs
> open "/Users/mauriciocomas/Downloads/YP_009020571.1 and 20 other
> sequences.aln"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 31, in open_file
seqs, file_attrs, file_markups = ns['read'](session, stream)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/io/readALN.py", line 33, in read
raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
with 'CLUSTAL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event
_open_dropped_file(self.session, event.file())
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 421, in collated_open
return func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/__init__.py", line 61, in open
return open_file(session, data, file_name,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
OSError: Syntax error in ALN file 'YP_009020571.1 and 20 other sequences.aln':
First non-blank line does not start with 'CLUSTAL'
OSError: Syntax error in ALN file 'YP_009020571.1 and 20 other sequences.aln':
First non-blank line does not start with 'CLUSTAL'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
See log for complete Python traceback.
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Alphavirus
> sequences/Madaragia YP_009020571.1 and 20 other sequences.aln"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 31, in open_file
seqs, file_attrs, file_markups = ns['read'](session, stream)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/io/readALN.py", line 33, in read
raise FormatSyntaxError("First non-blank line does not start with 'CLUSTAL'")
chimerax.seqalign.parse.FormatSyntaxError: First non-blank line does not start
with 'CLUSTAL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event
_open_dropped_file(self.session, event.file())
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 421, in collated_open
return func(*func_args, **func_kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/__init__.py", line 61, in open
return open_file(session, data, file_name,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
OSError: Syntax error in ALN file 'Madaragia YP_009020571.1 and 20 other
sequences.aln': First non-blank line does not start with 'CLUSTAL'
OSError: Syntax error in ALN file 'Madaragia YP_009020571.1 and 20 other
sequences.aln': First non-blank line does not start with 'CLUSTAL'
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/parse.py", line 33, in open_file
raise IOError("Syntax error in %s file '%s': %s" % (format_name, fname, err))
See log for complete Python traceback.
> hide #10 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
> 2/AlphaFold Colaboratory Middelburg virus.pdb"
Chain information for AlphaFold Colaboratory Middelburg virus.pdb #11
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain C (#1) with AlphaFold Colaboratory Middelburg
virus.pdb, chain A (#11), sequence alignment score = 810.9
RMSD between 151 pruned atom pairs is 0.862 angstroms; (across all 158 pairs:
1.359)
> show #10 models
> hide #10 models
> ui tool show "Show Sequence Viewer"
> sequence chain #11/A
Alignment identifier is 11/A
> select #11/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #11/A:132
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #11/A:158
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #11/A:161
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #11/A:182
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #11/A:187
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel dim gray
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:184-185
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:184
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #11/A:194
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #11/A:244
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image1.png supersample 3
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/structures.cxs"
——— End of log from Wed May 24 12:56:46 2023 ———
opened ChimeraX session
> hide #11 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
> 2/AlphaFold Colaboratory Everglades virus.pdb"
Chain information for AlphaFold Colaboratory Everglades virus.pdb #12
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #12 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain C (#1) with AlphaFold Colaboratory Everglades
virus.pdb, chain A (#12), sequence alignment score = 512.4
RMSD between 151 pruned atom pairs is 0.937 angstroms; (across all 158 pairs:
1.296)
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> ui mousemode right select
> select #12/A:132
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #12/A:134
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #12/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #12/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #12/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel dim gray
> select #12/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel dim gray
> select #12/A:159-160
28 atoms, 27 bonds, 2 residues, 1 model selected
> select #12/A:159-160
28 atoms, 27 bonds, 2 residues, 1 model selected
> style sel stick
Changed 28 atom styles
> show sel atoms
> select #12/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #12/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui tool show "Color Actions"
> color sel bychain
> select #12/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #2/I:152
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #12/A:165
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #12/A:165
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #12/A:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #12/A:189
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel medium blue
> select #12/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel dim gray
> select #12/A:247
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/A:246
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #12/A:246
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image2.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/structures.cxs"
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs"
——— End of log from Thu May 25 12:52:10 2023 ———
opened ChimeraX session
> hide #12 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
> 2/Alpha Fold Collaboratory Salmon Pancrease Disease.pdb"
Chain information for Alpha Fold Collaboratory Salmon Pancrease Disease.pdb
#13
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #13 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain C (#1) with Alpha Fold Collaboratory Salmon
Pancrease Disease.pdb, chain A (#13), sequence alignment score = 305.8
RMSD between 123 pruned atom pairs is 1.087 angstroms; (across all 157 pairs:
2.548)
> ui mousemode right rotate
> ui tool show "Show Sequence Viewer"
> sequence chain #13/A
Alignment identifier is 13/A
> ui mousemode right select
> select #13/A:141
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #13/A:144
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel dim gray
> select #13/A:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #13/A:142
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #13/A:172
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:169
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #13/A:172
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:174-175
42 atoms, 42 bonds, 2 residues, 1 model selected
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
Drag select of 5 residues
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:169
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 15 atom styles
> show sel atoms
> select #13/A:192
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #13/A:193
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:193
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel blue
> style sel stick
Changed 24 atom styles
> show sel atoms
> select #13/A:129
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #13/A:198
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> style sel stick
Changed 15 atom styles
> show sel atoms
> select #13/A:204
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #13/A:254
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> select clear
> ui mousemode right rotate
> save /Users/mauriciocomas/Desktop/image9.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs"
——— End of log from Thu May 25 17:54:54 2023 ———
opened ChimeraX session
> hide #13 models
> open "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/AlphaFold
> 2/Alpha Fold Collaboratory Fort Morgan virus.pdb"
Chain information for Alpha Fold Collaboratory Fort Morgan virus.pdb #14
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #14 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain C (#1) with Alpha Fold Collaboratory Fort Morgan
virus.pdb, chain A (#14), sequence alignment score = 506.1
RMSD between 152 pruned atom pairs is 0.926 angstroms; (across all 158 pairs:
1.271)
> ui tool show "Show Sequence Viewer"
> sequence chain #14/A
Alignment identifier is 14/A
> ui mousemode right select
> select #14/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #14/A:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #14/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #14/A:118
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #14/A:118
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #14/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #14/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #14/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #14/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #14/A:146
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #14/A:146
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #14/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #14/A:151-152
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #14/A:151-152
38 atoms, 37 bonds, 2 residues, 1 model selected
> select #14/A:152
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #14/A:152
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #14/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #14/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel medium blue
> style sel stick
Changed 22 atom styles
> show sel atoms
> select #14/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #14/A:184
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:184
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #14/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel dim gray
> select #14/A:234
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #14/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #14/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> save /Users/mauriciocomas/Desktop/image11.png supersample 3
> save "/Users/mauriciocomas/Documents/UASLP/Chikungunya/Assembly/Chimera X
> sessions/overlap of CP structures.cxs"
——— End of log from Fri May 26 15:30:48 2023 ———
opened ChimeraX session
> hide #14 models
> open "C:/Users/Carolina/Downloads/Ndumu virus Alphafold.pdb"
Chain information for Ndumu virus Alphafold.pdb #15
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #15 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Ndumu virus Alphafold.pdb, chain A
(#15), sequence alignment score = 653.9
RMSD between 144 pruned atom pairs is 0.776 angstroms; (across all 149 pairs:
1.015)
> matchmaker #15 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Ndumu virus Alphafold.pdb, chain A
(#15), sequence alignment score = 653.9
RMSD between 144 pruned atom pairs is 0.776 angstroms; (across all 149 pairs:
1.015)
> save "C:/Users/Carolina/Downloads/overlap of CP structures.cxs"
> ui mousemode right translate
> show #10 models
> hide #10 models
> color #15 #ff5500ff
> color #15 #ffaa00ff
> color #15 #ffaa7fff
> color #15 #ffa470ff
> color #15 #ff9c6bff
> color #15 #ff9a67ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Tue Jun 6 14:16:52 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #15/A
Alignment identifier is 15/A
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #15/A:128
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> show sel atoms
> style sel stick
Changed 15 atom styles
> style sel stick
Changed 15 atom styles
> show sel cartoons
> style sel stick
Changed 15 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel red
> ui mousemode right select
> select #15/A:242
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #15/A:159
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:156
15 atoms, 14 bonds, 1 residue, 1 model selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Tue Jun 6 14:34:43 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #15/A:127
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:128
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:242
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:192
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #15/A:193
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #15/A:192
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
Drag select of 1 residues
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:185
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:180
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:180
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #15/A:156
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:159
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Wed Jun 7 14:34:33 2023 ———
opened ChimeraX session
> show target m
> hide target m
> show #15 models
> show #2 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Everglades virus Alphafold.pdb"
Chain information for Everglades virus Alphafold.pdb #16
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-15#!5,7-8 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 3j2w.pdb, chain
I (#2), sequence alignment score = 536
RMSD between 147 pruned atom pairs is 0.728 angstroms; (across all 149 pairs:
0.822)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 1kxf.pdb, chain
A (#3), sequence alignment score = 570.4
RMSD between 149 pruned atom pairs is 0.682 angstroms; (across all 158 pairs:
2.151)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 7sfu.pdb, chain
F (#4), sequence alignment score = 808
RMSD between 147 pruned atom pairs is 0.721 angstroms; (across all 162 pairs:
2.067)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 4agk.pdb, chain
A (#6), sequence alignment score = 550.5
RMSD between 149 pruned atom pairs is 0.715 angstroms; (across all 151 pairs:
0.781)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 7ko8.pdb, chain
G (#9), sequence alignment score = 563
RMSD between 134 pruned atom pairs is 1.120 angstroms; (across all 152 pairs:
1.600)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797
RMSD between 150 pruned atom pairs is 0.554 angstroms; (across all 260 pairs:
18.148)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
788.3
RMSD between 152 pruned atom pairs is 0.630 angstroms; (across all 262 pairs:
22.549)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1435.7
RMSD between 274 pruned atom pairs is 0.060 angstroms; (across all 274 pairs:
0.060)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 549.1
RMSD between 134 pruned atom pairs is 0.953 angstroms; (across all 266 pairs:
27.039)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
1003.7
RMSD between 162 pruned atom pairs is 0.329 angstroms; (across all 254 pairs:
31.074)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 814.3
RMSD between 142 pruned atom pairs is 0.555 angstroms; (across all 266 pairs:
35.306)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 6xo4.pdb, chain
C (#5), sequence alignment score = 677.5
RMSD between 106 pruned atom pairs is 1.220 angstroms; (across all 151 pairs:
2.045)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 1vcp.pdb, chain
C (#7), sequence alignment score = 569.9
RMSD between 147 pruned atom pairs is 0.619 angstroms; (across all 149 pairs:
0.761)
Matchmaker Everglades virus Alphafold.pdb, chain A (#16) with 2yew.pdb, chain
G (#8), sequence alignment score = 512.3
RMSD between 55 pruned atom pairs is 1.276 angstroms; (across all 171 pairs:
11.421)
> hide #15 models
> color #16 #0055ffff
> color #16 #ff55ffff
> color #16 magenta
> hide #16 models
> show #16 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Wed Jun 7 16:42:56 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:132
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:134
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:246
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> view clip false
[Repeated 1 time(s)]Drag select of 4 atoms, 9 residues, 2 bonds
> ui mousemode right translate
> ui mousemode right select
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:195
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
Alignment identifier is 16/A
Drag select of 3 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:189
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #16/A:183
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> select clear
> ui mousemode right translate
> ui mousemode right select
Drag select of 1 residues
> select #16/A:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Thu Jun 8 09:54:20 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Bebaru virus Alphafold.pdb"
Chain information for Bebaru virus Alphafold.pdb #17
---
Chain | Description
A | No description available
> color #17 #00aa7fff
> ui tool show Matchmaker
> matchmaker #2-4,6,9-16#!5,7-8 to #17
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 3j2w.pdb, chain I
(#2), sequence alignment score = 675.4
RMSD between 148 pruned atom pairs is 0.764 angstroms; (across all 149 pairs:
0.786)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 1kxf.pdb, chain A
(#3), sequence alignment score = 566.3
RMSD between 148 pruned atom pairs is 0.837 angstroms; (across all 157 pairs:
1.897)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 7sfu.pdb, chain I
(#4), sequence alignment score = 593
RMSD between 143 pruned atom pairs is 0.808 angstroms; (across all 161 pairs:
2.693)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 4agk.pdb, chain A
(#6), sequence alignment score = 561
RMSD between 148 pruned atom pairs is 0.729 angstroms; (across all 150 pairs:
0.808)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 7ko8.pdb, chain D
(#9), sequence alignment score = 805.5
RMSD between 138 pruned atom pairs is 1.056 angstroms; (across all 152 pairs:
1.688)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 1142
RMSD between 163 pruned atom pairs is 0.340 angstroms; (across all 262 pairs:
25.400)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
1126.9
RMSD between 166 pruned atom pairs is 0.337 angstroms; (across all 260 pairs:
13.918)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
814.6
RMSD between 147 pruned atom pairs is 0.553 angstroms; (across all 256 pairs:
26.037)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 509.8
RMSD between 129 pruned atom pairs is 0.766 angstroms; (across all 258 pairs:
33.546)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
810.1
RMSD between 148 pruned atom pairs is 0.467 angstroms; (across all 255 pairs:
22.095)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 946.6
RMSD between 150 pruned atom pairs is 0.331 angstroms; (across all 257 pairs:
26.554)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 814.6
RMSD between 147 pruned atom pairs is 0.553 angstroms; (across all 256 pairs:
26.039)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 6xo4.pdb, chain C
(#5), sequence alignment score = 520.4
RMSD between 100 pruned atom pairs is 1.207 angstroms; (across all 150 pairs:
2.057)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 1vcp.pdb, chain C
(#7), sequence alignment score = 729.6
RMSD between 149 pruned atom pairs is 0.572 angstroms; (across all 149 pairs:
0.572)
Matchmaker Bebaru virus Alphafold.pdb, chain A (#17) with 2yew.pdb, chain G
(#8), sequence alignment score = 724.2
RMSD between 49 pruned atom pairs is 1.194 angstroms; (across all 171 pairs:
9.614)
> hide #16 models
> color #17 #007d5cff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 17/A
> select #17/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
Drag select of 1 atoms, 1 bonds
Drag select of 4 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #17/A:187
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #17/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #17/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #17/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #17/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #17/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #17/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #17/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/A:150
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> select clear
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Thu Jun 8 12:29:59 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Caaingua virus AlphaFold.pdb"
Chain information for Caaingua virus AlphaFold.pdb #18
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-17#!5,7-8 to #18
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 3j2w.pdb, chain I
(#2), sequence alignment score = 458.4
RMSD between 130 pruned atom pairs is 0.780 angstroms; (across all 149 pairs:
2.000)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 1kxf.pdb, chain A
(#3), sequence alignment score = 475.4
RMSD between 137 pruned atom pairs is 0.844 angstroms; (across all 158 pairs:
2.636)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 7sfu.pdb, chain I
(#4), sequence alignment score = 487.6
RMSD between 132 pruned atom pairs is 0.852 angstroms; (across all 162 pairs:
2.515)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 4agk.pdb, chain A
(#6), sequence alignment score = 508.1
RMSD between 138 pruned atom pairs is 0.816 angstroms; (across all 151 pairs:
1.682)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 7ko8.pdb, chain D
(#9), sequence alignment score = 485.3
RMSD between 124 pruned atom pairs is 1.036 angstroms; (across all 152 pairs:
2.096)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 707.3
RMSD between 138 pruned atom pairs is 0.591 angstroms; (across all 252 pairs:
19.368)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
732
RMSD between 133 pruned atom pairs is 0.547 angstroms; (across all 249 pairs:
27.925)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
681.8
RMSD between 151 pruned atom pairs is 0.608 angstroms; (across all 265 pairs:
18.650)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 529
RMSD between 121 pruned atom pairs is 0.853 angstroms; (across all 258 pairs:
27.133)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
675.6
RMSD between 139 pruned atom pairs is 0.598 angstroms; (across all 247 pairs:
34.105)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 669.2
RMSD between 135 pruned atom pairs is 0.619 angstroms; (across all 259 pairs:
38.678)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 681.8
RMSD between 151 pruned atom pairs is 0.608 angstroms; (across all 265 pairs:
18.649)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 705
RMSD between 117 pruned atom pairs is 0.563 angstroms; (across all 250 pairs:
34.618)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 6xo4.pdb, chain C
(#5), sequence alignment score = 413.1
RMSD between 95 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
2.833)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 1vcp.pdb, chain C
(#7), sequence alignment score = 489.6
RMSD between 136 pruned atom pairs is 0.711 angstroms; (across all 149 pairs:
1.711)
Matchmaker Caaingua virus AlphaFold.pdb, chain A (#18) with 2yew.pdb, chain G
(#8), sequence alignment score = 446.9
RMSD between 52 pruned atom pairs is 1.300 angstroms; (across all 171 pairs:
9.079)
> hide #17 models
> color #18 #ff5500ff
> color #18 #c54200ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Thu Jun 8 14:55:45 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:123
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 18/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #18/A:125
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:125
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:242
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:242
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> color #18 #f35100ff
> color #18 #eb4e00ff
> color sel red
> color #18 #ffaa00ff
> color #18 #ff9b0eff
> color #18 #ff790cff
> color #18 #ff850aff
> show #15 models
> hide #15 models
> color #18 #ee7c09ff
> color sel red
> ui mousemode right select
Drag select of 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #18/A:123
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #18/A:125
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #18/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #18/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel gray
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:182
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #18/A:181
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #18/A:182
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #18/A:174
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #18/A:151
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 3 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #18/A:182
14 atoms, 13 bonds, 1 residue, 1 model selected
Drag select of 11 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide #18 models
> show #16 models
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:196@CA
1 atom, 1 residue, 1 model selected
Alignment identifier is 16/A
> color sel orange
> style sel stick
Changed 1 atom style
> show sel atoms
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> color sel red
> color sel orange
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel gray
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Thu Jun 8 16:20:57 2023 ———
opened ChimeraX session
> hide #16 models
> show #18 models
> ui mousemode right select
Drag select of 1 residues
> select clear
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Cabassou virus Alphafold.pdb"
Chain information for Cabassou virus Alphafold.pdb #19
---
Chain | Description
A | No description available
> hide #18 models
> select add #18
4336 atoms, 4396 bonds, 269 residues, 1 model selected
> select subtract #18
Nothing selected
> ui tool show Matchmaker
> matchmaker #2-4,6,9-18#!5,7-8 to #19
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 3j2w.pdb, chain I
(#2), sequence alignment score = 523.2
RMSD between 146 pruned atom pairs is 0.713 angstroms; (across all 149 pairs:
0.884)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 1kxf.pdb, chain A
(#3), sequence alignment score = 557.2
RMSD between 150 pruned atom pairs is 0.659 angstroms; (across all 158 pairs:
2.145)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 7sfu.pdb, chain F
(#4), sequence alignment score = 796.5
RMSD between 148 pruned atom pairs is 0.761 angstroms; (across all 162 pairs:
2.057)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 4agk.pdb, chain A
(#6), sequence alignment score = 555.1
RMSD between 150 pruned atom pairs is 0.694 angstroms; (across all 151 pairs:
0.721)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 7ko8.pdb, chain G
(#9), sequence alignment score = 565
RMSD between 133 pruned atom pairs is 1.092 angstroms; (across all 152 pairs:
1.625)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 820.3
RMSD between 151 pruned atom pairs is 0.605 angstroms; (across all 258 pairs:
27.418)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
783.7
RMSD between 8 pruned atom pairs is 1.343 angstroms; (across all 261 pairs:
33.012)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1238.2
RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 273 pairs:
36.940)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 567.2
RMSD between 5 pruned atom pairs is 1.242 angstroms; (across all 269 pairs:
26.754)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
992.6
RMSD between 162 pruned atom pairs is 0.383 angstroms; (across all 255 pairs:
42.412)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 812.5
RMSD between 147 pruned atom pairs is 0.649 angstroms; (across all 265 pairs:
39.998)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1238.2
RMSD between 165 pruned atom pairs is 0.252 angstroms; (across all 273 pairs:
36.940)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 803.3
RMSD between 13 pruned atom pairs is 1.246 angstroms; (across all 257 pairs:
34.843)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 703.7
RMSD between 149 pruned atom pairs is 0.682 angstroms; (across all 261 pairs:
25.890)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 6xo4.pdb, chain C
(#5), sequence alignment score = 693.4
RMSD between 104 pruned atom pairs is 1.218 angstroms; (across all 151 pairs:
2.050)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 1vcp.pdb, chain C
(#7), sequence alignment score = 557.1
RMSD between 147 pruned atom pairs is 0.589 angstroms; (across all 149 pairs:
0.717)
Matchmaker Cabassou virus Alphafold.pdb, chain A (#19) with 2yew.pdb, chain G
(#8), sequence alignment score = 512.3
RMSD between 54 pruned atom pairs is 1.264 angstroms; (across all 171 pairs:
9.925)
> show #18 models
> hide #18 models
> color #19 #aaff7fff
> color #19 #92d96cff
> color #19 #90d56aff
> color #19 #88ca65ff
> color #19 #8fd46aff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Fri Jun 9 12:21:12 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Eilat virus Alphafold.pdb"
Chain information for Eilat virus Alphafold.pdb #20
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-19#!5,7-8 to #20
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 3j2w.pdb, chain I
(#2), sequence alignment score = 459.1
RMSD between 145 pruned atom pairs is 0.743 angstroms; (across all 149 pairs:
0.843)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 1kxf.pdb, chain A
(#3), sequence alignment score = 618.2
RMSD between 148 pruned atom pairs is 0.717 angstroms; (across all 159 pairs:
1.840)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 7sfu.pdb, chain I
(#4), sequence alignment score = 520.6
RMSD between 138 pruned atom pairs is 0.873 angstroms; (across all 162 pairs:
2.526)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 4agk.pdb, chain A
(#6), sequence alignment score = 660.7
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 152 pairs:
0.685)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 7ko8.pdb, chain G
(#9), sequence alignment score = 491.3
RMSD between 125 pruned atom pairs is 1.096 angstroms; (across all 152 pairs:
1.726)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphFold Colaboratory
Ross River.pdb, chain A (#10), sequence alignment score = 688.4
RMSD between 151 pruned atom pairs is 0.721 angstroms; (across all 251 pairs:
32.337)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
705.8
RMSD between 7 pruned atom pairs is 1.275 angstroms; (across all 248 pairs:
30.093)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
706.4
RMSD between 10 pruned atom pairs is 1.510 angstroms; (across all 254 pairs:
29.648)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 512.7
RMSD between 5 pruned atom pairs is 1.118 angstroms; (across all 251 pairs:
27.761)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
719.5
RMSD between 151 pruned atom pairs is 0.659 angstroms; (across all 245 pairs:
31.518)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 640.6
RMSD between 149 pruned atom pairs is 0.662 angstroms; (across all 252 pairs:
29.525)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 706.4
RMSD between 10 pruned atom pairs is 1.511 angstroms; (across all 254 pairs:
29.647)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 702.4
RMSD between 127 pruned atom pairs is 0.613 angstroms; (across all 251 pairs:
36.013)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 647.9
RMSD between 142 pruned atom pairs is 0.759 angstroms; (across all 242 pairs:
33.358)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 707.1
RMSD between 148 pruned atom pairs is 0.716 angstroms; (across all 253 pairs:
23.904)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 6xo4.pdb, chain C
(#5), sequence alignment score = 441.5
RMSD between 91 pruned atom pairs is 1.178 angstroms; (across all 150 pairs:
2.235)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 1vcp.pdb, chain C
(#7), sequence alignment score = 506.2
RMSD between 144 pruned atom pairs is 0.683 angstroms; (across all 149 pairs:
0.855)
Matchmaker Eilat virus Alphafold.pdb, chain A (#20) with 2yew.pdb, chain G
(#8), sequence alignment score = 461.4
RMSD between 55 pruned atom pairs is 1.242 angstroms; (across all 171 pairs:
7.961)
> color #20 #55aa00ff
> color #20 #00aa7fff
> color #20 #00b182ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> hide #20 models
> show #20 models
> hide #20 models
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 19/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select clear
Drag select of 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #19/A:45
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #19/A:198
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> ui mousemode right select
> select #19/A:198
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right select
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:190
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #19/A:189
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:184
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #19/A:191
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #19/A:190
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #19/A:184
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
Drag select of 2 residues
> select #19/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> show #18 models
> hide #18 models
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:190
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #19/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide #19 models
> show #20 models
Drag select of 1 atoms, 5 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #20/A:112
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
Alignment identifier is 20/A
> style sel stick
Changed 22 atom styles
> show sel atoms
Drag select of 1 bonds
> ui mousemode right translate
> ui mousemode right select
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:115
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:115
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #20/A:227
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:227
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:177
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:170
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
Drag select of 4 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:165
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #20/A:164
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #20/A:165
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
Drag select of 12 atoms, 40 residues, 8 bonds
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #20/A:144
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel orange
> style sel stick
Changed 11 atom styles
> show sel atoms
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #20/A:141
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel gray
> style sel stick
Changed 19 atom styles
> show sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Fri Jun 9 15:09:21 2023 ———
opened ChimeraX session
> hide #20 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/Highlands J. virus Alphafold.pdb"
Chain information for Highlands J. virus Alphafold.pdb #21
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-20#!5,7-8 to #21
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 3j2w.pdb,
chain I (#2), sequence alignment score = 534.6
RMSD between 147 pruned atom pairs is 0.672 angstroms; (across all 149 pairs:
0.755)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 1kxf.pdb,
chain A (#3), sequence alignment score = 584.9
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 158 pairs:
2.143)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 7sfu.pdb,
chain F (#4), sequence alignment score = 704.2
RMSD between 148 pruned atom pairs is 0.808 angstroms; (across all 162 pairs:
2.057)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 4agk.pdb,
chain A (#6), sequence alignment score = 563.1
RMSD between 150 pruned atom pairs is 0.643 angstroms; (across all 151 pairs:
0.671)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 7ko8.pdb,
chain G (#9), sequence alignment score = 593.5
RMSD between 134 pruned atom pairs is 1.109 angstroms; (across all 152 pairs:
1.587)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 804.8
RMSD between 148 pruned atom pairs is 0.558 angstroms; (across all 257 pairs:
26.440)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
818.8
RMSD between 151 pruned atom pairs is 0.625 angstroms; (across all 258 pairs:
21.384)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
996.4
RMSD between 163 pruned atom pairs is 0.346 angstroms; (across all 254 pairs:
15.033)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 539.8
RMSD between 132 pruned atom pairs is 0.906 angstroms; (across all 256 pairs:
30.694)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
1232.6
RMSD between 164 pruned atom pairs is 0.338 angstroms; (across all 259 pairs:
25.527)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 774.7
RMSD between 147 pruned atom pairs is 0.592 angstroms; (across all 251 pairs:
32.099)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Everglades
virus Alphafold.pdb, chain A (#16), sequence alignment score = 996.4
RMSD between 163 pruned atom pairs is 0.346 angstroms; (across all 254 pairs:
15.031)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 830.6
RMSD between 151 pruned atom pairs is 0.547 angstroms; (across all 256 pairs:
26.017)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 698.7
RMSD between 151 pruned atom pairs is 0.680 angstroms; (across all 248 pairs:
24.738)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1000.3
RMSD between 159 pruned atom pairs is 0.253 angstroms; (across all 255 pairs:
39.413)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 734.7
RMSD between 151 pruned atom pairs is 0.665 angstroms; (across all 244 pairs:
36.300)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 6xo4.pdb,
chain C (#5), sequence alignment score = 922.1
RMSD between 103 pruned atom pairs is 1.185 angstroms; (across all 151 pairs:
2.034)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 1vcp.pdb,
chain C (#7), sequence alignment score = 566.4
RMSD between 147 pruned atom pairs is 0.527 angstroms; (across all 149 pairs:
0.665)
Matchmaker Highlands J. virus Alphafold.pdb, chain A (#21) with 2yew.pdb,
chain G (#8), sequence alignment score = 540.8
RMSD between 53 pruned atom pairs is 1.232 angstroms; (across all 169 pairs:
7.986)
> color #21 #00aaffff
> color #21 #007cbaff
> select add #20
3966 atoms, 4011 bonds, 255 residues, 1 model selected
> select subtract #20
Nothing selected
> show #20 models
> hide #20 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Mon Jun 12 10:47:51 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel red
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 2/I
Alignment identifier is 2/I
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 21/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel orange
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #21/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> style sel stick
Changed 17 atom styles
> show sel atoms
Drag select of 8 atoms, 6 bonds
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #21/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel magenta
Drag select of 1 atoms, 9 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #21/A:175
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #21/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
Drag select of 2 residues
> select clear
[Repeated 3 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #21/A:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select clear
> select #21/A:148
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
Drag select of 6 residues
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #21/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select clear
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/Alpha fold/overlap of CP structures.cxs"
——— End of log from Mon Jun 12 13:04:04 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/prediction Madariaga virus.zip"
Unrecognized file suffix '.zip'
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Madariaga virus Alpha Fold.pdb"
Chain information for Madariaga virus Alpha Fold.pdb #22
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-21#!5,7-8 to #22
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 3j2w.pdb, chain
I (#2), sequence alignment score = 522
RMSD between 147 pruned atom pairs is 0.696 angstroms; (across all 149 pairs:
0.789)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 1kxf.pdb, chain
A (#3), sequence alignment score = 569.7
RMSD between 150 pruned atom pairs is 0.715 angstroms; (across all 158 pairs:
2.187)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 7sfu.pdb, chain
F (#4), sequence alignment score = 693.9
RMSD between 145 pruned atom pairs is 0.763 angstroms; (across all 162 pairs:
2.000)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 4agk.pdb, chain
A (#6), sequence alignment score = 550.5
RMSD between 150 pruned atom pairs is 0.691 angstroms; (across all 151 pairs:
0.721)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 7ko8.pdb, chain
G (#9), sequence alignment score = 589.5
RMSD between 133 pruned atom pairs is 1.135 angstroms; (across all 152 pairs:
1.607)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 785.6
RMSD between 150 pruned atom pairs is 0.551 angstroms; (across all 253 pairs:
30.619)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
784.8
RMSD between 149 pruned atom pairs is 0.602 angstroms; (across all 253 pairs:
31.010)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
991.5
RMSD between 147 pruned atom pairs is 0.277 angstroms; (across all 256 pairs:
36.174)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 557.2
RMSD between 107 pruned atom pairs is 0.830 angstroms; (across all 260 pairs:
49.521)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
1201.4
RMSD between 171 pruned atom pairs is 0.328 angstroms; (across all 259 pairs:
11.288)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 767.1
RMSD between 148 pruned atom pairs is 0.604 angstroms; (across all 253 pairs:
21.396)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 991.5
RMSD between 147 pruned atom pairs is 0.278 angstroms; (across all 256 pairs:
36.175)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 810.1
RMSD between 150 pruned atom pairs is 0.536 angstroms; (across all 249 pairs:
25.607)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 679.6
RMSD between 84 pruned atom pairs is 0.443 angstroms; (across all 250 pairs:
38.023)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 996.6
RMSD between 158 pruned atom pairs is 0.330 angstroms; (across all 257 pairs:
38.933)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 719.3
RMSD between 148 pruned atom pairs is 0.691 angstroms; (across all 243 pairs:
28.968)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with Highlands J.
virus Alphafold.pdb, chain A (#21), sequence alignment score = 1253.2
RMSD between 119 pruned atom pairs is 0.235 angstroms; (across all 259 pairs:
32.666)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 6xo4.pdb, chain
C (#5), sequence alignment score = 1014.1
RMSD between 100 pruned atom pairs is 1.163 angstroms; (across all 151 pairs:
2.109)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 1vcp.pdb, chain
C (#7), sequence alignment score = 555.2
RMSD between 147 pruned atom pairs is 0.560 angstroms; (across all 149 pairs:
0.708)
Matchmaker Madariaga virus Alpha Fold.pdb, chain A (#22) with 2yew.pdb, chain
G (#8), sequence alignment score = 534.1
RMSD between 54 pruned atom pairs is 1.237 angstroms; (across all 171 pairs:
10.062)
> hide #21 models
> show #21 models
> hide #22 models
> show #22 models
> hide #21 models
> color #22 #ff5500ff
> color #22 #eb4e00ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:118
19 atoms, 18 bonds, 1 residue, 1 model selected
Alignment identifier is 22/A
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> style sel stick
Changed 17 atom styles
> show sel atoms
> hide sel atoms
> style sel stick
Changed 17 atom styles
> show sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> hide sel atoms
> show sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel magenta
> ui mousemode right translate
> color #22 #ffaa7fff
> color #22 #ee9e77ff
> color #22 #ffaa00ff
> color #22 #cc8800ff
> color #22 #b37700ff
> color #22 #b57900ff
> color #22 #ce8900ff
> color #22 #ff5500ff
> ui mousemode right select
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 13 11:14:29 2023 ———
opened ChimeraX session
> select #22/A:1-30
505 atoms, 519 bonds, 30 residues, 1 model selected
> select #22/A:1-30
505 atoms, 519 bonds, 30 residues, 1 model selected
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #22/A:170
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #22/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 5 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> style sel stick
Changed 17 atom styles
> show sel atoms
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #22/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #22/A:149
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #22/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
Drag select of 3 residues, 2 atoms, 4 bonds
> select #22/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 13 12:23:11 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Mosso das Pedras virus AlphaFold.pdb"
Chain information for Mosso das Pedras virus AlphaFold.pdb #23
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-22#!5,7-8 to #23
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 3j2w.pdb,
chain I (#2), sequence alignment score = 525
RMSD between 147 pruned atom pairs is 0.747 angstroms; (across all 149 pairs:
0.843)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 1kxf.pdb,
chain A (#3), sequence alignment score = 555.1
RMSD between 150 pruned atom pairs is 0.697 angstroms; (across all 158 pairs:
2.182)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 7sfu.pdb,
chain F (#4), sequence alignment score = 774.4
RMSD between 146 pruned atom pairs is 0.748 angstroms; (across all 162 pairs:
2.048)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 4agk.pdb,
chain A (#6), sequence alignment score = 564
RMSD between 151 pruned atom pairs is 0.736 angstroms; (across all 151 pairs:
0.736)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 7ko8.pdb,
chain G (#9), sequence alignment score = 530.6
RMSD between 138 pruned atom pairs is 1.162 angstroms; (across all 152 pairs:
1.566)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 796.6
RMSD between 151 pruned atom pairs is 0.563 angstroms; (across all 261 pairs:
34.344)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
791.9
RMSD between 135 pruned atom pairs is 0.567 angstroms; (across all 263 pairs:
37.641)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1181.5
RMSD between 13 pruned atom pairs is 1.031 angstroms; (across all 272 pairs:
39.100)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 560.8
RMSD between 25 pruned atom pairs is 0.636 angstroms; (across all 270 pairs:
41.007)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
979.8
RMSD between 164 pruned atom pairs is 0.325 angstroms; (across all 255 pairs:
31.044)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Ndumu
virus Alphafold.pdb, chain A (#15), sequence alignment score = 808.2
RMSD between 149 pruned atom pairs is 0.627 angstroms; (across all 267 pairs:
30.210)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Everglades
virus Alphafold.pdb, chain A (#16), sequence alignment score = 1181.5
RMSD between 13 pruned atom pairs is 1.030 angstroms; (across all 272 pairs:
39.103)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Bebaru
virus Alphafold.pdb, chain A (#17), sequence alignment score = 796.3
RMSD between 147 pruned atom pairs is 0.540 angstroms; (across all 258 pairs:
32.949)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Caaingua
virus AlphaFold.pdb, chain A (#18), sequence alignment score = 669.3
RMSD between 143 pruned atom pairs is 0.659 angstroms; (across all 254 pairs:
36.135)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Cabassou
virus Alphafold.pdb, chain A (#19), sequence alignment score = 1176
RMSD between 165 pruned atom pairs is 0.262 angstroms; (across all 274 pairs:
29.984)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Eilat
virus Alphafold.pdb, chain A (#20), sequence alignment score = 704.1
RMSD between 148 pruned atom pairs is 0.693 angstroms; (across all 253 pairs:
13.728)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Highlands
J. virus Alphafold.pdb, chain A (#21), sequence alignment score = 962.3
RMSD between 12 pruned atom pairs is 1.277 angstroms; (across all 255 pairs:
27.902)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with Madariaga
virus Alpha Fold.pdb, chain A (#22), sequence alignment score = 976.4
RMSD between 163 pruned atom pairs is 0.314 angstroms; (across all 257 pairs:
25.593)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 6xo4.pdb,
chain C (#5), sequence alignment score = 680.4
RMSD between 103 pruned atom pairs is 1.187 angstroms; (across all 151 pairs:
2.065)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 1vcp.pdb,
chain C (#7), sequence alignment score = 558.9
RMSD between 147 pruned atom pairs is 0.584 angstroms; (across all 149 pairs:
0.736)
Matchmaker Mosso das Pedras virus AlphaFold.pdb, chain A (#23) with 2yew.pdb,
chain G (#8), sequence alignment score = 499.1
RMSD between 55 pruned atom pairs is 1.261 angstroms; (across all 170 pairs:
9.233)
> hide #22 models
> select add #22
4167 atoms, 4228 bonds, 261 residues, 1 model selected
> select subtract #22
Nothing selected
> color #23 #aaaa7fff
> color #23 #999972ff
> color #23 #94946eff
> color #23 #9e9e76ff
> color #23 #a3a379ff
> color #23 #a5a57bff
> color #23 #a1a178ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:137
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
Alignment identifier is 23/A
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:139
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:251
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:189
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:168
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #23/A:165
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #23/A:168
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #23/A:165
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
[Repeated 1 time(s)]
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:137
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #23/A:139
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #23/A:251
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #23/A:189
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #23/A:168@CA
1 atom, 1 residue, 1 model selected
> select #23/A:165
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 14 15:40:04 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Southern Elephant Seal virus AlphaFold.pdb"
Chain information for Southern Elephant Seal virus AlphaFold.pdb #24
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-23#!5,7-8 to #24
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
3j2w.pdb, chain I (#2), sequence alignment score = 595.1
RMSD between 149 pruned atom pairs is 0.700 angstroms; (across all 149 pairs:
0.700)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
1kxf.pdb, chain A (#3), sequence alignment score = 543.6
RMSD between 147 pruned atom pairs is 0.771 angstroms; (across all 157 pairs:
1.959)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
7sfu.pdb, chain I (#4), sequence alignment score = 577.8
RMSD between 143 pruned atom pairs is 0.786 angstroms; (across all 161 pairs:
2.477)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
4agk.pdb, chain A (#6), sequence alignment score = 575.4
RMSD between 147 pruned atom pairs is 0.663 angstroms; (across all 150 pairs:
0.772)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
7ko8.pdb, chain D (#9), sequence alignment score = 657.3
RMSD between 133 pruned atom pairs is 1.065 angstroms; (across all 152 pairs:
1.706)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
AlphFold Colaboratory Ross River.pdb, chain A (#10), sequence alignment score
= 914
RMSD between 154 pruned atom pairs is 0.396 angstroms; (across all 251 pairs:
23.072)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
AlphaFold Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment
score = 910.1
RMSD between 156 pruned atom pairs is 0.463 angstroms; (across all 251 pairs:
24.684)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
AlphaFold Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment
score = 745.1
RMSD between 147 pruned atom pairs is 0.547 angstroms; (across all 258 pairs:
29.865)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Alpha Fold Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence
alignment score = 561.1
RMSD between 132 pruned atom pairs is 0.772 angstroms; (across all 265 pairs:
33.702)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Alpha Fold Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence
alignment score = 747.2
RMSD between 150 pruned atom pairs is 0.471 angstroms; (across all 258 pairs:
22.727)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Ndumu virus Alphafold.pdb, chain A (#15), sequence alignment score = 876.2
RMSD between 153 pruned atom pairs is 0.454 angstroms; (across all 260 pairs:
16.995)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Everglades virus Alphafold.pdb, chain A (#16), sequence alignment score =
745.1
RMSD between 147 pruned atom pairs is 0.547 angstroms; (across all 258 pairs:
29.865)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Bebaru virus Alphafold.pdb, chain A (#17), sequence alignment score = 885.6
RMSD between 154 pruned atom pairs is 0.323 angstroms; (across all 250 pairs:
25.775)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Caaingua virus AlphaFold.pdb, chain A (#18), sequence alignment score = 686.5
RMSD between 101 pruned atom pairs is 0.541 angstroms; (across all 257 pairs:
34.122)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Cabassou virus Alphafold.pdb, chain A (#19), sequence alignment score = 746.3
RMSD between 5 pruned atom pairs is 0.781 angstroms; (across all 261 pairs:
39.736)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Eilat virus Alphafold.pdb, chain A (#20), sequence alignment score = 688.6
RMSD between 154 pruned atom pairs is 0.690 angstroms; (across all 238 pairs:
27.995)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Highlands J. virus Alphafold.pdb, chain A (#21), sequence alignment score =
761.8
RMSD between 150 pruned atom pairs is 0.515 angstroms; (across all 252 pairs:
24.621)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Madariaga virus Alpha Fold.pdb, chain A (#22), sequence alignment score =
744.9
RMSD between 150 pruned atom pairs is 0.532 angstroms; (across all 254 pairs:
26.232)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
Mosso das Pedras virus AlphaFold.pdb, chain A (#23), sequence alignment score
= 761.8
RMSD between 150 pruned atom pairs is 0.559 angstroms; (across all 260 pairs:
36.762)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
6xo4.pdb, chain C (#5), sequence alignment score = 496.9
RMSD between 101 pruned atom pairs is 1.204 angstroms; (across all 150 pairs:
2.038)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
1vcp.pdb, chain C (#7), sequence alignment score = 628.6
RMSD between 149 pruned atom pairs is 0.536 angstroms; (across all 149 pairs:
0.536)
Matchmaker Southern Elephant Seal virus AlphaFold.pdb, chain A (#24) with
2yew.pdb, chain G (#8), sequence alignment score = 628.5
RMSD between 56 pruned atom pairs is 1.258 angstroms; (across all 171 pairs:
5.304)
> hide #23 models
> select add #23
4449 atoms, 4504 bonds, 279 residues, 1 model selected
> select subtract #23
Nothing selected
> show #23 models
> hide #23 models
> color #24 #555500ff
> color #24 black
> color #24 #550000ff
> color #24 #aaaa7fff
> color #24 #aaaa00ff
> color #24 #555500ff
> color #24 #6c6c00ff
> color #24 #7f7f00ff
> color #24 #666600ff
> color #24 #aaaa7fff
> color #24 #757557ff
> color #24 #707053ff
> color #24 #68684dff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 24/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:129
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:191
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:184
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:179
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> set bgColor black
> set bgColor white
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:158
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:155
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:129
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:129
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:184
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:179
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #24/A:158
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #24/A:155
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jun 15 13:33:00 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Mucambo virus AlphaFold.pdb"
Chain information for Mucambo virus AlphaFold.pdb #25
---
Chain | Description
A | No description available
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #2-4,6,9-24#!5,7-8 to #25
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 3j2w.pdb, chain I
(#2), sequence alignment score = 529.5
RMSD between 148 pruned atom pairs is 0.719 angstroms; (across all 149 pairs:
0.763)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1kxf.pdb, chain A
(#3), sequence alignment score = 561.4
RMSD between 150 pruned atom pairs is 0.671 angstroms; (across all 158 pairs:
1.955)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7sfu.pdb, chain F
(#4), sequence alignment score = 791.4
RMSD between 148 pruned atom pairs is 0.732 angstroms; (across all 162 pairs:
2.042)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 4agk.pdb, chain A
(#6), sequence alignment score = 559.3
RMSD between 150 pruned atom pairs is 0.713 angstroms; (across all 151 pairs:
0.739)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7ko8.pdb, chain G
(#9), sequence alignment score = 568.5
RMSD between 129 pruned atom pairs is 1.055 angstroms; (across all 152 pairs:
1.523)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797.8
RMSD between 148 pruned atom pairs is 0.605 angstroms; (across all 261 pairs:
27.742)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
775.8
RMSD between 151 pruned atom pairs is 0.653 angstroms; (across all 262 pairs:
24.551)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1240.9
RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
24.227)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 569.6
RMSD between 132 pruned atom pairs is 0.920 angstroms; (across all 267 pairs:
15.674)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
974.5
RMSD between 155 pruned atom pairs is 0.353 angstroms; (across all 255 pairs:
37.484)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 830.2
RMSD between 137 pruned atom pairs is 0.550 angstroms; (across all 267 pairs:
41.448)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1240.9
RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
24.231)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 795.9
RMSD between 146 pruned atom pairs is 0.593 angstroms; (across all 258 pairs:
29.444)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 680.9
RMSD between 130 pruned atom pairs is 0.713 angstroms; (across all 261 pairs:
27.031)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1287
RMSD between 13 pruned atom pairs is 0.146 angstroms; (across all 274 pairs:
25.862)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 686.9
RMSD between 11 pruned atom pairs is 1.306 angstroms; (across all 254 pairs:
32.777)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 984.3
RMSD between 156 pruned atom pairs is 0.293 angstroms; (across all 255 pairs:
25.661)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 988.9
RMSD between 135 pruned atom pairs is 0.294 angstroms; (across all 257 pairs:
42.924)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1167.1
RMSD between 20 pruned atom pairs is 1.361 angstroms; (across all 274 pairs:
38.794)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 764.6
RMSD between 147 pruned atom pairs is 0.552 angstroms; (across all 262 pairs:
31.695)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 6xo4.pdb, chain C
(#5), sequence alignment score = 701.7
RMSD between 104 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
2.018)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1vcp.pdb, chain C
(#7), sequence alignment score = 563.4
RMSD between 147 pruned atom pairs is 0.576 angstroms; (across all 149 pairs:
0.688)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 2yew.pdb, chain G
(#8), sequence alignment score = 508.8
RMSD between 54 pruned atom pairs is 1.257 angstroms; (across all 171 pairs:
5.382)
> hide #24 models
> color #25 #ff557fff
> color #25 #f4517aff
> color #25 #e64d73ff
> color #25 #da496dff
> color #25 #e34c72ff
> color #25 #f8537cff
> color #25 #ff007fff
> color #25 #ff557fff
> color #25 #be3f5fff
> color #25 #e14b71ff
> color #25 #ef5078ff
> color #25 #ffaaffff
> color #25 #ff557fff
> color #25 #ff679cff
> color #25 #ff82baff
> color #25 #ff97dbff
> color #25 #ff86c7ff
> color #25 #ff81d9ff
> color #25 #ff7bcaff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 25/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
Alignment identifier is 2/I
> select #25/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> style sel stick
Changed 15 atom styles
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #25/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #25/A:164
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #25/A:164
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> hide sel atoms
> show sel atoms
> style sel stick
Changed 11 atom styles
> color sel orange
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Fri Jun 16 15:07:56 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Onyong-nyong virus AlphaFold.pdb"
Chain information for Onyong-nyong virus AlphaFold.pdb #26
---
Chain | Description
A | No description available
> select add #25
4421 atoms, 4479 bonds, 275 residues, 1 model selected
> hide #25 models
> select subtract #25
Nothing selected
> ui tool show Matchmaker
> matchmaker #2-4,6,9-25#!5,7-8 to #26
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 3j2w.pdb,
chain I (#2), sequence alignment score = 693.1
RMSD between 145 pruned atom pairs is 0.692 angstroms; (across all 149 pairs:
0.928)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 1kxf.pdb,
chain A (#3), sequence alignment score = 550.8
RMSD between 145 pruned atom pairs is 0.764 angstroms; (across all 157 pairs:
1.974)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 7sfu.pdb,
chain I (#4), sequence alignment score = 571.5
RMSD between 141 pruned atom pairs is 0.808 angstroms; (across all 161 pairs:
2.633)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 4agk.pdb,
chain A (#6), sequence alignment score = 554.2
RMSD between 145 pruned atom pairs is 0.645 angstroms; (across all 150 pairs:
0.967)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 7ko8.pdb,
chain D (#9), sequence alignment score = 789.3
RMSD between 135 pruned atom pairs is 1.096 angstroms; (across all 152 pairs:
1.761)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 1011.1
RMSD between 161 pruned atom pairs is 0.532 angstroms; (across all 259 pairs:
26.498)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
990.1
RMSD between 166 pruned atom pairs is 0.493 angstroms; (across all 260 pairs:
12.774)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
745.5
RMSD between 148 pruned atom pairs is 0.549 angstroms; (across all 253 pairs:
25.234)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 521
RMSD between 129 pruned atom pairs is 0.751 angstroms; (across all 253 pairs:
34.504)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
761.6
RMSD between 148 pruned atom pairs is 0.466 angstroms; (across all 257 pairs:
22.771)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 883
RMSD between 153 pruned atom pairs is 0.307 angstroms; (across all 255 pairs:
28.508)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Everglades
virus Alphafold.pdb, chain A (#16), sequence alignment score = 745.5
RMSD between 148 pruned atom pairs is 0.549 angstroms; (across all 253 pairs:
25.235)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 1010.1
RMSD between 168 pruned atom pairs is 0.393 angstroms; (across all 256 pairs:
13.447)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 714.7
RMSD between 131 pruned atom pairs is 0.592 angstroms; (across all 248 pairs:
30.461)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 737.3
RMSD between 12 pruned atom pairs is 0.503 angstroms; (across all 255 pairs:
37.820)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 665.2
RMSD between 146 pruned atom pairs is 0.659 angstroms; (across all 248 pairs:
33.950)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Highlands J.
virus Alphafold.pdb, chain A (#21), sequence alignment score = 778.5
RMSD between 148 pruned atom pairs is 0.516 angstroms; (across all 257 pairs:
23.355)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Madariaga
virus Alpha Fold.pdb, chain A (#22), sequence alignment score = 752.9
RMSD between 148 pruned atom pairs is 0.535 angstroms; (across all 255 pairs:
24.725)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Mosso das
Pedras virus AlphaFold.pdb, chain A (#23), sequence alignment score = 734.5
RMSD between 148 pruned atom pairs is 0.559 angstroms; (across all 255 pairs:
31.406)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Southern
Elephant Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score =
881.1
RMSD between 151 pruned atom pairs is 0.324 angstroms; (across all 248 pairs:
23.757)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 737.4
RMSD between 147 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
32.618)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 6xo4.pdb,
chain C (#5), sequence alignment score = 495.9
RMSD between 99 pruned atom pairs is 1.202 angstroms; (across all 150 pairs:
2.096)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 1vcp.pdb,
chain C (#7), sequence alignment score = 720.3
RMSD between 145 pruned atom pairs is 0.504 angstroms; (across all 149 pairs:
0.805)
Matchmaker Onyong-nyong virus AlphaFold.pdb, chain A (#26) with 2yew.pdb,
chain G (#8), sequence alignment score = 682.7
RMSD between 54 pruned atom pairs is 1.188 angstroms; (across all 171 pairs:
9.494)
> color #26 #55557fff
> color #26 #67679aff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Sat Jun 17 16:13:53 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:119
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 26/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #26/A:119
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:119
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:121
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #26/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #26/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #26/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:150
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #26/A:150
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #26/A:147
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
Drag select of 9 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:237
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Pixuna virus AlphaFold.pdb"
Chain information for Pixuna virus AlphaFold.pdb #27
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-26#!5,7-8 to #27
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
(#2), sequence alignment score = 521
RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
0.820)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
(#3), sequence alignment score = 570.9
RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
1.897)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
(#4), sequence alignment score = 784.4
RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
2.028)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
(#6), sequence alignment score = 557.4
RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
0.770)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
(#9), sequence alignment score = 555.5
RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
1.573)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
31.415)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
757.5
RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
32.104)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 600.2
RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
45.726)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
931.2
RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
24.821)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
16.320)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
26.677)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
31.729)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
39.936)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
22.031)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
36.964)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
20.809)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
22.847)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
24.355)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
36.851)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
28.486)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
(#5), sequence alignment score = 676.1
RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
2.057)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
(#7), sequence alignment score = 554.2
RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
0.747)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
(#8), sequence alignment score = 518.2
RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
6.032)
> hide #26 models
> color #27 #ff5500ff
> color #27 #aa007fff
> color #27 #a7007dff
> color #27 #a10079ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:133
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 27/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:135
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:135
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #27/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #27/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel cartoons
> style sel stick
Changed 15 atom styles
> show sel cartoons
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #27/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #27/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #27/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #27/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #27/A:161
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> ui mousemode right translate
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jun 19 14:50:40 2023 ———
opened ChimeraX session
> hide #27 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/RioNegro virus AlphaFold.pdb"
Chain information for RioNegro virus AlphaFold.pdb #28
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #2-4,6,9-27#!5,7-8 to #28
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 3j2w.pdb, chain I
(#2), sequence alignment score = 527.8
RMSD between 147 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
0.789)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1kxf.pdb, chain A
(#3), sequence alignment score = 566.3
RMSD between 150 pruned atom pairs is 0.681 angstroms; (across all 158 pairs:
1.969)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7sfu.pdb, chain F
(#4), sequence alignment score = 787.7
RMSD between 147 pruned atom pairs is 0.760 angstroms; (across all 162 pairs:
2.092)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 4agk.pdb, chain A
(#6), sequence alignment score = 560.5
RMSD between 150 pruned atom pairs is 0.690 angstroms; (across all 151 pairs:
0.725)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7ko8.pdb, chain G
(#9), sequence alignment score = 543.1
RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 152 pairs:
1.558)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 810.7
RMSD between 149 pruned atom pairs is 0.612 angstroms; (across all 260 pairs:
26.607)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
814.9
RMSD between 150 pruned atom pairs is 0.655 angstroms; (across all 262 pairs:
19.991)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1186.9
RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
22.699)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 570
RMSD between 129 pruned atom pairs is 0.916 angstroms; (across all 274 pairs:
14.045)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
971.5
RMSD between 153 pruned atom pairs is 0.346 angstroms; (across all 255 pairs:
34.468)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 805.7
RMSD between 110 pruned atom pairs is 0.481 angstroms; (across all 266 pairs:
39.937)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1186.9
RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
22.702)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 803.1
RMSD between 150 pruned atom pairs is 0.602 angstroms; (across all 255 pairs:
27.125)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 690.7
RMSD between 142 pruned atom pairs is 0.666 angstroms; (across all 260 pairs:
24.522)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1172
RMSD between 14 pruned atom pairs is 1.444 angstroms; (across all 275 pairs:
24.262)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 686
RMSD between 13 pruned atom pairs is 1.555 angstroms; (across all 251 pairs:
32.745)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 974.3
RMSD between 154 pruned atom pairs is 0.271 angstroms; (across all 255 pairs:
21.224)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 972.7
RMSD between 133 pruned atom pairs is 0.245 angstroms; (across all 257 pairs:
43.677)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1260.3
RMSD between 23 pruned atom pairs is 1.168 angstroms; (across all 278 pairs:
34.771)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 777
RMSD between 148 pruned atom pairs is 0.570 angstroms; (across all 265 pairs:
31.463)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1175.9
RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
6.018)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 731.4
RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 255 pairs:
29.382)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Pixuna virus
AlphaFold.pdb, chain A (#27), sequence alignment score = 1160.6
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
35.129)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 6xo4.pdb, chain C
(#5), sequence alignment score = 670.2
RMSD between 100 pruned atom pairs is 1.164 angstroms; (across all 151 pairs:
2.092)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1vcp.pdb, chain C
(#7), sequence alignment score = 561.7
RMSD between 146 pruned atom pairs is 0.547 angstroms; (across all 149 pairs:
0.720)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 2yew.pdb, chain G
(#8), sequence alignment score = 489.8
RMSD between 57 pruned atom pairs is 1.297 angstroms; (across all 171 pairs:
6.267)
> color #28 #55557fff
> color #28 #55007fff
> color #28 black
> color #28 #545454ff
> color #28 #868686ff
> color #28 #212121ff
> color #28 #414141ff
> color #28 #4c4c4cff
> color #28 #55557fff
> color #28 #4e4e75ff
> color #28 #414161ff
> color #28 black
> color #28 #2c2c2cff
> color #28 #474747ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 13:21:24 2023 ———
opened ChimeraX session
Alignment identifier is 27/A
> select add #27
4429 atoms, 4485 bonds, 275 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #28
4421 atoms, 4477 bonds, 278 residues, 1 model selected
Alignment identifier is 28/A
> select subtract #28
Nothing selected
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:136
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> hide sel atoms
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:138
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:250
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:200
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:193
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:193
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:188
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #28/A:167
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #28/A:164
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> hide #28 models
> show #28 models
> hide #28 models
> show #27 models
> select add #28
4421 atoms, 4477 bonds, 278 residues, 1 model selected
> select subtract #28
Nothing selected
> show #26 models
> hide #26 models
> hide #27 models
> show #27 models
> ui tool show Matchmaker
> matchmaker #2-4,6,9-26,28#!5,7-8 to #27
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
(#2), sequence alignment score = 521
RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
0.820)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
(#3), sequence alignment score = 570.9
RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
1.897)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
(#4), sequence alignment score = 784.4
RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
2.028)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
(#6), sequence alignment score = 557.4
RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
0.770)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
(#9), sequence alignment score = 555.5
RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
1.573)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
31.415)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
757.5
RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
32.104)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 600.2
RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
45.726)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
931.2
RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
24.821)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
16.320)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
26.677)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
31.729)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
39.936)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
22.031)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
36.964)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
20.809)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
22.847)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
24.355)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
36.851)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
28.486)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with RioNegro virus
AlphaFold.pdb, chain A (#28), sequence alignment score = 1160.6
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
35.129)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
(#5), sequence alignment score = 676.1
RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
2.057)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
(#7), sequence alignment score = 554.2
RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
0.747)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
(#8), sequence alignment score = 518.2
RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
6.032)
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 13:33:55 2023 ———
opened ChimeraX session
> hide #27 models
> show #28 models
> show #26 models
> hide #26 models
> ui tool show Matchmaker
> matchmaker #2-4,6,9-27#!5,7-8 to #28
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 3j2w.pdb, chain I
(#2), sequence alignment score = 527.8
RMSD between 147 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
0.789)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1kxf.pdb, chain A
(#3), sequence alignment score = 566.3
RMSD between 150 pruned atom pairs is 0.681 angstroms; (across all 158 pairs:
1.969)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7sfu.pdb, chain F
(#4), sequence alignment score = 787.7
RMSD between 147 pruned atom pairs is 0.760 angstroms; (across all 162 pairs:
2.092)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 4agk.pdb, chain A
(#6), sequence alignment score = 560.5
RMSD between 150 pruned atom pairs is 0.690 angstroms; (across all 151 pairs:
0.725)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 7ko8.pdb, chain G
(#9), sequence alignment score = 543.1
RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 152 pairs:
1.558)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 810.7
RMSD between 149 pruned atom pairs is 0.612 angstroms; (across all 260 pairs:
26.607)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
814.9
RMSD between 150 pruned atom pairs is 0.655 angstroms; (across all 262 pairs:
19.991)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1186.9
RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
22.699)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 570
RMSD between 129 pruned atom pairs is 0.916 angstroms; (across all 274 pairs:
14.045)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
971.5
RMSD between 153 pruned atom pairs is 0.346 angstroms; (across all 255 pairs:
34.468)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 805.7
RMSD between 110 pruned atom pairs is 0.481 angstroms; (across all 266 pairs:
39.937)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1186.9
RMSD between 153 pruned atom pairs is 0.275 angstroms; (across all 273 pairs:
22.702)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 803.1
RMSD between 150 pruned atom pairs is 0.602 angstroms; (across all 255 pairs:
27.125)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 690.7
RMSD between 142 pruned atom pairs is 0.666 angstroms; (across all 260 pairs:
24.522)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1172
RMSD between 14 pruned atom pairs is 1.444 angstroms; (across all 275 pairs:
24.262)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 686
RMSD between 13 pruned atom pairs is 1.555 angstroms; (across all 251 pairs:
32.745)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 974.3
RMSD between 154 pruned atom pairs is 0.271 angstroms; (across all 255 pairs:
21.224)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 972.7
RMSD between 133 pruned atom pairs is 0.245 angstroms; (across all 257 pairs:
43.677)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1260.3
RMSD between 23 pruned atom pairs is 1.168 angstroms; (across all 278 pairs:
34.771)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 777
RMSD between 148 pruned atom pairs is 0.570 angstroms; (across all 265 pairs:
31.463)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1175.9
RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
6.018)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 731.4
RMSD between 148 pruned atom pairs is 0.584 angstroms; (across all 255 pairs:
29.382)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with Pixuna virus
AlphaFold.pdb, chain A (#27), sequence alignment score = 1160.6
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
35.129)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 6xo4.pdb, chain C
(#5), sequence alignment score = 670.2
RMSD between 100 pruned atom pairs is 1.164 angstroms; (across all 151 pairs:
2.092)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 1vcp.pdb, chain C
(#7), sequence alignment score = 561.7
RMSD between 146 pruned atom pairs is 0.547 angstroms; (across all 149 pairs:
0.720)
Matchmaker RioNegro virus AlphaFold.pdb, chain A (#28) with 2yew.pdb, chain G
(#8), sequence alignment score = 489.8
RMSD between 57 pruned atom pairs is 1.297 angstroms; (across all 171 pairs:
6.267)
> show #26 models
> hide #26 models
> hide #28 models
> show #27 models
> ui tool show Matchmaker
> matchmaker #2-4,6,9-26,28#!5,7-8 to #27
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 3j2w.pdb, chain I
(#2), sequence alignment score = 521
RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
0.820)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1kxf.pdb, chain A
(#3), sequence alignment score = 570.9
RMSD between 149 pruned atom pairs is 0.684 angstroms; (across all 158 pairs:
1.897)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7sfu.pdb, chain F
(#4), sequence alignment score = 784.4
RMSD between 148 pruned atom pairs is 0.745 angstroms; (across all 162 pairs:
2.028)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 4agk.pdb, chain A
(#6), sequence alignment score = 557.4
RMSD between 149 pruned atom pairs is 0.706 angstroms; (across all 151 pairs:
0.770)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 7ko8.pdb, chain G
(#9), sequence alignment score = 555.5
RMSD between 135 pruned atom pairs is 1.130 angstroms; (across all 152 pairs:
1.573)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 768.3
RMSD between 150 pruned atom pairs is 0.552 angstroms; (across all 258 pairs:
31.415)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
757.5
RMSD between 140 pruned atom pairs is 0.581 angstroms; (across all 263 pairs:
32.104)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 600.2
RMSD between 92 pruned atom pairs is 0.792 angstroms; (across all 268 pairs:
45.726)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
931.2
RMSD between 153 pruned atom pairs is 0.312 angstroms; (across all 255 pairs:
24.821)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 849.5
RMSD between 148 pruned atom pairs is 0.597 angstroms; (across all 266 pairs:
16.320)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1176.1
RMSD between 24 pruned atom pairs is 0.507 angstroms; (across all 273 pairs:
32.005)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 755.1
RMSD between 140 pruned atom pairs is 0.521 angstroms; (across all 258 pairs:
26.677)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 629.3
RMSD between 10 pruned atom pairs is 0.489 angstroms; (across all 258 pairs:
31.729)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1205.6
RMSD between 149 pruned atom pairs is 0.247 angstroms; (across all 274 pairs:
39.936)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 645.7
RMSD between 152 pruned atom pairs is 0.709 angstroms; (across all 247 pairs:
22.031)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 931.4
RMSD between 139 pruned atom pairs is 0.323 angstroms; (across all 254 pairs:
36.964)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 930.4
RMSD between 155 pruned atom pairs is 0.321 angstroms; (across all 256 pairs:
20.809)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1156
RMSD between 144 pruned atom pairs is 0.209 angstroms; (across all 275 pairs:
22.847)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 743.4
RMSD between 148 pruned atom pairs is 0.534 angstroms; (across all 265 pairs:
24.355)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Mucambo virus
AlphaFold.pdb, chain A (#25), sequence alignment score = 1188.8
RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
36.851)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 689.8
RMSD between 144 pruned atom pairs is 0.546 angstroms; (across all 255 pairs:
28.486)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with RioNegro virus
AlphaFold.pdb, chain A (#28), sequence alignment score = 1160.6
RMSD between 44 pruned atom pairs is 1.121 angstroms; (across all 275 pairs:
35.129)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 6xo4.pdb, chain C
(#5), sequence alignment score = 676.1
RMSD between 104 pruned atom pairs is 1.210 angstroms; (across all 151 pairs:
2.057)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 1vcp.pdb, chain C
(#7), sequence alignment score = 554.2
RMSD between 147 pruned atom pairs is 0.608 angstroms; (across all 149 pairs:
0.747)
Matchmaker Pixuna virus AlphaFold.pdb, chain A (#27) with 2yew.pdb, chain G
(#8), sequence alignment score = 518.2
RMSD between 51 pruned atom pairs is 1.245 angstroms; (across all 171 pairs:
6.032)
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> hide #27 models
> show #26 models
> hide #26 models
> show #26 models
> hide #26 models
> show #25 models
> show #24 models
> hide #24 models
> show #23 models
> hide #23 models
> ui tool show Matchmaker
> matchmaker #2-4,6,9-24,26-28#!5,7-8 to #25
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 3j2w.pdb, chain I
(#2), sequence alignment score = 529.5
RMSD between 148 pruned atom pairs is 0.719 angstroms; (across all 149 pairs:
0.763)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1kxf.pdb, chain A
(#3), sequence alignment score = 561.4
RMSD between 150 pruned atom pairs is 0.671 angstroms; (across all 158 pairs:
1.955)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7sfu.pdb, chain F
(#4), sequence alignment score = 791.4
RMSD between 148 pruned atom pairs is 0.732 angstroms; (across all 162 pairs:
2.042)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 4agk.pdb, chain A
(#6), sequence alignment score = 559.3
RMSD between 150 pruned atom pairs is 0.713 angstroms; (across all 151 pairs:
0.739)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 7ko8.pdb, chain G
(#9), sequence alignment score = 568.5
RMSD between 129 pruned atom pairs is 1.055 angstroms; (across all 152 pairs:
1.523)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphFold
Colaboratory Ross River.pdb, chain A (#10), sequence alignment score = 797.8
RMSD between 148 pruned atom pairs is 0.605 angstroms; (across all 261 pairs:
27.742)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
Colaboratory Middelburg virus.pdb, chain A (#11), sequence alignment score =
775.8
RMSD between 151 pruned atom pairs is 0.653 angstroms; (across all 262 pairs:
24.551)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with AlphaFold
Colaboratory Everglades virus.pdb, chain A (#12), sequence alignment score =
1240.9
RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
24.227)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
Collaboratory Salmon Pancrease Disease.pdb, chain A (#13), sequence alignment
score = 569.6
RMSD between 132 pruned atom pairs is 0.920 angstroms; (across all 267 pairs:
15.674)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Alpha Fold
Collaboratory Fort Morgan virus.pdb, chain A (#14), sequence alignment score =
974.5
RMSD between 155 pruned atom pairs is 0.353 angstroms; (across all 255 pairs:
37.484)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Ndumu virus
Alphafold.pdb, chain A (#15), sequence alignment score = 830.2
RMSD between 137 pruned atom pairs is 0.550 angstroms; (across all 267 pairs:
41.448)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Everglades virus
Alphafold.pdb, chain A (#16), sequence alignment score = 1240.9
RMSD between 152 pruned atom pairs is 0.330 angstroms; (across all 274 pairs:
24.231)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Bebaru virus
Alphafold.pdb, chain A (#17), sequence alignment score = 795.9
RMSD between 146 pruned atom pairs is 0.593 angstroms; (across all 258 pairs:
29.444)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Caaingua virus
AlphaFold.pdb, chain A (#18), sequence alignment score = 680.9
RMSD between 130 pruned atom pairs is 0.713 angstroms; (across all 261 pairs:
27.031)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 1287
RMSD between 13 pruned atom pairs is 0.146 angstroms; (across all 274 pairs:
25.862)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 686.9
RMSD between 11 pruned atom pairs is 1.306 angstroms; (across all 254 pairs:
32.777)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Highlands J. virus
Alphafold.pdb, chain A (#21), sequence alignment score = 984.3
RMSD between 156 pruned atom pairs is 0.293 angstroms; (across all 255 pairs:
25.661)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Madariaga virus
Alpha Fold.pdb, chain A (#22), sequence alignment score = 988.9
RMSD between 135 pruned atom pairs is 0.294 angstroms; (across all 257 pairs:
42.924)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 1167.1
RMSD between 20 pruned atom pairs is 1.361 angstroms; (across all 274 pairs:
38.794)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Southern Elephant
Seal virus AlphaFold.pdb, chain A (#24), sequence alignment score = 764.6
RMSD between 147 pruned atom pairs is 0.552 angstroms; (across all 262 pairs:
31.695)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Onyong-nyong virus
AlphaFold.pdb, chain A (#26), sequence alignment score = 737.4
RMSD between 147 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
32.618)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with Pixuna virus
AlphaFold.pdb, chain A (#27), sequence alignment score = 1188.8
RMSD between 41 pruned atom pairs is 0.760 angstroms; (across all 274 pairs:
36.851)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with RioNegro virus
AlphaFold.pdb, chain A (#28), sequence alignment score = 1175.9
RMSD between 159 pruned atom pairs is 0.307 angstroms; (across all 274 pairs:
6.018)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 6xo4.pdb, chain C
(#5), sequence alignment score = 701.7
RMSD between 104 pruned atom pairs is 1.212 angstroms; (across all 151 pairs:
2.018)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 1vcp.pdb, chain C
(#7), sequence alignment score = 563.4
RMSD between 147 pruned atom pairs is 0.576 angstroms; (across all 149 pairs:
0.688)
Matchmaker Mucambo virus AlphaFold.pdb, chain A (#25) with 2yew.pdb, chain G
(#8), sequence alignment score = 508.8
RMSD between 54 pruned atom pairs is 1.257 angstroms; (across all 171 pairs:
5.382)
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 13:41:59 2023 ———
opened ChimeraX session
> hide #25 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #27 models
> show #26 models
> hide #26 models
> show #25 models
> hide #25 models
> hide #27 models
> show #28 models
> show #26 models
> hide #26 models
> show #27 models
> hide #28 models
> ui tool show Matchmaker
> matchmaker #27 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Pixuna virus AlphaFold.pdb, chain A
(#27), sequence alignment score = 521
RMSD between 147 pruned atom pairs is 0.730 angstroms; (across all 149 pairs:
0.820)
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> show #28 models
> show #26 models
> hide #28 models
> hide #26 models
> show #26 models
> hide #27 models
> show #25 models
> hide #26 models
> show #24 models
> hide #25 models
> show #13 models
> hide #24 models
> show #25 models
> show #26 models
> hide #26 models
> hide #25 models
> show #27 models
> show #28 models
> hide #28 models
> show #28 models
> hide #28 models
> hide #27 models
> hide #13 models
> show #28 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 13:59:27 2023 ———
opened ChimeraX session
> show #27 models
> hide #27 models
> hide #28 models
> show #28 models
> hide #28 models
> show #27 models
> hide #27 models
> show #28 models
> show #26 models
> show #25 models
> hide #25 models
> hide #26 models
> hide #28 models
> show #28 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 20 14:01:06 2023 ———
opened ChimeraX session
> show #27 models
> hide #27 models
> show #26 models
> hide #26 models
> show #25 models
> hide #25 models
> hide #28 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Tonate virus AlphaFold.pdb"
Chain information for Tonate virus AlphaFold.pdb #29
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #29 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Tonate virus AlphaFold.pdb, chain A
(#29), sequence alignment score = 516.2
RMSD between 147 pruned atom pairs is 0.812 angstroms; (across all 149 pairs:
0.929)
> color #29 #555500ff
> color #29 #550000ff
> color #29 #0055ffff
> color #29 #0042c7ff
> color #29 #00007fff
> color #29 #0000a6ff
> color #29 #0000ecff
> color #29 #00007cff
> color #29 #200e7cff
> color #29 #27167cff
> color #29 #2e1e7cff
> color #29 #36287cff
> color #29 #40237cff
> color #29 #3b2e7cff
> color #29 #5240adff
> color #29 #3638adff
> color #29 #585cadff
> color #29 #4b54adff
> color #29 #333a76ff
> color #29 #404894ff
> color #29 #616ee1ff
> color #29 #434c9cff
> color #29 #3d458dff
> color #29 #394084ff
> color #29 #363d7dff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
Alignment identifier is 29/A
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #29/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #29/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #29/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #29/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #29/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #29/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> select #29/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> show #27 models
> hide #2 models
> show #2 models
> hide #27 models
> select add #29
4432 atoms, 4487 bonds, 275 residues, 1 model selected
> select subtract #29
Nothing selected
> hide #29 models
> show #17 models
> ui tool show Matchmaker
> matchmaker #17 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Bebaru virus Alphafold.pdb, chain A
(#17), sequence alignment score = 675.4
RMSD between 148 pruned atom pairs is 0.764 angstroms; (across all 149 pairs:
0.786)
> show #29 models
> hide #29 models
> show #14 models
> hide #17 models
> hide #14 models
> show #29 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 21 13:00:17 2023 ———
opened ChimeraX session
> ui tool show Registration
> hide #29 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Trocara virus AlphaFold.pdb"
Chain information for Trocara virus AlphaFold.pdb #30
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #30 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Trocara virus AlphaFold.pdb, chain A
(#30), sequence alignment score = 500.7
RMSD between 144 pruned atom pairs is 0.680 angstroms; (across all 149 pairs:
0.933)
> color #30 #550000ff
> color #30 #670000ff
> color #30 #740000ff
> color #30 #940000ff
> color #30 #750000ff
> color #30 #750b0bff
> color #30 #752616ff
> color #30 #752620ff
> color #30 #751414ff
> color #30 #750b0bff
> color #30 #b51212ff
> color #30 #620a0aff
> color #30 #810d0dff
> color #30 #8f0e0eff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 30/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 1 bonds
> select #30/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240@CA
1 atom, 1 residue, 1 model selected
> select #30/A:236
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:236
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190@CA
1 atom, 1 residue, 1 model selected
> select #30/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #30/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> show #28 models
> hide #28 models
> show #28 models
> show #27 models
> hide #27 models
> hide #28 models
> select add #30
4192 atoms, 4243 bonds, 264 residues, 1 model selected
> select subtract #30
Nothing selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jun 22 13:48:19 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Una virus AlphaFold.pdb"
Chain information for Una virus AlphaFold.pdb #31
---
Chain | Description
A | No description available
> hide #30 models
> ui tool show Matchmaker
> matchmaker #31 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Una virus AlphaFold.pdb, chain A (#31),
sequence alignment score = 668.1
RMSD between 144 pruned atom pairs is 0.726 angstroms; (across all 149 pairs:
0.900)
> color #31 #ff557fff
> color #31 #ff007fff
> color #31 #55557fff
> color #31 #ff557fff
> color #31 #ff5580ff
> color #31 #ffaaffff
> color #31 #ff557fff
> color #31 #ff5a99ff
> color #31 #ff5ea4ff
> color #31 #ff67abff
> color #31 #ff69a2ff
> color #31 #ff5496ff
> color #31 #ff557fff
> color #31 #ff5892ff
> color #31 #ff4f8dff
> color #31 #ff52a6ff
> color #31 #ff54a1ff
> ui mousemode right select
Drag select of 2 atoms, 1 bonds
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 31/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 6 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #31/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 19 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #31/A:150
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> show #30 models
> hide #31 models
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #30/A:236
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide #30 models
> show #31 models
> ui mousemode right translate
> show #30 models
> show #29 models
> hide #29 models
> hide #30 models
> hide #31 models
> show #31 models
> select add #30
4192 atoms, 4243 bonds, 264 residues, 1 model selected
> select subtract #30
Nothing selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Fri Jun 23 14:27:32 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Whataroa virus AlphaFold.pdb"
Chain information for Whataroa virus AlphaFold.pdb #32
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #32 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Whataroa virus AlphaFold.pdb, chain A
(#32), sequence alignment score = 516.5
RMSD between 146 pruned atom pairs is 0.667 angstroms; (across all 149 pairs:
0.786)
> hide #31 models
> color #32 #ffaa7fff
> color #32 #ffaa00ff
> color #32 #ffff7fff
> color #32 yellow
> color #32 #ffcb0eff
> color #32 #ffcd07ff
> color #32 #ffca0cff
> color #32 #ffd711ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:123
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 32/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:126
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 2 atoms, 2 residues, 3 bonds
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:181
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> color #32 #ffec20ff
> color #32 #ffd70cff
> color #32 #ffff7fff
> color #32 #ffaa00ff
> color #32 #ffff7fff
> color #32 #ffff5cff
> color #32 #fcff4aff
> color #32 #ddff43ff
> color #32 #ffff38ff
> color #32 #ff9cd9ff
> color #32 #ffa7d2ff
> color #32 #ffa4d3ff
> color #32 #fcff39ff
> color #32 #ffef3aff
> style sel stick
Changed 14 atom styles
> hide sel atoms
> show sel atoms
> color sel orange
> ui mousemode right select
> select #32/A:123
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> select #32/A:126
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #32/A:123
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #32/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #32/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:152
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32/A:152
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> hide sel atoms
> show sel atoms
> color sel gray
> select #32/A:155
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #32/A:155
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/AguaSalud alphavirus AlphaFold.pdb"
Chain information for AguaSalud alphavirus AlphaFold.pdb #33
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #33 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with AguaSalud alphavirus AlphaFold.pdb,
chain A (#33), sequence alignment score = 497.5
RMSD between 147 pruned atom pairs is 0.696 angstroms; (across all 149 pairs:
0.798)
> hide #32 models
> select add #32
4214 atoms, 4273 bonds, 266 residues, 1 model selected
> select subtract #32
Nothing selected
> color #33 #56344dff
> color #33 #4e3256ff
> color #33 #562651ff
> color #33 #561b3cff
> color #33 #ffaaffff
> color #33 #f78affff
> color #33 #ff66f0ff
> color #33 #f352ffff
> color #33 #55ffffff
> color #33 #ffaaffff
> color #33 #ffb3feff
> color #33 #fcb0ffff
> color #33 #ffa1efff
> color #33 #ffb9e9ff
> color #33 #ffb2e7ff
> color #33 #ffaed8ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:123
11 atoms, 10 bonds, 1 residue, 1 model selected
Alignment identifier is 33/A
> select #33/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #33/A:123
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #33/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> set bgColor black
[Repeated 1 time(s)]
> set bgColor white
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:126
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #33/A:127
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #33/A:126
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> show #32 models
> select #32/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide #32 models
> select add #32
4214 atoms, 4273 bonds, 266 residues, 1 model selected
> select subtract #32
Nothing selected
> select #33/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190@CA
1 atom, 1 residue, 1 model selected
> select #33/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:181
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel cartoons
> style sel stick
Changed 24 atom styles
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #33/A:155
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #33/A:152
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> show #32 models
> hide #33 models
> show #33 models
> hide #32 models
> select add #33
4198 atoms, 4258 bonds, 266 residues, 1 model selected
> select subtract #33
Nothing selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
[Repeated 1 time(s)]
——— End of log from Mon Jun 26 10:11:19 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Comber alphavirus AlphaFold.pdb"
Chain information for Comber alphavirus AlphaFold.pdb #34
---
Chain | Description
A | No description available
> hide #33 models
> ui tool show Matchmaker
> matchmaker #34 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Comber alphavirus AlphaFold.pdb, chain
A (#34), sequence alignment score = 336.5
RMSD between 118 pruned atom pairs is 0.991 angstroms; (across all 144 pairs:
3.924)
> color #34 #cd7248ff
> color #34 #cd4a33ff
> color #34 #cd5647ff
> color #34 #cd7d44ff
> color #34 #bd733fff
> color #34 #b36d3cff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Harbor porpoise alphavirus AlphaFold.pdb"
Chain information for Harbor porpoise alphavirus AlphaFold.pdb #35
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #35 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Harbor porpoise alphavirus
AlphaFold.pdb, chain A (#35), sequence alignment score = 612.2
RMSD between 146 pruned atom pairs is 0.708 angstroms; (across all 149 pairs:
0.922)
> hide #34 models
> color #35 #ff557fff
> color #35 #ffff7fff
> color #35 yellow
> color #35 #ffff7fff
> color #35 #fff049ff
> color #35 #f6ff42ff
> color #35 #e0ff6eff
> color #35 #d3ff73ff
> color #35 #ddff61ff
> color #35 #cbea59ff
> color #35 #bcd953ff
> color #35 #bad94aff
> color #35 #c9d93cff
> color #35 #bdd92fff
> color #35 #c0d941ff
> color #35 #cad946ff
> color #35 #d1d93cff
> color #35 #bad931ff
> color #35 #d9d93fff
> color #35 #bfd93cff
> color #35 #d1d93cff
> color #35 #b7d93cff
> color #35 #bfd93cff
> color #35 #bed938ff
> color #35 #cae63cff
> color #35 #c2e640ff
> color #35 #cae63eff
> color #35 #c9e53eff
> show #34 models
> hide #35 models
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:161
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 34/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel blue
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #34/A:274
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 1 atoms, 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #34/A:274
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:224
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:224
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:224
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:224
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> style sel stick
Changed 7 atom styles
> hide sel atoms
> show sel atoms
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:190@CA
1 atom, 1 residue, 1 model selected
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> show sel cartoons
> show sel atoms
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:218
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> style sel stick
Changed 7 atom styles
> show sel atoms
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:213
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157@CA
1 atom, 1 residue, 1 model selected
> select #34/A:192
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #34/A:192
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #34/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 27 12:45:33 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #34/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> hide #34 models
> select add #34
4798 atoms, 4847 bonds, 303 residues, 1 model selected
> select subtract #34
Nothing selected
> show #35 models
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #35/A:95
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:95
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:95
12 atoms, 11 bonds, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Alignment identifier is 35/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:97
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:209
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #35/A:152
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> hide sel atoms
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:147
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #35/A:126
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 1 residues
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #35/A:123
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #35/A:123
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jun 27 13:05:48 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Mwinilunga alphavirus AlphaFold.pdb"
Chain information for Mwinilunga alphavirus AlphaFold.pdb #36
---
Chain | Description
A | No description available
> hide #35 models
> select add #35
3771 atoms, 3815 bonds, 236 residues, 1 model selected
> select subtract #35
Nothing selected
> color #36 #cd4e7aff
> color #36 #cd4355ff
> color #36 #8d81cdff
> color #36 #7867cdff
> color #36 #574fcdff
> color #36 #7272cdff
> color #36 #8383ebff
> color #36 #888debff
> ui tool show Angles/Torsions
> ui tool show Matchmaker
> matchmaker #36 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Mwinilunga alphavirus AlphaFold.pdb,
chain A (#36), sequence alignment score = 461.6
RMSD between 143 pruned atom pairs is 0.699 angstroms; (across all 149 pairs:
0.975)
> color #36 #8086dcff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:113
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 36/A
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:113
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:116
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:228
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #36/A:178
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #36/A:172
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #36/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 28 16:04:54 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #36/A:178
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> ui mousemode right translate
> color sel orange
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:166
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> style sel stick
Changed 24 atom styles
> ui mousemode right translate
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #36/A:145
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #36/A:145
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #36/A:142
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> set bgColor white
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/selected_prediction Pirahy virus.pdb"
Chain information for selected_prediction Pirahy virus.pdb #37
---
Chain | Description
A | No description available
> hide #36 models
> select add #36
3980 atoms, 4027 bonds, 256 residues, 1 model selected
> select subtract #36
Nothing selected
> ui tool show Matchmaker
> matchmaker #37 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with selected_prediction Pirahy virus.pdb,
chain A (#37), sequence alignment score = 544.4
RMSD between 147 pruned atom pairs is 0.769 angstroms; (across all 149 pairs:
0.873)
> color #37 #55557fff
> color #37 #550000ff
> color #37 #0055ffff
> color #37 #aaff7fff
> color #37 #55ff00ff
> color #37 #4ade00ff
> color #37 #4cde0dff
> color #37 #47de1dff
> color #37 #65de39ff
> color #37 #6bde41ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:134
12 atoms, 11 bonds, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Alignment identifier is 37/A
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:136
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:136
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:248
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:248
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:198
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
[Repeated 1 time(s)]
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #37/A:191
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:186
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #37/A:185
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #37/A:186
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:186
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #37/A:165
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #37/A:162
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> hide #37 models
> select add #37
4402 atoms, 4459 bonds, 276 residues, 1 model selected
> show #37 models
> select subtract #37
Nothing selected
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/selected_prediction tai forest alphavirus
> .pdb"
Chain information for selected_prediction tai forest alphavirus .pdb #38
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #38 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with selected_prediction tai forest
alphavirus .pdb, chain A (#38), sequence alignment score = 454.7
RMSD between 140 pruned atom pairs is 0.831 angstroms; (across all 149 pairs:
1.170)
> hide #37 models
> color #38 #348d22ff
> color #38 #aaaa00ff
> color #38 #aaaa7fff
> color #38 #93936eff
> color #38 #939362ff
> color #38 #939360ff
> color #38 #938f54ff
> color #38 #93934bff
> color #38 #a6a655ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:115
17 atoms, 16 bonds, 1 residue, 1 model selected
Alignment identifier is 38/A
> select #38/A:114
12 atoms, 11 bonds, 1 residue, 1 model selected
Drag select of 12 residues
> select clear
> select #38/A:114
12 atoms, 11 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 38/A
Alignment identifier is 38/A
> ui mousemode right zoom
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:117
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> ui mousemode right translate
> color sel gray
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:229
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:179
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:172
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #38/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> select clear
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
Drag select of 1 atoms, 6 residues
> select clear
> select #38/A:146
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> select #38/A:147
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #38/A:143
19 atoms, 18 bonds, 1 residue, 1 model selected
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 28 17:55:43 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/selected_prediction Weglinng hagfish
> alphavirus consensus.pdb"
Chain information for selected_prediction Weglinng hagfish alphavirus
consensus.pdb #39
---
Chain | Description
A | No description available
> hide #38 models
> select add #38
4010 atoms, 4055 bonds, 257 residues, 1 model selected
> select subtract #38
Nothing selected
> color #39 #550000ff
> color #39 #aa5500ff
> color #39 #550000ff
> color #39 #6b0000ff
> color #39 #810000ff
> color #39 #814a3dff
> ui tool show Matchmaker
> matchmaker #39 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with selected_prediction Weglinng hagfish
alphavirus consensus.pdb, chain A (#39), sequence alignment score = 364.7
RMSD between 66 pruned atom pairs is 0.877 angstroms; (across all 134 pairs:
4.771)
> set bgColor white
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 39/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #39/A:188
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel magenta
> show sel atoms
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #39/A:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #39/A:299
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #39/A:250
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #39/A:263
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #39/A:299
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #39/A:243
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #39/A:238
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:238
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:217
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:214
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> color #39 #965647ff
> color #39 #ba6a58ff
> color #39 #7f483cff
> color #39 #8f5043ff
> color #39 #8c4e42ff
> color #39 #8c5444ff
> color #39 #8c4545ff
> color #39 #8c4b49ff
> color #39 #9d5452ff
> color #39 #96514eff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:188
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #39/A:300
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #39/A:299
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> set bgColor black
> set bgColor white
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #39/A:243
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color sel blue
> ui mousemode right select
> select #39/A:238
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel blue
Drag select of 4 residues
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A:214
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> color sel red
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A:217
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel orange
[Repeated 1 time(s)]
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
Drag select of 44 residues
> select #39/A:187
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jun 28 18:20:41 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Norwegian salmonid alphavirus AlphaFold.pdb"
Chain information for Norwegian salmonid alphavirus AlphaFold.pdb #40
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #40 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Norwegian salmonid alphavirus
AlphaFold.pdb, chain A (#40), sequence alignment score = 379.7
RMSD between 128 pruned atom pairs is 0.984 angstroms; (across all 148 pairs:
1.791)
> hide #39 models
> select add #39
4950 atoms, 4999 bonds, 312 residues, 1 model selected
> select subtract #39
Nothing selected
> color #40 #cd8444ff
> color #40 #cd6c58ff
> color #40 #cd8b4aff
> color #40 #966636ff
> color #40 #ba7f43ff
> color #40 #b57b41ff
> color #40 #b58a34ff
> color #40 #9e782dff
> color #40 #ba8e35ff
> color #40 #b08632ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40/A:140
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 40/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:142
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:253
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:204
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #40/A:204
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> set bgColor white
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:192
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #40/A:140
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #40/A:142
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #40/A:253
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #40/A:192
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #40/A:171
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #40/A:167
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #40/A:168
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #40/A:168
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #40/A:171
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #40/A:167
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #40/A:168
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #40/A:192
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/selected_prediction Wenling fish
> alphavirus.pdb"
Chain information for selected_prediction Wenling fish alphavirus.pdb #41
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #41 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with selected_prediction Wenling fish
alphavirus.pdb, chain A (#41), sequence alignment score = 320.8
RMSD between 130 pruned atom pairs is 0.918 angstroms; (across all 148 pairs:
1.592)
> hide #40 models
> select add #40
4420 atoms, 4461 bonds, 281 residues, 1 model selected
> select subtract #40
Nothing selected
> color #41 #286b1aff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:155
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #41/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:155
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #41/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
Alignment identifier is 41/A
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:158
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide #41 models
> select add #41
4748 atoms, 4801 bonds, 296 residues, 1 model selected
> select subtract #41
Nothing selected
> show #26 models
> hide #26 models
> show #39 models
> show #40 models
> hide #39 models
> show #38 models
> hide #40 models
> hide #38 models
> show #41 models
> ui mousemode right select
> select #41/A:158
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:158
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:269
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 1 residues
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #41/A:219
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:219
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jun 29 15:37:27 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:138
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:213
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:208
17 atoms, 17 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:187
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #41/A:187
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 15 atom styles
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 3 atoms, 6 residues, 2 bonds
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #41/A:184
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 19 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Yada yada virus AlphaFold.pdb"
Chain information for Yada yada virus AlphaFold.pdb #42
---
Chain | Description
A | No description available
> color #42 #5555ffff
> color #42 #5500ffff
> color #42 #ff007fff
> color #42 #ca0065ff
> color #42 #5dcac6ff
> color #42 #6647caff
> color #42 #ca6d89ff
> color #42 #ca758cff
> color #42 #ca7585ff
> color #42 #77ca53ff
> color #42 #ca78c3ff
> color #42 #ca7894ff
> color #42 #ca6d83ff
> color #42 magenta
> color #42 #ff2ad8ff
> color #42 #ff1ebbff
> color #42 #b623ffff
> color #42 #da23ffff
> color #42 #e837ffff
> color #42 #ff4c91ff
> color #42 #ff3acaff
> color #42 #ff2fd2ff
> color #42 #ff11b4ff
> color #42 #c30d89ff
> color #42 #c340abff
> color #42 #5d6fc3ff
> color #42 #7a73c3ff
> color #42 #c35344ff
> color #42 #a8473bff
> color #42 #a84e37ff
> color #42 #a8412fff
> color #42 #a83931ff
> color #42 #b63d35ff
> color #42 #b6877bff
> color #42 #b67d6fff
> color #42 #b65b5bff
> color #42 #a65353ff
> color #42 #b15959ff
> color #42 #b13e3aff
> color #42 #b13227ff
> color #42 #89b19eff
> ui tool show Matchmaker
> matchmaker #42 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Yada yada virus AlphaFold.pdb, chain A
(#42), sequence alignment score = 480
RMSD between 140 pruned atom pairs is 0.706 angstroms; (across all 149 pairs:
0.975)
> hide #41 models
> select add #41
4748 atoms, 4801 bonds, 296 residues, 1 model selected
> select subtract #41
Nothing selected
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:125
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 42/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select clear
Drag select of 1 atoms, 1 bonds
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:190
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:183
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> color #42 #a5d6beff
> color #42 #9eccb6ff
> color sel gray
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel red
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #42/A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:125
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> select #42/A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color sel blue
> ui mousemode right select
> select #42/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color sel red
> ui mousemode right select
> select #42/A:190
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #42/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #42/A:157
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel orange
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #42/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #42/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jun 29 18:48:25 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Aura virus AlphaFold.pdb"
Chain information for Aura virus AlphaFold.pdb #43
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #43 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Aura virus AlphaFold.pdb, chain A
(#43), sequence alignment score = 493.2
RMSD between 143 pruned atom pairs is 0.738 angstroms; (across all 149 pairs:
1.063)
> color #43 #55007fff
> color #43 #8d00d3ff
> hide #42 models
> select add #42
4151 atoms, 4199 bonds, 268 residues, 1 model selected
> select subtract #42
Nothing selected
> ui mousemode right select
> select #43/A:124
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 43/A
> select #43/A:125
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #43/A:124
15 atoms, 14 bonds, 1 residue, 1 model selected
Drag select of 15 residues
> select clear
Drag select of 31 residues
> ui mousemode right translate
> ui mousemode right select
> select #43/A:125
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right select
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel light sea green
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:239
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #43/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #43/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel magenta
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
[Repeated 3 time(s)]
> hide sel atoms
> show sel atoms
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:177
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> color #43 #ff55ffff
> color #43 #aaaaffff
> color #43 #8d8dd3ff
> color #43 #9696e1ff
> color #43 #a391e1ff
> color #43 #b58ae1ff
> color #43 #bb8ee8ff
> color sel blue
> ui mousemode right select
> select #43/A:182
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> hide sel atoms
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 7 atom styles
> show sel atoms
> color sel magenta
> ui mousemode right translate
> color #43 #c797f7ff
> color sel magenta
> color sel blue
> color sel magenta
> ui mousemode right select
> select #43/A:177
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:189@CA
1 atom, 1 residue, 1 model selected
> select #43/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #43/A:239
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> select #43/A:125
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #43/A:239
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #43/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #43/A:153
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jul 3 21:54:16 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/BFV AlphaFold.pdb"
Chain information for BFV AlphaFold.pdb #44
---
Chain | Description
A | No description available
> hide #43 models
> select add #43
4223 atoms, 4279 bonds, 267 residues, 1 model selected
> select subtract #43
Nothing selected
> color #44 #ffaa7fff
> color #44 #ffb375ff
> color #44 #ffa77bff
> color #44 #ffae6cff
> color #44 #c78854ff
> color #44 #d18f59ff
> color #44 #dc965dff
> color #44 #cf8d58ff
> color #44 #d18f59ff
> ui tool show Matchmaker
> matchmaker #44 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with BFV AlphaFold.pdb, chain A (#44),
sequence alignment score = 630.2
RMSD between 144 pruned atom pairs is 0.775 angstroms; (across all 149 pairs:
1.027)
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:112
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 44/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #44/A:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #44/A:226
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> set bgColor black
> set bgColor white
> ui mousemode right select
Drag select of 1 residues
> select #44/A:176
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
Drag select of 3 residues
> select clear
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:164
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #44/A:143
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #44/A:140
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #44/A:140
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #44/A:140
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jul 3 22:05:56 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/WEEV AlphaFold.pdb"
Chain information for WEEV AlphaFold.pdb #45
---
Chain | Description
A | No description available
> color #45 #00aaffff
> color #45 blue
> color #45 #00007fff
> color #45 #5500ffff
> color #45 #00aaffff
> color #45 #0093ddff
> color #45 #0083c5ff
> color #45 #0079b6ff
> hide #44 models
> color #45 #0084c6ff
> color #45 #2f78c6ff
> color #45 #4075c6ff
> color #45 #5581c6ff
> color #45 #6a92c6ff
> show #36 models
> hide #36 models
> select add #44
4047 atoms, 4099 bonds, 253 residues, 1 model selected
> select subtract #44
Nothing selected
> ui tool show Matchmaker
> matchmaker #45 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with WEEV AlphaFold.pdb, chain A (#45),
sequence alignment score = 514.5
RMSD between 148 pruned atom pairs is 0.714 angstroms; (across all 149 pairs:
0.757)
> ui mousemode right select
> select #45/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 45/A
> ui mousemode right translate
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #45/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #45/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select #2/I:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #45/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 15 atom styles
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #45/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel magenta
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jul 4 13:42:21 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #45/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #45/A:148
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 10 atom styles
> show sel atoms
[Repeated 1 time(s)]
> color sel gray
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #45/A:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Tue Jul 4 14:24:08 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/EEEV AlphaFold.pdb"
Chain information for EEEV AlphaFold.pdb #46
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #46 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with EEEV AlphaFold.pdb, chain A (#46),
sequence alignment score = 506.1
RMSD between 148 pruned atom pairs is 0.711 angstroms; (across all 149 pairs:
0.764)
> hide #45 models
> select add #45
4153 atoms, 4213 bonds, 259 residues, 1 model selected
> select subtract #45
Nothing selected
> color #46 black
> color #46 #444444ff
> color #46 #646464ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 46/A
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> set bgColor black
> set bgColor white
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #46/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel magenta
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #46/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> style sel stick
Changed 17 atom styles
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> color sel gray
Drag select of 2 residues
> select #2/I:156
5 atoms, 4 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #46/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> style sel stick
Changed 17 atom styles
> show sel atoms
> color sel orange
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jul 5 13:32:58 2023 ———
opened ChimeraX session
> color #46 #424242ff
> color #46 #323232ff
> color #46 #3a3a3aff
> ui mousemode right select
> select #46/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #46/A:171@CA
1 atom, 1 residue, 1 model selected
> color #46 #28293aff
> color #46 #aaaa7fff
> color #46 #55007fff
> color #46 magenta
> color #46 #550000ff
> color #46 #660000ff
> color #46 #710000ff
> color #46 #6f0000ff
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> show #30 models
> hide #30 models
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #46/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> color sel orange
> select #46/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #46/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
Drag select of 2 residues
> select #46/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #46/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #46/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #46/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #46/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Wed Jul 5 13:38:28 2023 ———
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Getah virus AlphaFold.pdb"
Chain information for Getah virus AlphaFold.pdb #47
---
Chain | Description
A | No description available
> color #47 #aaaa7fff
> color #47 #aa5500ff
> color #47 #a15100ff
> color #47 #8c4600ff
> color #47 #8c4b0aff
> color #47 #8c5512ff
> color #47 #8c5d0cff
> color #47 #9c680dff
> color #47 #8c5d0cff
> color #47 #aa5500ff
> color #47 #a35200ff
> color #47 #ad5700ff
> hide #46 models
> select add #46
4167 atoms, 4228 bonds, 261 residues, 1 model selected
> select subtract #46
Nothing selected
> ui tool show Matchmaker
> matchmaker #47 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Getah virus AlphaFold.pdb, chain A
(#47), sequence alignment score = 673.5
RMSD between 145 pruned atom pairs is 0.778 angstroms; (across all 149 pairs:
0.993)
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 47/A
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #47/A:129
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:191
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:184
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #47/A:158
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #47/A:155
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Mayaro virus AlphaFold.pdb"
Chain information for Mayaro virus AlphaFold.pdb #48
---
Chain | Description
A | No description available
> hide #47 models
> select add #47
4298 atoms, 4353 bonds, 268 residues, 1 model selected
> select subtract #47
Nothing selected
> color #48 #ffaa00ff
> color #48 #55aa00ff
> color #48 #51a200ff
> ui tool show Matchmaker
> matchmaker #48 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Mayaro virus AlphaFold.pdb, chain A
(#48), sequence alignment score = 674.3
RMSD between 147 pruned atom pairs is 0.759 angstroms; (across all 149 pairs:
0.801)
> color #48 #59b100ff
> color #48 #5bb600ff
[Repeated 1 time(s)]
> color #48 #5bb500ff
> color #48 #5ab300ff
> color #48 #60ba00ff
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:117
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 48/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:119
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel orange red
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:181
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Thu Jul 6 13:25:11 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #48/A:117
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #48/A:119
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #48/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #48/A:181
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel red
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #48/A:148
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel red
> color sel blue
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #48/A:145
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #48/A:145
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #48/A:145
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/SFV AlphaFold.pdb"
Chain information for SFV AlphaFold.pdb #49
---
Chain | Description
A | No description available
> color #49 #cd965eff
> color #49 #ffaaffff
> color #49 #ff007fff
> color #49 #ff257cff
> color #49 #ff478eff
> color #49 #ff66b5ff
> color #49 #ff8abfff
> color #49 #ff74b3ff
> color #49 #ff576dff
> select add #48
4180 atoms, 4234 bonds, 258 residues, 1 model selected
> select subtract #48
Nothing selected
> ui tool show Matchmaker
> matchmaker #49 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with SFV AlphaFold.pdb, chain A (#49),
sequence alignment score = 688.6
RMSD between 147 pruned atom pairs is 0.722 angstroms; (across all 149 pairs:
0.761)
> hide #48 models
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 49/A
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #49/A:128
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #49/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> color #49 #ff6b75ff
> color #49 #ff8c98ff
> color #49 #ff878fff
> color #49 #ff7d7fff
> ui mousemode right rotate
> ui mousemode right select
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> select #49/A:128
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #49/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:190
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color sel red
> style sel stick
Changed 15 atom styles
> show sel atoms
> ui mousemode right select
Drag select of 1 residues
> select #2/I:183@CA
1 atom, 1 residue, 1 model selected
> select #49/A:183
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jul 10 15:59:37 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:157
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #49/A:154
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel blue
> color sel red
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/Sindbis virus AlphaFold.pdb"
Chain information for Sindbis virus AlphaFold.pdb #50
---
Chain | Description
A | No description available
> color #50 white
> color #50 #ccccccff
> color #50 #c5c5c5ff
> color #50 #b0b0b0ff
> color #50 #b8b8b8ff
> hide #49 models
> select add #49
4263 atoms, 4315 bonds, 267 residues, 1 model selected
> select subtract #49
Nothing selected
> ui tool show Matchmaker
> matchmaker #50 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j2w.pdb, chain I (#2) with Sindbis virus AlphaFold.pdb, chain A
(#50), sequence alignment score = 517.9
RMSD between 146 pruned atom pairs is 0.676 angstroms; (across all 149 pairs:
0.789)
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 50/A
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> show #49 models
Drag select of 2 residues
> select clear
> hide #50 models
> ui mousemode right translate
> ui mousemode right select
> select #49/A:183
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
Alignment identifier is 49/A
> show #50 models
> select add #49
4263 atoms, 4315 bonds, 267 residues, 1 model selected
> select subtract #49
Nothing selected
Drag select of 2 residues
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
Alignment identifier is 49/A
Drag select of 3 residues
> select #50/A:110
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide #50 models
> select add #50
4183 atoms, 4237 bonds, 264 residues, 1 model selected
> select subtract #50
Nothing selected
> ui mousemode right select
> select #49/A:183
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #49/A:157
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #49/A:157
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide #49 models
> select add #49
4263 atoms, 4315 bonds, 267 residues, 1 model selected
> select subtract #49
Nothing selected
> show #50 models
> ui mousemode right select
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
Drag select of 8 residues
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
Drag select of 2 residues
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel orange red
> ui mousemode right translate
> ui mousemode right select
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel light gray
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> color sel byhetero
> color sel byelement
> color #50 #bcbcbcff
Drag select of 5 residues
> select clear
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:236
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 12 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:179
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #50/A:179
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #50/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 22 atom styles
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #50/A:150
16 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/overlap of CP structures.cxs"
——— End of log from Mon Jul 10 18:33:01 2023 ———
opened ChimeraX session
> hide #2 models
> ui tool show Matchmaker
> matchmaker #43 to #50
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 Sindbis virus AlphaFold.pdb, chain A (#50) with Aura virus
AlphaFold.pdb, chain A (#43), sequence alignment score = 980.1
RMSD between 167 pruned atom pairs is 0.483 angstroms; (across all 262 pairs:
15.441)
> ui tool show Matchmaker
> matchmaker #43 to #50
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 Sindbis virus AlphaFold.pdb, chain A (#50) with Aura virus
AlphaFold.pdb, chain A (#43), sequence alignment score = 980.1
RMSD between 167 pruned atom pairs is 0.483 angstroms; (across all 262 pairs:
15.441)
> show #43 models
> ui mousemode right select
> ui mousemode right translate
> select #50/A:150
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #50/A:150
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select clear
> select #50/A:179
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 21 atom styles
> show sel atoms
> 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
> hide sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> show sel cartoons
> color #50 #bfbfbfff
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel gray
Drag select of 2 residues
[Repeated 1 time(s)]
> select #43/A:229
16 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 22 atom styles
> show sel cartoons
> hide sel atoms
> select #43/A:125
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #43/A:125
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #50/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #50/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #43/A:127
22 atoms, 21 bonds, 1 residue, 1 model selected
> color #43 #c898f8ff
> ui mousemode right translate
> color #43 #c092eeff
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #43/A:239
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #50/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #43/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #43/A:177
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 8 residues
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #50/A:150
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #43/A:153@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select #43/A:153
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 7 residues
> select #50/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #43/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #43/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> color #50 #d6d6d6ff
> color #50 blue
> color #50 #0055ffff
> color #50 #55aaffff
> color #50 #4e9debff
> color #50 #61a4ebff
> color #50 #5997d9ff
> color #50 #5092d9ff
> color #50 #579eebff
> color #50 #549ae5ff
Drag select of 4 residues
> select #43/A:228
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel gray
> select #43/A:183
21 atoms, 21 bonds, 1 residue, 1 model selected
Alignment identifier is 43/A
> color sel gray
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #43/A:183
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #43/A:183
21 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 21 atom styles
> show sel cartoons
> show sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #43/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
Drag select of 2 residues
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #50/A:246
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #50/A:245
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #50/A:246
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #43/A:249
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #50/A:246
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> select #43/A:250
24 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> style sel stick
Changed 24 atom styles
> show sel atoms
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel light gray
> color sel gray
> ui mousemode right translate
> hide #43 models
> show #43 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures.cxs"
——— End of log from Tue Jul 18 20:54:16 2023 ———
opened ChimeraX session
> hide #43 models
> select add #43
4223 atoms, 4279 bonds, 267 residues, 1 model selected
> select subtract #43
Nothing selected
> show #44 models
> color #44 #e19a60ff
> set bgColor black
> set bgColor white
> ui mousemode right select
> select #44/A:112
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> select #44/A:114
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right select
> select #44/A:226
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #44/A:176
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #44/A:173
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #44/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #44/A:173
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 44/A
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #44/A:173
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 #44/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #44/A:237
24 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> select #44/A:170
20 atoms, 20 bonds, 1 residue, 1 model selected
> style sel stick
Changed 20 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/overlap of CP structures comp. Sindbis.cxs"
> ui mousemode right select
> select #44/A:164
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #44/A:143
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> show sel atoms
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right select
> select #44/A:140
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Tue Jul 18 21:16:37 2023 ———
opened ChimeraX session
> show #17 models
> hide #44 models
> select add #44
4047 atoms, 4099 bonds, 253 residues, 1 model selected
> select subtract #44
Nothing selected
> color #17 #007f5dff
> ui mousemode right select
> select #17/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #17/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #17/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #17/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
Alignment identifier is 17/A
> show sel atoms
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #17/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #17/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> hide sel atoms
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #17/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #17/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #17/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #17/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right select
> select #17/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #17/A:150
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #17/A:150
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #18 models
> hide #17 models
> select add #17
4212 atoms, 4263 bonds, 263 residues, 1 model selected
> select subtract #17
Nothing selected
> color #18 #f07d09ff
> color #18 #ef7c09ff
> ui mousemode right rotate
> ui mousemode right select
> select #18/A:125
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #18/A:123
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #18/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right select
> select #18/A:190
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #18/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
Alignment identifier is 18/A
> select #18/A:186
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #18/A:186
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #18/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #18/A:185
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 blue
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #18/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> select #18/A:183
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #18/A:183
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #18/A:183
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 16 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select clear
Drag select of 1 residues
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #18/A:175
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #18/A:151
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #18/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Wed Jul 19 11:49:32 2023 ———
opened ChimeraX session
> hide #18 models
> select add #18
4336 atoms, 4396 bonds, 269 residues, 1 model selected
> select subtract #18
Nothing selected
> show #19 models
> ui tool show Matchmaker
> matchmaker #19 to #50
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 Sindbis virus AlphaFold.pdb, chain A (#50) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 773.2
RMSD between 10 pruned atom pairs is 1.228 angstroms; (across all 254 pairs:
35.143)
> hide #19 models
> show #19 models
> hide #19 models
> ui tool show Matchmaker
> matchmaker #19 to #50
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 Sindbis virus AlphaFold.pdb, chain A (#50) with Cabassou virus
Alphafold.pdb, chain A (#19), sequence alignment score = 773.2
RMSD between 10 pruned atom pairs is 1.228 angstroms; (across all 254 pairs:
35.143)
> show #19 models
> show #18 models
> hide #19 models
> hide #18 models
> show #18 models
> hide #18 models
> show #19 models
> ui tool show Matchmaker
> matchmaker #19 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 Cabassou virus Alphafold.pdb, chain A
(#19), sequence alignment score = 523.2
RMSD between 146 pruned atom pairs is 0.713 angstroms; (across all 149 pairs:
0.884)
> color #19 #90d66bff
> color #19 #92d86cff
> color #19 #90d66bff
> ui mousemode right select
> select #19/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #19/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #19/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #19/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 1 residues
> select #50/A:185
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #19/A:194
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 19/A
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #19/A:194
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 #19/A:190
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #19/A:258
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #19/A:191
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #19/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #19/A:206
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #19/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #19/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #19/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #19
4422 atoms, 4482 bonds, 275 residues, 1 model selected
> select subtract #19
Nothing selected
> hide #19 models
> show #19 models
> hide #19 models
> show #18 models
> ui mousemode right select
> select #18/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #18/A:183
16 atoms, 15 bonds, 1 residue, 1 model selected
> select add #18
4336 atoms, 4396 bonds, 269 residues, 1 model selected
> select subtract #18
Nothing selected
> hide #18 models
> show #20 models
> hide #20 models
> show #2 models
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> color #2 #20e0eeff
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
Alignment identifier is 2/I
> style sel stick
Changed 9 atom styles
> show sel atoms
> color sel red
> select clear
[Repeated 1 time(s)]
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> hide sel atoms
> ui mousemode right select
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 14 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:184
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel gray
> hide sel atoms
> show sel atoms
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> hide #2 models
> select add #2
30928 atoms, 31759 bonds, 4020 residues, 1 model selected
> select subtract #2
Nothing selected
> show #20 models
> hide #20 models
> show #46 models
> hide #46 models
> show #46 models
> color #46 #750000ff
> ui mousemode right select
> select #46/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #46/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #46/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> 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
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #46/A:180
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 46/A
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #46/A:180
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #46/A:180
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
> select add #46
4167 atoms, 4228 bonds, 261 residues, 1 model selected
> select subtract #46
Nothing selected
> ui mousemode right select
> select #50/A:179
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #46/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> style sel ball
Changed 17 atom styles
> ui mousemode right select
> select #46/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #46/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #46/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #46/A:244
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180@CA
1 atom, 1 residue, 1 model selected
> select #46/A:177
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> select add #46
4167 atoms, 4228 bonds, 261 residues, 1 model selected
> select subtract #46
Nothing selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> hide #46 models
> show #20 models
> ui tool show Matchmaker
> matchmaker #20 to #50
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 Sindbis virus AlphaFold.pdb, chain A (#50) with Eilat virus
Alphafold.pdb, chain A (#20), sequence alignment score = 850
RMSD between 154 pruned atom pairs is 0.618 angstroms; (across all 248 pairs:
35.914)
> color #20 #00b383ff
> ui mousemode right select
> select #20/A:113
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #20/A:115
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #20/A:227
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #20/A:177
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #20/A:174
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 20/A
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> hide sel atoms
> show sel atoms
> color sel red
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #20/A:238
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #20/A:238
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #20/A:238
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #20/A:171
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #20/A:165
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #20/A:141@CA
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> show sel atoms
> ui mousemode right select
> select #20/A:141
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #20/A:141@CA
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> show sel atoms
> ui mousemode right select
> select #20/A:141
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #20/A:144
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #20/A:238
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #20/A:171
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> hide #20 models
> select add #20
3966 atoms, 4011 bonds, 255 residues, 1 model selected
> select subtract #20
Nothing selected
> show #15 models
> hide #15 models
> show #16 models
> color #16 #fe00feff
> ui mousemode right select
> select #16/A:134
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #16/A:132
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #16/A:246
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #16/A:246
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #16/A:196
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select clear
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #16/A:193
15 atoms, 14 bonds, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Alignment identifier is 16/A
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #16/A:257
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #16/A:190
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #16/A:189@CA
1 atom, 1 residue, 1 model selected
> select #16/A:189
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #16/A:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #16/A:184
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #16/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel cartoons
> hide sel atoms
> ui mousemode right select
> select #16/A:160
16 atoms, 15 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #16/A:193
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #16/A:257
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #16/A:190
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #16/A:190
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Mon Jul 31 10:36:12 2023 ———
opened ChimeraX session
> show #47 models
> hide #16 models
> select add #16
4411 atoms, 4467 bonds, 274 residues, 1 model selected
> select subtract #16
Nothing selected
> color #47 #b05800ff
> color #47 #ad5700ff
> ui mousemode right select
> select #47/A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #47/A:129
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> ui mousemode right select
> select #47/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #47/A:191@CA
1 atom, 1 residue, 1 model selected
> select #47/A:191
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 50/A
Alignment identifier is 50/A
> select #47/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 47/A
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #50/A:179
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #47/A:184
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #47/A:179@CA
1 atom, 1 residue, 1 model selected
> select #47/A:179@CA
1 atom, 1 residue, 1 model selected
Drag select of 4 residues
> select #47/A:177
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #47/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #47/A:158
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #47/A:155
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #47/A:155
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #47/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #47/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
Drag select of 2 residues
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #47/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #47/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> show sel atoms
> color sel gray
> ui mousemode right select
> select #47/A:185
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel dark gray
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> open "C:/Users/Carolina/Downloads/Fort Morgan virus AlphaFold.pdb"
Chain information for Fort Morgan virus AlphaFold.pdb #51
---
Chain | Description
A | No description available
> color #51 #55557fff
> color #51 #00aa7fff
> color #51 #aaff7fff
> color #51 #00557fff
> color #51 #006999ff
> color #51 #1d5999ff
> color #51 #2f7999ff
> color #51 #3a6899ff
> color #51 #4276adff
> color #51 #4f81adff
> hide #47 models
> select add #47
4298 atoms, 4353 bonds, 268 residues, 1 model selected
> select subtract #47
Nothing selected
> ui tool show Matchmaker
> matchmaker #51 to #50
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 Sindbis virus AlphaFold.pdb, chain A (#50) with Fort Morgan virus
AlphaFold.pdb, chain A (#51), sequence alignment score = 836.3
RMSD between 167 pruned atom pairs is 0.504 angstroms; (across all 260 pairs:
13.821)
> color #51 #00557fff
> color #51 #006c9eff
> color #51 #00608cff
> color #51 #17448cff
> color #51 #311f8cff
> color #51 #00007fff
> color #51 blue
> color #51 #0000d6ff
> color #51 #00007fff
> color #51 #0000a8ff
> color #51 #0000c5ff
> color #51 #0000b4ff
> color #51 #0e27b4ff
> color #51 #171eb4ff
> color #51 #2129b4ff
> color #51 #2836b4ff
> color #51 #272eb4ff
> ui mousemode right rotate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #51/A:180
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 51/A
> ui mousemode right translate
> style sel stick
Changed 15 atom styles
> show sel atoms
> color sel red
> ui mousemode right select
[Repeated 1 time(s)]
> select #51/A:244
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #51/A:244
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> hide sel atoms
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #51/A:177
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> hide #51 models
> select add #51
4193 atoms, 4251 bonds, 261 residues, 1 model selected
> select subtract #51
Nothing selected
> show #47 models
> hide #47 models
> show #21 models
> color #21 #0077b3ff
> color #21 #006ea5ff
> color #21 #0073adff
> color #21 #006fa6ff
> ui mousemode right select
> select #21/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #21/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right select
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #21/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #21/A:181@N
1 atom, 1 residue, 1 model selected
> select #21/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #21/A:178
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 #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #21/A:242
24 atoms, 25 bonds, 1 residue, 1 model selected
Alignment identifier is 21/A
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #21/A:175
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #21/A:175
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Mon Jul 31 12:55:07 2023 ———
opened ChimeraX session
> show #22 models
> hide #21 models
> select add #21
4166 atoms, 4222 bonds, 259 residues, 1 model selected
> select subtract #21
Nothing selected
> color #22 #fa5300ff
> color #22 #ff5500ff
> color #22 #ff7a0eff
> ui mousemode right rotate
> ui mousemode right select
> select #22/A:121
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #22/A:119
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #22/A:147@CB
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #22/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #22/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #22/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #22/A:147
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #22/A:176
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #22/A:183
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #22/A:180
15 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #22/A:180
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #22/A:180
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 22/A
> color sel red
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #22/A:244
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #22/A:177
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #48 models
> select add #22
4167 atoms, 4228 bonds, 261 residues, 1 model selected
> select subtract #22
Nothing selected
> hide #22 models
> ui mousemode right select
> select #48/A:238
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #48/A:238
11 atoms, 10 bonds, 1 residue, 1 model selected
Alignment identifier is 48/A
> ui mousemode right translate
> color #48 #62bd00ff
> color #48 #60ba00ff
> ui mousemode right select
> select #48/A:119
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #48/A:117
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> 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
> hide sel atoms
> ui mousemode right select
> select #48/A:181
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #48/A:178
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #48/A:178
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
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Tue Aug 1 09:36:23 2023 ———
opened ChimeraX session
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #48/A:242
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel gray
> set bgColor white
> ui mousemode right rotate
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/A:175
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> style sel stick
Changed 21 atom styles
> show sel atoms
> color sel gray
> ui mousemode right select
> select #48/A:174@CA
1 atom, 1 residue, 1 model selected
> select #48/A:174@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #48/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/A:174
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #48/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #48/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #48/A:145
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #48/A:147
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> select #48/A:147
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #48/A:148
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #48
4180 atoms, 4234 bonds, 258 residues, 1 model selected
> select subtract #48
Nothing selected
> hide #48 models
> show #43 models
> hide #43 models
> show #44 models
> hide #44 models
> show #17 models
> hide #17 models
> show #18 models
> hide #18 models
> show #19 models
> hide #19 models
> show #2 models
> hide #2 models
> show #46 models
> hide #46 models
> show #20 models
> ui mousemode right select
> select #20/A:170
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> hide #20 models
> select add #20
3966 atoms, 4011 bonds, 255 residues, 1 model selected
> show #21 models
> select subtract #20
Nothing selected
> select add #20
3966 atoms, 4011 bonds, 255 residues, 1 model selected
> select subtract #20
Nothing selected
> hide #21 models
> show #16 models
> hide #50 models
> show #51 models
> hide #51 models
> show #47 models
> hide #47 models
> show #21 models
> ui mousemode right select
> select #16/A:193
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide #16 models
> show #50 models
Drag select of 2 residues
> select #21/A:178
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #21/A:242
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #21/A:175
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #21/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #21/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #21/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #21/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #21/A:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #21/A:148
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #51 models
> hide #51 models
> hide #50 models
> show #50 models
> hide #50 models
> show #50 models
> select add #21
4166 atoms, 4222 bonds, 259 residues, 1 model selected
> select subtract #21
Nothing selected
> hide #21 models
> show #21 models
> show #43 models
> hide #43 models
> hide #21 models
> show #22 models
> hide #22 models
> show #48 models
> hide #48 models
> show #11 models
> color #11 #5a43cfff
> ui mousemode right select
> select #11/A:132
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #11/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #11/A:244
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #11/A:194
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #11/A:192
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #11/A:191
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 11/A
> show sel atoms
> ui mousemode right translate
> color sel red
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #11/A:255
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #11/A:188
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #11/A:187@CA
1 atom, 1 residue, 1 model selected
> select #11/A:187@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select #11/A:187
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #11/A:182
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #11/A:161
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #11/A:158
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #44 models
> hide #11 models
> select add #11
4348 atoms, 4410 bonds, 271 residues, 1 model selected
> select subtract #11
Nothing selected
> ui mousemode right select
> select #44/A:173
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #44/A:237
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #44/A:170
20 atoms, 20 bonds, 1 residue, 1 model selected
Alignment identifier is 44/A
> hide #44 models
> select add #44
4047 atoms, 4099 bonds, 253 residues, 1 model selected
> select subtract #44
Nothing selected
> show #18 models
> show #23 models
> hide #18 models
> hide #23 models
> show #23 models
> ui tool show Matchmaker
> matchmaker #23 to #50
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 Sindbis virus AlphaFold.pdb, chain A (#50) with Mosso das Pedras
virus AlphaFold.pdb, chain A (#23), sequence alignment score = 753.4
RMSD between 159 pruned atom pairs is 0.501 angstroms; (across all 252 pairs:
36.942)
Drag select of 1 residues
> select #50/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> color #23 #a2a279ff
Drag select of 79 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #23/A:139
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #23/A:137
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #23/A:251
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #23/A:201
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right select
> select #23/A:198
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #23/A:198
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 23/A
> color sel red
> select clear
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #23/A:262
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #23/A:262
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right select
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #23/A:195
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
Drag select of 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #23/A:194@CA
1 atom, 1 residue, 1 model selected
> select #23/A:194
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select #23/A:189
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #23/A:165
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #23/A:168
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> hide #23 models
> select add #23
4449 atoms, 4504 bonds, 279 residues, 1 model selected
> select subtract #23
Nothing selected
> show #25 models
> color #25 #fd7ac9ff
> color #25 #ff7bcaff
> ui mousemode right select
Drag select of 4 residues
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #25/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #25/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #25/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select #25/A:194
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #25/A:194
12 atoms, 11 bonds, 1 residue, 1 model selected
Alignment identifier is 25/A
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #25/A:258
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #25/A:191
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #25/A:191
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #25/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #25/A:190@CA
1 atom, 1 residue, 1 model selected
> select #25/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #25/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #25/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 2 time(s)]
> select #25/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #25/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #25/A:164@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #25/A:164@CA
1 atom, 1 residue, 1 model selected
> select #25/A:164
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #23 models
> show #24 models
> hide #24 models
> hide #23 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Tue Aug 1 14:51:39 2023 ———
opened ChimeraX session
> hide #25 models
> show #25 models
> select add #25
4421 atoms, 4479 bonds, 275 residues, 1 model selected
> hide #25 models
> select subtract #25
Nothing selected
> show #15 models
> color #15 #fa9765ff
> color #15 #ff9a67ff
> ui mousemode right select
> select #15/A:130
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 1 residues
> select #15/A:128
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #15/A:242
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #15/A:192
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #15/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> ~hbonds
Alignment identifier is 15/A
> ui mousemode right translate
> show sel atoms
> color sel red
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #15/A:253
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select clear
> select #15/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #15/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #15/A:186
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #15/A:185
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #15/A:180
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #15/A:159
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #15/A:156
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #15
4293 atoms, 4344 bonds, 269 residues, 1 model selected
> select subtract #15
Nothing selected
> hide #15 models
> show #26 models
> color #26 #69699cff
> color #26 #7171a8ff
> color #26 #8686c8ff
> color #26 #7979b4ff
> color #26 #5d5d8aff
> color #26 #646495ff
> color #26 #7676b0ff
> ui mousemode right rotate
> ui mousemode right select
> select #26/A:121
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #26/A:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #26/A:119
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #26/A:233
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #26/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #26/A:180
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 26/A
> ui mousemode right translate
> show sel atoms
> color sel red
> ui mousemode right select
> select #26/A:244
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel light gray
> color sel gray
> ui mousemode right select
> select clear
> select #26/A:177
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #26/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #26/A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #26/A:150
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #26/A:147
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #26
4242 atoms, 4287 bonds, 260 residues, 1 model selected
> select subtract #26
Nothing selected
> hide #26 models
> show #27 models
> color #27 #a3007dff
> color #27 #a2007cff
> ui mousemode right select
> select #27/A:135
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #27/A:133
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #27/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #27/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #27/A:194
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 27/A
> ui mousemode right translate
> show sel atoms
> color sel red
> ui mousemode right select
> select #27/A:258
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #27/A:191
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #27/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #27/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #27/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #27/A:161
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #27
4429 atoms, 4485 bonds, 275 residues, 1 model selected
> select subtract #27
Nothing selected
> hide #27 models
> show #28 models
> color #28 #4b4b4bff
> color #28 #464646ff
> color #28 #3a3a3aff
> ui mousemode right select
> select #28/A:138
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #28/A:136
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #28/A:250
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #28/A:250
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #28/A:250
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #28/A:200
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #28/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 28/A
> ui mousemode right translate
> show sel atoms
> color sel red
> ui mousemode right select
> select #28/A:261
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #28/A:194
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #28/A:193
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #28/A:188
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #28/A:164
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #28/A:167
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #28
4421 atoms, 4477 bonds, 278 residues, 1 model selected
> select subtract #28
Nothing selected
> show #10 models
> hide #28 models
> color #10 #810081ff
> ui mousemode right select
> select #10/A:131
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #10/A:129
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #10/A:243
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #10/A:193
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #10/A:190
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 10/A
> ui mousemode right translate
> show sel atoms
> color sel red
> ui mousemode right select
> select #10/A:254
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #10/A:187
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #10/A:186
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #10/A:186
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #10/A:181
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #10/A:157
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #10/A:156
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #10/A:156
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #10/A:157
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #10/A:160
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #10
4349 atoms, 4399 bonds, 270 residues, 1 model selected
> select subtract #10
Nothing selected
> show #13 models
> hide #10 models
> color #13 #5e45d8ff
> color #13 #6248e1ff
> ui mousemode right select
> select #13/A:143
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #13/A:141
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #13/A:254
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #13/A:204
12 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #13/A:202
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #13/A:201
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 13/A
> select #13/A:202
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #13/A:265
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #13/A:265
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #13/A:265
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #13/A:199
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel magenta
> ui mousemode right select
> select #13/A:172
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #13/A:169
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #13/A:198
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #13/A:193
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> color #13 #7757e1ff
> color #13 #886de1ff
> color #13 #7865e1ff
> color #13 #8956e1ff
> color #13 #7856e1ff
> color #13 #7865e1ff
> color #13 #7461e1ff
> color #13 #7763e6ff
> color #13 #5446a3ff
> color #13 #6b59cfff
> color #13 #795fcfff
> color #13 #8a62cfff
> color #13 #6d59cfff
> color #13 #6b57cfff
> color #13 #675dcfff
> color #13 #6c62d9ff
> color #13 #6960d4ff
> set bgColor white
> ui mousemode right select
> select #13/A:202
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #13/A:265
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel gray
> select #13/A:199
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel magenta
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Wed Aug 2 11:23:08 2023 ———
opened ChimeraX session
> select add #13
4435 atoms, 4474 bonds, 282 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #13 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #49 models
> color #49 #fe7d7fff
> color #49 #ff7d7fff
> ui mousemode right select
> select #49/A:129
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #49/A:128
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #49/A:126
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #49/A:157
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #49/A:154
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #49/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #49/A:190
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #49/A:187
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel red
Alignment identifier is 49/A
> ui mousemode right select
> select #49/A:251
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #49/A:184
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #49/A:183
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #49/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #49
4263 atoms, 4315 bonds, 267 residues, 1 model selected
> select subtract #49
Nothing selected
> hide #49 models
> show #24 models
> color #24 #6b6b4fff
> color #24 #6c6c50ff
> color #24 #828260ff
> color #24 #5b5b43ff
> color #24 #636349ff
> color #24 #707053ff
> ui mousemode right select
> select #24/A:129
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #24/A:127
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #24/A:158
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #24/A:155
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #24/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #24/A:241
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #24/A:191
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #24/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
Alignment identifier is 24/A
> color sel red
> select #24/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #24/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #24/A:185
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel dark gray
> color sel gray
> ui mousemode right translate
> color #24 #6a7045ff
> color #24 #54704cff
> color #24 #567045ff
> color #24 #6e7057ff
> color #24 #706d5aff
> color #24 #6f704fff
> color #24 #a5a676ff
> color #24 #c9ca8fff
> ui mousemode right rotate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #24/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel red
> select #24/A:252
24 atoms, 25 bonds, 1 residue, 1 model selected
> color sel gray
> select #24/A:185
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel light gray
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #24/A:184
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #24/A:179
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #29 models
> color #29 #373e7fff
> color #29 #363d7dff
> select add #24
4246 atoms, 4299 bonds, 268 residues, 1 model selected
> select subtract #24
Nothing selected
> hide #24 models
> ui mousemode right select
> select #29/A:135
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #29/A:133
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #29/A:247
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #29/A:197
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #29/A:194
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 29/A
> ui mousemode right translate
> show sel atoms
> color sel red
> ui mousemode right select
> select #29/A:258
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #29/A:191
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #29/A:190
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #29/A:161
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #50/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #29/A:185
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 17 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #29/A:164
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 8 residues
> select #29/A:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #30 models
> select add #29
4432 atoms, 4487 bonds, 275 residues, 1 model selected
> select subtract #29
Nothing selected
> hide #29 models
> color #30 #910e0eff
> show #46 models
> hide #46 models
> color #30 #9c0f0fff
> ui mousemode right select
> select #30/A:121
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #30/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #30/A:236
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #30/A:186@CA
1 atom, 1 residue, 1 model selected
> select #30/A:186@CA
1 atom, 1 residue, 1 model selected
> select #50/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #30/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #30/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel red
> color #30 #960f0fff
> color #30 #930e0eff
> show #46 models
> hide #46 models
> color sel red
> ui mousemode right select
> select #30/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
Alignment identifier is 30/A
> show sel atoms
> color sel gray
> select #30/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #30/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #30/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #30/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #30/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #30/A:150
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #30
4192 atoms, 4243 bonds, 264 residues, 1 model selected
> select subtract #30
Nothing selected
> show #31 models
> hide #30 models
> color #31 #ff54a4ff
> ui mousemode right select
> select #31/A:124
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #31/A:122
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #31/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #31/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #31/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #31/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #31/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
Alignment identifier is 31/A
> select #31/A:180
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> show #30 models
> hide #30 models
> select add #31
4258 atoms, 4310 bonds, 263 residues, 1 model selected
> select subtract #31
Nothing selected
> select #31/A:174
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #31/A:153
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #31/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Wed Aug 2 11:55:29 2023 ———
opened ChimeraX session
> select add #31
4258 atoms, 4310 bonds, 263 residues, 1 model selected
> select subtract #31
Nothing selected
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold/VEEV AlphaFold.pdb"
Chain information for VEEV AlphaFold.pdb #52
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #52 to #50
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 Sindbis virus AlphaFold.pdb, chain A (#50) with VEEV AlphaFold.pdb,
chain A (#52), sequence alignment score = 780
RMSD between 162 pruned atom pairs is 0.545 angstroms; (across all 256 pairs:
21.851)
> color #52 yellow
> color #52 #e6e600ff
> hide #31 models
> ui mousemode right select
> select #52/A:194
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #52/A:258
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #52/A:191
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #45 models
> hide #52 models
> color #45 #678ebfff
> ui mousemode right select
> select #45/A:119
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #45/A:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #45/A:231
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> ui mousemode right translate
> ui mousemode right select
> select #45/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #45/A:181
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #45/A:178
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
Alignment identifier is 45/A
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #45/A:242
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #45/A:175
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #45/A:242
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #45/A:174
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #45/A:169
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #45/A:148
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #45/A:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> select add #45
4153 atoms, 4213 bonds, 259 residues, 1 model selected
> select subtract #45
Nothing selected
> show #32 models
> color #32 #ffef3aff
> hide #45 models
> ui mousemode right select
> select #32/A:126
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #32/A:123
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:236
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #32/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #32/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #32/A:185
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel red
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> ui mousemode right select
> select #32/A:249
24 atoms, 25 bonds, 1 residue, 1 model selected
Alignment identifier is 32/A
> show sel atoms
> color sel gray
Drag select of 4 residues
> select clear
> select #32/A:182
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #32/A:181
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #32/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #32/A:155
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #32/A:115
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #32/A:152
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Wed Aug 2 13:12:02 2023 ———
opened ChimeraX session
> show #33 models
> hide #33 models
> hide #32 models
> select add #32
4214 atoms, 4273 bonds, 266 residues, 1 model selected
> select subtract #32
Nothing selected
> show #33 models
> color #33 #ffaed9ff
> ui mousemode right select
> select #33/A:124
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #33/A:126
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #33/A:238
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #33/A:188
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #33/A:185
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 50/A
Alignment identifier is 50/A
> select #33/A:185
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 33/A
> ui mousemode right translate
> show sel atoms
> color sel red
> ui mousemode right select
> select #33/A:181
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #33/A:249
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #50/A:246
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #33/A:249
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #33/A:182
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #33/A:182
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #33/A:155
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #33/A:152
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #33/A:176
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #33
4198 atoms, 4258 bonds, 266 residues, 1 model selected
> select subtract #33
Nothing selected
> hide #33 models
> show #34 models
> color #34 #b56d3cff
> color #34 #b06a3bff
> ui mousemode right select
> select #34/A:163
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #34/A:161
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #34/A:192
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #34/A:274
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #34/A:218
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #34/A:189
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #34/A:213
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #34/A:222
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #34/A:221
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #34/A:222
19 atoms, 18 bonds, 1 residue, 1 model selected
Alignment identifier is 34/A
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #34/A:298
14 atoms, 14 bonds, 1 residue, 1 model selected
> color #34 #bd713fff
> color #34 #c77742ff
> select #34/A:222
19 atoms, 18 bonds, 1 residue, 1 model selected
> color sel gray
> select #34/A:285
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> color sel magenta
> color sel gray
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #34/A:285
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #34/A:219
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #34/A:220
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #34/A:219
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel purple
> color sel magenta
> show sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #34
4798 atoms, 4847 bonds, 303 residues, 1 model selected
> select subtract #34
Nothing selected
> hide #34 models
> show #35 models
> color #35 #cce83fff
> color #35 #cae63eff
> ui mousemode right select
> select #35/A:97
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #35/A:95
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> color #35 #cbe73fff
> ui mousemode right select
> select #35/A:209
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #35/A:173
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #35/A:159
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #35/A:156
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #35/A:156
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #35/A:157
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #35/A:156
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
Alignment identifier is 35/A
Drag select of 2 residues
> ui mousemode right translate
> ui mousemode right select
> select #35/A:152
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #35/A:220
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #35/A:220
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #35/A:153
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel gray
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #35/A:147
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #35/A:123
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #35/A:126
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #35
3771 atoms, 3815 bonds, 236 residues, 1 model selected
> select subtract #35
Nothing selected
> hide #35 models
> show #36 models
> show #34 models
> hide #34 models
> show #34 models
> hide #36 models
> hide #34 models
> show #36 models
> color #36 #8187deff
> color #36 #8086dcff
> ui mousemode right rotate
> ui mousemode right select
> select #36/A:116
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #36/A:116
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #36/A:113
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #36/A:228
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #36/A:178
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #36/A:175
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #36/A:175
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
Alignment identifier is 36/A
> ui mousemode right translate
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #36/A:239
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
Drag select of 3 residues, 1 atoms
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #36/A:172
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #36/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #36/A:166
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #36/A:145
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #36/A:142
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #36
3980 atoms, 4027 bonds, 256 residues, 1 model selected
> select subtract #36
Nothing selected
> hide #36 models
> show #40 models
> color #40 #b18732ff
> color #40 #b88c34ff
> ui mousemode right select
> select #40/A:142
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #40/A:140
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #40/A:253
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #40/A:203
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #40/A:201
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #40/A:200
14 atoms, 13 bonds, 1 residue, 1 model selected
Alignment identifier is 40/A
> select #40/A:201
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #50/A:253
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> color #40 #c19336ff
> color #40 #c69738ff
> ui mousemode right select
> select #40/A:201
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel red
> color sel gray
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #40/A:264
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #40/A:198
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel magenta
> ui mousemode right rotate
> ui mousemode right select
> select #40/A:197
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #40/A:192
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #40/A:171
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #40/A:168
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #40
4420 atoms, 4461 bonds, 281 residues, 1 model selected
> select subtract #40
Nothing selected
> show #37 models
> hide #40 models
> color #37 #6edf42ff
> color #37 #6ddc41ff
> ui mousemode right select
> select #37/A:136
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #37/A:134
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #37/A:248
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #37/A:198
17 atoms, 16 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #37/A:195
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 37/A
> show sel atoms
> color sel red
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #37/A:259
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel dark gray
> color sel gray
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #37/A:192
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #37/A:191
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #37/A:186
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #37/A:162
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #37/A:165
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #37
4402 atoms, 4459 bonds, 276 residues, 1 model selected
> select subtract #37
Nothing selected
> show #36 models
> hide #36 models
> show #40 models
> hide #37 models
> hide #40 models
> show #37 models
> hide #37 models
> show #38 models
> color #38 #a7a756ff
> color #38 #a6a655ff
> color #38 #b0b05aff
Drag select of 15 atoms, 22 residues, 15 bonds
Drag select of 19 residues, 2 atoms, 1 bonds
> ui mousemode right translate
> ui mousemode right select
> select #38/A:117
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #38/A:114
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #38/A:229
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #38/A:179
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #38/A:176
15 atoms, 14 bonds, 1 residue, 1 model selected
Alignment identifier is 38/A
> show sel atoms
> color sel gray
> color sel red
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #38/A:240
24 atoms, 25 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #38/A:173
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #38/A:172
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #38/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #38/A:143
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #38/A:146
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #38
4010 atoms, 4055 bonds, 257 residues, 1 model selected
> select subtract #38
Nothing selected
> show #39 models
> hide #38 models
> color #39 #9e5552ff
> color #39 #a35855ff
> ui mousemode right select
> select #39/A:186
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #39/A:217
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #39/A:299
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #39/A:249
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #39/A:246
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #39/A:247
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #39/A:246
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #39/A:245
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #39/A:246
10 atoms, 9 bonds, 1 residue, 1 model selected
Alignment identifier is 39/A
> select #39/A:245
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #39/A:246
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #39/A:245
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #39/A:246
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right select
> select #39/A:214
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #39/A:238
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #39/A:243
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #39/A:244
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> select add #39
4950 atoms, 4999 bonds, 312 residues, 1 model selected
> select subtract #39
Nothing selected
> hide #39 models
> show #41 models
> color #41 #2c731cff
> color #41 #399123ff
> ui mousemode right select
> select #41/A:158
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right select
> hide sel atoms
> select #41/A:156
22 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #41/A:269
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #41/A:219
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #41/A:217
21 atoms, 21 bonds, 1 residue, 1 model selected
Alignment identifier is 41/A
> select #41/A:221
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #41/A:221
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #41/A:217
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:216
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:217
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:218
22 atoms, 21 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #41/A:217
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:217
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> color sel gray
> ui mousemode right rotate
> ui mousemode right select
> select #41/A:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> color #41 #45b02bff
> color #41 #54d634ff
> select #41/A:217
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel gray
> select #50/A:180
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:214
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #50/A:247
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #41/A:280
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #41/A:281
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #41/A:280
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel gray
> select #41/A:217
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #41/A:214
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #41/A:187
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #41/A:184
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #41/A:213
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #41/A:208
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> hide #41 models
> select add #41
4748 atoms, 4801 bonds, 296 residues, 1 model selected
> select subtract #41
Nothing selected
> show #42 models
> color #42 #a1cfb9ff
[Repeated 1 time(s)]
> color #42 #9bc7b2ff
> ui mousemode right rotate
> ui mousemode right select
> select #42/A:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #42/A:125@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #42/A:125
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #42/A:240
15 atoms, 14 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> hide sel atoms
> ui mousemode right select
> select #42/A:190
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #42/A:187
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #50/A:183
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #42/A:187
22 atoms, 21 bonds, 1 residue, 1 model selected
Alignment identifier is 42/A
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #42/A:183
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #42/A:251
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #42/A:184
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> select #42/A:178
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #42/A:154
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #42/A:157
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui mousemode right translate
> ui mousemode right select
> select #42/A:187
22 atoms, 21 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
> show #34 models
> hide #50 models
> ui mousemode right select
> select #34/A:222
19 atoms, 18 bonds, 1 residue, 1 model selected
> ui mousemode right translate
Alignment identifier is 34/A
> select add #34
4798 atoms, 4847 bonds, 303 residues, 1 model selected
> select subtract #34
Nothing selected
> hide #34 models
> show #50 models
> show #34 models
> ui mousemode right select
> select #34/A:222
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #34
4798 atoms, 4847 bonds, 303 residues, 1 model selected
> select subtract #34
Nothing selected
> hide #34 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/overlap of CP structures comp. Sindbis.cxs"
——— End of log from Wed Aug 9 11:27:54 2023 ———
> view name session-start
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/fold_sec1_model_0.cif"
Chain information for fold_sec1_model_0.cif #53
---
Chain | Description
A | .
Computing secondary structure
> hide #50 models
> hide #42 models
> show #1 models
> show #2 models
> hide #1 models
> hide #2 models
> show #2 models
> ui tool show Matchmaker
> matchmaker #53 to #2
Computing secondary structure
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 fold_sec1_model_0.cif, chain A (#53),
sequence alignment score = 527.8
RMSD between 147 pruned atom pairs is 0.715 angstroms; (across all 148 pairs:
0.768)
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> show target m
> view clip false
> log metadata #1
The model has no metadata
> log chains #1
Chain information for 7vga.pdb #1
---
Chain | Description | UniProt
A D G J | No description available | POLS_GETV 1-438
B E H K | No description available | POLS_GETV 1-422
C F I L | No description available | POLS_GETV 1-268
> log metadata #2
The model has no metadata
> log chains #2
Chain information for 3j2w.pdb #2
---
Chain | Description | UniProt
A B C D | No description available | Q1H8W5_CHIKV 1-393 1001-1393 2001-2393 3001-3393
E F G H | No description available | POLS_CHIK3 394-439 1394-1439 2394-2439 3394-3439
I | capsid protein | POLS_CHIK3 119-267
J K L | No description available | POLS_CHIK3 1119-1267 2119-2267 3119-3267
M N O | No description available | Q1H8W5_CHIKV 507-842 1507-1842 2507-2842
P | No description available | Q1H8W5_CHIKV 3507-3842
Q R S T | No description available | POLS_CHIK3 843-923 1843-1923 2843-2923 3843-3923
> log metadata #3
The model has no metadata
> log chains #3
Chain information for 1kxf.pdb #3
---
Chain | Description | UniProt
A | No description available | POLS_SINDV 106-264
> log metadata #4
The model has no metadata
> log chains #4
Chain information for 7sfu.pdb #4
---
Chain | Description | UniProt
A D G J | No description available | POLS_EEVV8 1-442
B E H K | No description available | POLS_EEVV8 1-423
C F I L | No description available | POLS_EEVV8 114-275
> log metadata #5
No models had metadata
> log chains #5
Chain information for 6xo4.pdb #5
---
Chain | Description | UniProt
A D G J | No description available | Q88678_EEEV 1-441
B E H K | No description available | Q88678_EEEV 1-420
C F I L | No description available | Q88678_EEEV 1-261
> log metadata #6
The model has no metadata
> log chains #6
Chain information for 4agk.pdb #6
---
Chain | Description | UniProt
A | No description available | POLS_AURAV 110-267
> log metadata #7
No models had metadata
> log chains #7
Chain information for 1vcp.pdb #7
---
Chain | Description | UniProt
A B C | No description available | POLS_SFV 119-267
> log metadata #8
No models had metadata
> log chains #8
Chain information for 2yew.pdb #8
---
Chain | Description | UniProt
A D G J | No description available | POLS_BFV 1-253
B E H K | No description available | POLS_BFV 1-439
C F I L | No description available | POLS_BFV 1-421
> log metadata #9
The model has no metadata
> log chains #9
Chain information for 7ko8.pdb #9
---
Chain | Description
A D G J | No description available
B E H L | No description available
C F I M | No description available
> log metadata #10
The model has no metadata
> log chains #10
Chain information for AlphFold Colaboratory Ross River.pdb #10
---
Chain | Description
A | No description available
> log metadata #11
The model has no metadata
> log chains #11
Chain information for AlphaFold Colaboratory Middelburg virus.pdb #11
---
Chain | Description
A | No description available
> log metadata #12
The model has no metadata
> log chains #12
Chain information for AlphaFold Colaboratory Everglades virus.pdb #12
---
Chain | Description
A | No description available
> log metadata #13
The model has no metadata
> log chains #13
Chain information for Alpha Fold Collaboratory Salmon Pancrease Disease.pdb
#13
---
Chain | Description
A | No description available
> log metadata #14
The model has no metadata
> log chains #14
Chain information for Alpha Fold Collaboratory Fort Morgan virus.pdb #14
---
Chain | Description
A | No description available
> log metadata #15
The model has no metadata
> log chains #15
Chain information for Ndumu virus Alphafold.pdb #15
---
Chain | Description
A | No description available
> log metadata #16
The model has no metadata
> log chains #16
Chain information for Everglades virus Alphafold.pdb #16
---
Chain | Description
A | No description available
> log metadata #17
The model has no metadata
> log chains #17
Chain information for Bebaru virus Alphafold.pdb #17
---
Chain | Description
A | No description available
> log metadata #18
The model has no metadata
> log chains #18
Chain information for Caaingua virus AlphaFold.pdb #18
---
Chain | Description
A | No description available
> log metadata #19
The model has no metadata
> log chains #19
Chain information for Cabassou virus Alphafold.pdb #19
---
Chain | Description
A | No description available
> log metadata #20
The model has no metadata
> log chains #20
Chain information for Eilat virus Alphafold.pdb #20
---
Chain | Description
A | No description available
> log metadata #21
The model has no metadata
> log chains #21
Chain information for Highlands J. virus Alphafold.pdb #21
---
Chain | Description
A | No description available
> log metadata #22
The model has no metadata
> log chains #22
Chain information for Madariaga virus Alpha Fold.pdb #22
---
Chain | Description
A | No description available
> log metadata #23
The model has no metadata
> log chains #23
Chain information for Mosso das Pedras virus AlphaFold.pdb #23
---
Chain | Description
A | No description available
> log metadata #24
The model has no metadata
> log chains #24
Chain information for Southern Elephant Seal virus AlphaFold.pdb #24
---
Chain | Description
A | No description available
> log metadata #25
The model has no metadata
> log chains #25
Chain information for Mucambo virus AlphaFold.pdb #25
---
Chain | Description
A | No description available
> log metadata #26
The model has no metadata
> log chains #26
Chain information for Onyong-nyong virus AlphaFold.pdb #26
---
Chain | Description
A | No description available
> log metadata #27
The model has no metadata
> log chains #27
Chain information for Pixuna virus AlphaFold.pdb #27
---
Chain | Description
A | No description available
> log metadata #28
The model has no metadata
> log chains #28
Chain information for RioNegro virus AlphaFold.pdb #28
---
Chain | Description
A | No description available
> log metadata #29
The model has no metadata
> log chains #29
Chain information for Tonate virus AlphaFold.pdb #29
---
Chain | Description
A | No description available
> log metadata #30
The model has no metadata
> log chains #30
Chain information for Trocara virus AlphaFold.pdb #30
---
Chain | Description
A | No description available
> log metadata #31
The model has no metadata
> log chains #31
Chain information for Una virus AlphaFold.pdb #31
---
Chain | Description
A | No description available
> log metadata #32
The model has no metadata
> log chains #32
Chain information for Whataroa virus AlphaFold.pdb #32
---
Chain | Description
A | No description available
> log metadata #33
The model has no metadata
> log chains #33
Chain information for AguaSalud alphavirus AlphaFold.pdb #33
---
Chain | Description
A | No description available
> log metadata #34
The model has no metadata
> log chains #34
Chain information for Comber alphavirus AlphaFold.pdb #34
---
Chain | Description
A | No description available
> log metadata #35
The model has no metadata
> log chains #35
Chain information for Harbor porpoise alphavirus AlphaFold.pdb #35
---
Chain | Description
A | No description available
> log metadata #36
The model has no metadata
> log chains #36
Chain information for Mwinilunga alphavirus AlphaFold.pdb #36
---
Chain | Description
A | No description available
> log metadata #37
The model has no metadata
> log chains #37
Chain information for selected_prediction Pirahy virus.pdb #37
---
Chain | Description
A | No description available
> log metadata #38
The model has no metadata
> log chains #38
Chain information for selected_prediction tai forest alphavirus .pdb #38
---
Chain | Description
A | No description available
> log metadata #39
The model has no metadata
> log chains #39
Chain information for selected_prediction Weglinng hagfish alphavirus
consensus.pdb #39
---
Chain | Description
A | No description available
> log metadata #40
The model has no metadata
> log chains #40
Chain information for Norwegian salmonid alphavirus AlphaFold.pdb #40
---
Chain | Description
A | No description available
> log metadata #41
The model has no metadata
> log chains #41
Chain information for selected_prediction Wenling fish alphavirus.pdb #41
---
Chain | Description
A | No description available
> log metadata #42
The model has no metadata
> log chains #42
Chain information for Yada yada virus AlphaFold.pdb #42
---
Chain | Description
A | No description available
> log metadata #43
The model has no metadata
> log chains #43
Chain information for Aura virus AlphaFold.pdb #43
---
Chain | Description
A | No description available
> log metadata #44
The model has no metadata
> log chains #44
Chain information for BFV AlphaFold.pdb #44
---
Chain | Description
A | No description available
> log metadata #45
The model has no metadata
> log chains #45
Chain information for WEEV AlphaFold.pdb #45
---
Chain | Description
A | No description available
> log metadata #46
The model has no metadata
> log chains #46
Chain information for EEEV AlphaFold.pdb #46
---
Chain | Description
A | No description available
> log metadata #47
The model has no metadata
> log chains #47
Chain information for Getah virus AlphaFold.pdb #47
---
Chain | Description
A | No description available
> log metadata #48
The model has no metadata
> log chains #48
Chain information for Mayaro virus AlphaFold.pdb #48
---
Chain | Description
A | No description available
> log metadata #49
The model has no metadata
> log chains #49
Chain information for SFV AlphaFold.pdb #49
---
Chain | Description
A | No description available
> log metadata #50
The model has no metadata
> log chains #50
Chain information for Sindbis virus AlphaFold.pdb #50
---
Chain | Description
A | No description available
> log metadata #51
The model has no metadata
> log chains #51
Chain information for Fort Morgan virus AlphaFold.pdb #51
---
Chain | Description
A | No description available
> log metadata #52
The model has no metadata
> log chains #52
Chain information for VEEV AlphaFold.pdb #52
---
Chain | Description
A | No description available
> log metadata #53
The model has no metadata
> log chains #53
Chain information for fold_sec1_model_0.cif #53
---
Chain | Description
A | .
> hide target m
> show #2 models
> show #53 models
> ui tool show Distances
> ui tool show "Similar Structures"
Must choose a chain in the similar structures panel before running search
You must press the similar structures Search button before you can open
matching structures.
Must run search first
> similarstructures blast #2/A
Webservices job id: BNOXPZ45QADI1K8E
Must run search first
Found 441 similar structures to 3j2w.pdb #2/A in pdb database using blast,
name bl1
> save "C:/Users/Carolina/Documents/Prueba Chimera.cxs"
[Repeated 1 time(s)]
——— End of log from Tue Jan 21 18:31:41 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #53/A
Alignment identifier is 53/A
> ui tool show "Show Sequence Viewer"
> sequence chain #2/I
Alignment identifier is 2/I
> ui mousemode right select
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> ui mousemode right select
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui mousemode right select
[Repeated 1 time(s)]
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel red
> select #2/I:189
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel red
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/I:190@CG
1 atom, 1 residue, 1 model selected
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/I:184
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> save C:/Users/Carolina/Documents/CHIKVaaint.cxs
> hide #53 models
> select #2/I:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel cyan
> select #2/I:251
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel cyan
> select #2/I:184
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel cyan
> save C:/Users/Carolina/Documents/CHIKVaaint.cxs
——— End of log from Wed Jan 29 09:08:51 2025 ———
> view name session-start
opened ChimeraX session
> show #53 models
> ui tool show Matchmaker
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/32/fold_sec1_summary_confidences_1.json"
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
UASLP/Lab Virología/AlphaFold3/32/fold_sec1_summary_confidences_1.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/32/fold_sec1_model_1.cif"
Chain information for fold_sec1_model_1.cif #54
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #54 to #2
Computing secondary structure
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 fold_sec1_model_1.cif, chain A (#54),
sequence alignment score = 527.8
RMSD between 147 pruned atom pairs is 0.713 angstroms; (across all 148 pairs:
0.764)
> hide #53 models
> show #53 models
> hide #53 models
> hide #54 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/32/fold_sec1_summary_confidences_2.json"
JSON file "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis
Potosi - UASLP/Lab
Virología/AlphaFold3/32/fold_sec1_summary_confidences_2.json" is not AlphaFold
predicted aligned error data, expected a top level list
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/32/fold_sec1_model_2.cif"
Chain information for fold_sec1_model_2.cif #55
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #55 to #2
Computing secondary structure
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 fold_sec1_model_2.cif, chain A (#55),
sequence alignment score = 527.8
RMSD between 146 pruned atom pairs is 0.727 angstroms; (across all 148 pairs:
0.814)
> hide #55 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/32/fold_sec1_model_3.cif"
Chain information for fold_sec1_model_3.cif #56
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #56 to #2
Computing secondary structure
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 fold_sec1_model_3.cif, chain A (#56),
sequence alignment score = 527.8
RMSD between 145 pruned atom pairs is 0.737 angstroms; (across all 148 pairs:
0.823)
> hide #56 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/32/fold_sec1_model_4.cif"
Chain information for fold_sec1_model_4.cif #57
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #57 to #2
Computing secondary structure
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 fold_sec1_model_4.cif, chain A (#57),
sequence alignment score = 527.8
RMSD between 145 pruned atom pairs is 0.742 angstroms; (across all 148 pairs:
0.906)
> hide #57 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_0.cif"
Chain information for fold_sec2_model_0.cif #58
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #58 to #2
Computing secondary structure
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 fold_sec2_model_0.cif, chain A (#58),
sequence alignment score = 547.5
RMSD between 148 pruned atom pairs is 0.718 angstroms; (across all 149 pairs:
0.771)
> hide #58 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_1.cif"
Chain information for fold_sec2_model_1.cif #59
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #59 to #2
Computing secondary structure
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 fold_sec2_model_1.cif, chain A (#59),
sequence alignment score = 536.7
RMSD between 148 pruned atom pairs is 0.686 angstroms; (across all 149 pairs:
0.740)
> hide #59 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_2.cif"
Chain information for fold_sec2_model_2.cif #60
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #60 to #2
Computing secondary structure
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 fold_sec2_model_2.cif, chain A (#60),
sequence alignment score = 536.7
RMSD between 148 pruned atom pairs is 0.686 angstroms; (across all 149 pairs:
0.733)
> hide #60 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_3.cif"
Chain information for fold_sec2_model_3.cif #61
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #61 to #2
Computing secondary structure
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 fold_sec2_model_3.cif, chain A (#61),
sequence alignment score = 536.7
RMSD between 148 pruned atom pairs is 0.663 angstroms; (across all 149 pairs:
0.706)
> hide #61 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/35/fold_sec2_summary_confidences_4.json"
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
UASLP/Lab Virología/AlphaFold3/35/fold_sec2_summary_confidences_4.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/35/fold_sec2_model_4.cif"
Chain information for fold_sec2_model_4.cif #62
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #62 to #2
Computing secondary structure
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 fold_sec2_model_4.cif, chain A (#62),
sequence alignment score = 536.7
RMSD between 148 pruned atom pairs is 0.666 angstroms; (across all 149 pairs:
0.699)
> color #60 white
> color #60 #d4d4d4ff
> color #62 #737f82ff
> color #62 #757682ff
> show #61 models
> hide #62 models
> color #59 #bfd6d8ff
> color #58 #53605cff
> color #58 #5b5e60ff
> color #58 #5e605eff
> color #58 white
> color #58 #c2c2c2ff
> color #58 #d6d6d6ff
> hide #61 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_0.cif"
Chain information for fold_sec3_model_0.cif #63
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #63 to #2
Computing secondary structure
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 fold_sec3_model_0.cif, chain A (#63),
sequence alignment score = 544.6
RMSD between 148 pruned atom pairs is 0.694 angstroms; (across all 149 pairs:
0.756)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/41/fold_sec3_full_data_1.json"
Opened AlphaFold PAE with values for 270 residues and atoms
> color #63/A:126-184 lime
> ui tool show Matchmaker
> matchmaker #63 to #2
Computing secondary structure
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 fold_sec3_model_0.cif, chain A (#63),
sequence alignment score = 544.6
RMSD between 148 pruned atom pairs is 0.694 angstroms; (across all 149 pairs:
0.756)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_1.cif"
Chain information for fold_sec3_model_1.cif #64
---
Chain | Description
A | .
Computing secondary structure
> ui mousemode right select
> select #63/A:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> hide #!63 models
> ui tool show Matchmaker
> matchmaker #64 to #2
Computing secondary structure
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 fold_sec3_model_1.cif, chain A (#64),
sequence alignment score = 544.6
RMSD between 148 pruned atom pairs is 0.678 angstroms; (across all 149 pairs:
0.736)
> select add #63
2159 atoms, 2218 bonds, 270 residues, 2 models selected
> select subtract #63
1 model selected
> hide #64 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_2.cif"
Chain information for fold_sec3_model_2.cif #65
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #65 to #2
Computing secondary structure
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 fold_sec3_model_2.cif, chain A (#65),
sequence alignment score = 544.6
RMSD between 148 pruned atom pairs is 0.697 angstroms; (across all 149 pairs:
0.753)
> color #65 #d5bbd7ff
> color #65 #d7cccdff
> hide #65 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_3.cif"
Chain information for fold_sec3_model_3.cif #66
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #66 to #2
Computing secondary structure
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 fold_sec3_model_3.cif, chain A (#66),
sequence alignment score = 544.6
RMSD between 148 pruned atom pairs is 0.695 angstroms; (across all 149 pairs:
0.742)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/41/fold_sec3_model_4.cif"
Chain information for fold_sec3_model_4.cif #67
---
Chain | Description
A | .
Computing secondary structure
> hide #66 models
> ui tool show Matchmaker
> matchmaker #67 to #2
Computing secondary structure
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 fold_sec3_model_4.cif, chain A (#67),
sequence alignment score = 544.6
RMSD between 148 pruned atom pairs is 0.675 angstroms; (across all 149 pairs:
0.740)
> color #66 white
> color #66 #eeeeeeff
> color #64 white
> color #64 #e3e3e3ff
> color #61 #ffaa00ff
> color #61 #ffaa7fff
> hide #67 models
> show #54 models
> color #53 #656770ff
> color #55 white
> color #55 #e6e6e6ff
> color #56 white
> color #56 #f3f3f3ff
> color #57 white
> color #57 #f1f1f1ff
> color #53 #bdc0d1ff
> show #67 models
> hide #54 models
> save C:/Users/Carolina/Documents/CHIKVaaint.cxs
——— End of log from Wed Jan 29 14:59:10 2025 ———
> view name session-start
opened ChimeraX session
> hide #67 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_0.cif"
Chain information for fold_sec4_model_0.cif #68
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #68 to #2
Computing secondary structure
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 fold_sec4_model_0.cif, chain A (#68),
sequence alignment score = 556.6
RMSD between 147 pruned atom pairs is 0.631 angstroms; (across all 149 pairs:
0.720)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_1.cif"
Chain information for fold_sec4_model_1.cif #69
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #69 to #2
Computing secondary structure
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 fold_sec4_model_1.cif, chain A (#69),
sequence alignment score = 545.8
RMSD between 147 pruned atom pairs is 0.669 angstroms; (across all 149 pairs:
0.764)
> hide #68 models
> hide #69 models
> color #69 white
> color #69 #ffe4edff
> color #69 white
> color #69 #fff7f9ff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_2.cif"
Chain information for fold_sec4_model_2.cif #70
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #70 to #2
Computing secondary structure
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 fold_sec4_model_2.cif, chain A (#70),
sequence alignment score = 567.4
RMSD between 147 pruned atom pairs is 0.660 angstroms; (across all 149 pairs:
0.753)
> color #70 white
> color #70 #fae9ffff
> color #70 #fbf0ffff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_3.cif"
Chain information for fold_sec4_model_3.cif #71
---
Chain | Description
A | .
Computing secondary structure
> hide #70 models
> ui tool show Matchmaker
> matchmaker #71 to #2
Computing secondary structure
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 fold_sec4_model_3.cif, chain A (#71),
sequence alignment score = 556.6
RMSD between 146 pruned atom pairs is 0.623 angstroms; (across all 149 pairs:
0.740)
> color #68 #d3dbd3ff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/43/fold_sec4_model_4.cif"
Chain information for fold_sec4_model_4.cif #72
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #72 to #2
Computing secondary structure
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 fold_sec4_model_4.cif, chain A (#72),
sequence alignment score = 567.4
RMSD between 147 pruned atom pairs is 0.619 angstroms; (across all 149 pairs:
0.709)
> hide #71-72 target m
> show #1 target m
> hide #2 target m
> show #72 target m
> hide #1 target m
> show #71 target m
> hide #72 target m
> show #2 models
> show #72 models
> hide #71 models
> color #71 #969e96ff
> color #71 #9c9e9cff
> color #71 #969e96ff
> color #71 #bbc5bbff
> color #71 #ced9ceff
> hide #72 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_0.cif"
Chain information for fold_sec5_model_0.cif #73
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #73 to #2
Computing secondary structure
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 fold_sec5_model_0.cif, chain A (#73),
sequence alignment score = 651.1
RMSD between 148 pruned atom pairs is 0.618 angstroms; (across all 149 pairs:
0.661)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_1.cif"
Chain information for fold_sec5_model_1.cif #74
---
Chain | Description
A | .
Computing secondary structure
> hide #73 models
> ui tool show H-Bonds
> ui tool show Matchmaker
> matchmaker #74 to #2
Computing secondary structure
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 fold_sec5_model_1.cif, chain A (#74),
sequence alignment score = 661.9
RMSD between 148 pruned atom pairs is 0.611 angstroms; (across all 149 pairs:
0.654)
> color #73 #7f8b8dff
> color #73 #c8dbdeff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_2.cif"
Chain information for fold_sec5_model_2.cif #75
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #75 to #2
Computing secondary structure
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 fold_sec5_model_2.cif, chain A (#75),
sequence alignment score = 670.9
RMSD between 148 pruned atom pairs is 0.595 angstroms; (across all 149 pairs:
0.636)
> color #74 #7c8078ff
> color #74 #e1e7d9ff
> hide #74 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_3.cif"
Chain information for fold_sec5_model_3.cif #76
---
Chain | Description
A | .
Computing secondary structure
> hide #75 models
> ui tool show Matchmaker
> matchmaker #76 to #2
Computing secondary structure
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 fold_sec5_model_3.cif, chain A (#76),
sequence alignment score = 651.1
RMSD between 148 pruned atom pairs is 0.598 angstroms; (across all 149 pairs:
0.637)
> color #76 #676b65ff
> color #76 #d6ded1ff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/44/fold_sec5_model_4.cif"
Chain information for fold_sec5_model_4.cif #77
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #77 to #2
Computing secondary structure
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 fold_sec5_model_4.cif, chain A (#77),
sequence alignment score = 640.3
RMSD between 148 pruned atom pairs is 0.642 angstroms; (across all 149 pairs:
0.683)
> color #77 #44523cff
> color #77 #cef8b7ff
> color #77 #d3ffbcff
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> color #77 #edffe1ff
> hide #77 models
> hide #76 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_0.cif"
Chain information for fold_sec6_model_0.cif #78
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #78 to #2
Computing secondary structure
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 fold_sec6_model_0.cif, chain A (#78),
sequence alignment score = 627.1
RMSD between 148 pruned atom pairs is 0.614 angstroms; (across all 149 pairs:
0.681)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_1.cif"
Chain information for fold_sec6_model_1.cif #79
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #79 to #2
Computing secondary structure
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 fold_sec6_model_1.cif, chain A (#79),
sequence alignment score = 631.3
RMSD between 148 pruned atom pairs is 0.635 angstroms; (across all 149 pairs:
0.703)
> hide #78 models
> color #79 #b1a7a0ff
> color #79 #f4e7dcff
> hide #79 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_2.cif"
Chain information for fold_sec6_model_2.cif #80
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #80 to #2
Computing secondary structure
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 fold_sec6_model_2.cif, chain A (#80),
sequence alignment score = 630.7
RMSD between 148 pruned atom pairs is 0.627 angstroms; (across all 149 pairs:
0.699)
> color #80 #e1e6f1ff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_3.cif"
Chain information for fold_sec6_model_3.cif #81
---
Chain | Description
A | .
Computing secondary structure
> hide #80 models
> ui tool show H-Bonds
> ui tool show Matchmaker
> matchmaker #81 to #2
Computing secondary structure
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 fold_sec6_model_3.cif, chain A (#81),
sequence alignment score = 631.3
RMSD between 148 pruned atom pairs is 0.632 angstroms; (across all 149 pairs:
0.694)
> color #81 #88838eff
> color #81 #d0c8d9ff
> hide #81 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/45/fold_sec6_model_4.cif"
Chain information for fold_sec6_model_4.cif #82
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #82 to #2
Computing secondary structure
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 fold_sec6_model_4.cif, chain A (#82),
sequence alignment score = 630.7
RMSD between 148 pruned atom pairs is 0.634 angstroms; (across all 149 pairs:
0.696)
> color #82 #baf82aff
> color #82 #e2f8b8ff
> hide #82 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_0.cif"
Chain information for fold_sec7_model_0.cif #83
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #83 to #2
Computing secondary structure
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 fold_sec7_model_0.cif, chain A (#83),
sequence alignment score = 680.9
RMSD between 148 pruned atom pairs is 0.665 angstroms; (across all 149 pairs:
0.690)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_1.cif"
Chain information for fold_sec7_model_1.cif #84
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #84 to #2
Computing secondary structure
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 fold_sec7_model_1.cif, chain A (#84),
sequence alignment score = 689.9
RMSD between 148 pruned atom pairs is 0.674 angstroms; (across all 149 pairs:
0.722)
> color #84 #c192aaff
> color #84 #f8bcdbff
> color #84 #f8dbe7ff
> hide #84 models
> hide #83 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_2.cif"
Chain information for fold_sec7_model_2.cif #85
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #85 to #2
Computing secondary structure
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 fold_sec7_model_2.cif, chain A (#85),
sequence alignment score = 683.9
RMSD between 148 pruned atom pairs is 0.676 angstroms; (across all 149 pairs:
0.695)
> color #85 #777571ff
> color #85 #f8f5ecff
> hide #85 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_3.cif"
Chain information for fold_sec7_model_3.cif #86
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #86 to #2
Computing secondary structure
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 fold_sec7_model_3.cif, chain A (#86),
sequence alignment score = 680.9
RMSD between 148 pruned atom pairs is 0.641 angstroms; (across all 149 pairs:
0.694)
> color #83 #bbbdd1ff
> color #83 #dee0f8ff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/50/fold_sec7_model_4.cif"
Chain information for fold_sec7_model_4.cif #87
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #87 to #2
Computing secondary structure
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 fold_sec7_model_4.cif, chain A (#87),
sequence alignment score = 702.5
RMSD between 148 pruned atom pairs is 0.659 angstroms; (across all 149 pairs:
0.696)
> hide #86 models
> color #87 #4e5d56ff
> color #87 #cdf5e2ff
> color #86 #13a85eff
> hide #87 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_0.cif"
Chain information for fold_sec8_model_0.cif #88
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #88 to #2
Computing secondary structure
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 fold_sec8_model_0.cif, chain A (#88),
sequence alignment score = 685.7
RMSD between 149 pruned atom pairs is 0.662 angstroms; (across all 149 pairs:
0.662)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_1.cif"
Chain information for fold_sec8_model_1.cif #89
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #89 to #2
Computing secondary structure
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 fold_sec8_model_1.cif, chain A (#89),
sequence alignment score = 700.7
RMSD between 148 pruned atom pairs is 0.648 angstroms; (across all 149 pairs:
0.684)
> hide #88 models
> color #88 #666776ff
> color #88 #d6d9f8ff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_1.cif"
Chain information for fold_sec8_model_1.cif #90
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #90 to #2
Computing secondary structure
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 fold_sec8_model_1.cif, chain A (#90),
sequence alignment score = 700.7
RMSD between 148 pruned atom pairs is 0.648 angstroms; (across all 149 pairs:
0.684)
> hide #90 models
> color #90 white
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_2.cif"
Chain information for fold_sec8_model_2.cif #91
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #91 to #2
Computing secondary structure
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 fold_sec8_model_2.cif, chain A (#91),
sequence alignment score = 691.7
RMSD between 148 pruned atom pairs is 0.679 angstroms; (across all 149 pairs:
0.714)
> color #91 #a0a0aeff
> color #91 #e1e2f5ff
> hide #91 models
> show #91 models
> hide #91 models
> hide #89 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_3.cif"
Chain information for fold_sec8_model_3.cif #92
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #92 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7vga.pdb, chain C (#1) with fold_sec8_model_3.cif, chain A (#92),
sequence alignment score = 838.6
RMSD between 151 pruned atom pairs is 0.830 angstroms; (across all 158 pairs:
1.156)
> color #89 #dbb4dbff
> color #89 #f8ccf8ff
> color #89 #e975f8ff
> color #89 #f87cc7ff
> color #92 #9da198ff
> color #92 #f3faebff
> hide #92 models
> show #92 models
> hide #92 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/54/fold_sec8_model_4.cif"
Chain information for fold_sec8_model_4.cif #93
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #93 to #2
Computing secondary structure
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 fold_sec8_model_4.cif, chain A (#93),
sequence alignment score = 679.7
RMSD between 148 pruned atom pairs is 0.624 angstroms; (across all 149 pairs:
0.678)
> color #89 #f8e5efff
> color #93 #8d3e78ff
> color #93 #f16acdff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
——— End of log from Sun Feb 2 22:29:43 2025 ———
> view name session-start
opened ChimeraX session
> show #54 models
> hide #93 models
> ui mousemode right select
> select #54/A:134
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> show sel atoms
Alignment identifier is 54/A
> color sel red
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #54/A:248
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #54/A:198
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #54/A:199
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #54/A:198
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
[Repeated 1 time(s)]
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #54/A:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #54/A:186
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/I:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #54/A:186
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #54/A:162
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #54/A:162
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #54/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #54/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #54/A:165
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> show sel atoms
> color sel orange
> ui mousemode right select
> select #54/A:162
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #54/A:198
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
——— End of log from Tue Feb 11 09:48:29 2025 ———
> view name session-start
opened ChimeraX session
> show #61 models
> hide #61 models
> show #61 models
> hide #54 models
> ui mousemode right select
> select #61/A:242
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #61/A
Alignment identifier is 61/A
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #61/A:234
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:234
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
Drag select of 1 residues
> ui mousemode right translate
> ui mousemode right select
> select #61/A:184
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:184
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/A:185
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #61/A:184
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> select #61/A:184
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> 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 #61/A:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel blue
> ui mousemode right translate
> color #61 #d18b68ff
> color #61 #d48d6aff
> color #61 #ff5500ff
> color #61 #ff7c11ff
> color #61 #ff7f23ff
> color #61 #ffc44fff
> color #61 #ffaa7fff
> color #61 #ffa86eff
> color #61 #ff9580ff
> ui mousemode right "crop volume"
> ui mousemode right translate
> ui mousemode right select
> select #61/A:234
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> select #61/A:184
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select #61/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #61/A:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #61/A:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #61/A:151
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:151
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:151
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right select
> select #61/A:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #61/A:151
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
> hide sel atoms
> show sel atoms
[Repeated 1 time(s)]
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #61/A:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:234
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:177
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #61/A:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select #61/A:151
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #61/A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:122
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #61/A:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
——— End of log from Fri Feb 21 21:14:08 2025 ———
> view name session-start
opened ChimeraX session
> hide #61 models
> show #67 models
> ui mousemode right rotate
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
> select #67/A:242
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:242
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #67/A
Alignment identifier is 67/A
> show sel atoms
> color sel red
> select #2/I:240
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 #67/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:185
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:180
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:180
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:180
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #67/A:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:130
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:130
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right select
[Repeated 1 time(s)]
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #67/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> show #72 models
> hide #67 models
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui mousemode right select
[Repeated 1 time(s)]
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #72/A:242
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #72/A
Alignment identifier is 72/A
> show sel atoms
> color sel red
> show sel cartoons
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:242
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 #72/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #72/A:185
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:185
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> 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 #72/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
[Repeated 1 time(s)]
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:130
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:130
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel blue
> 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
> ui mousemode right translate
> ui mousemode right select
> select #72/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:126@CG
1 atom, 1 residue, 1 model selected
Drag select of 1 residues
> select #72/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #72/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> select #2/I:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:226-250
171 atoms, 170 bonds, 25 residues, 1 model selected
> select #72/A:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #72/A:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #72 models
> show #72 models
> show #75 models
> hide #75 models
> show #75 models
> hide #75 models
> hide #72 models
> show #72 models
> hide #72 models
> show #75 models
> hide #75 models
> show #75 models
> hide #75 models
> show #74 models
> show #75 models
> hide #75 models
> show #75 models
> hide #75 models
> show #75 models
> hide #75 models
> hide #74 models
> show #75 models
> hide #75 models
> show #75 models
> hide #75 models
> show #75 models
> color #75 #a39c0fff
> color #75 #aaaaffff
> color #75 #7f7fbfff
> color #75 #7c7cbaff
> color #75 #7676b1ff
> color #75 #7777b3ff
> color #75 #8181c2ff
> ui mousemode right "crop volume"
> ui mousemode right translate
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:226-250
171 atoms, 170 bonds, 25 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 #75/A:250
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #75/A
Alignment identifier is 75/A
> select #75/A:250
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
[Repeated 1 time(s)]
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:200
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
[Repeated 1 time(s)]
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select #75/A:188
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:188
9 atoms, 8 bonds, 1 residue, 1 model selected
> 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 #75/A:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> rainbow sel
> select #75/A:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #75/A:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #75/A:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #75/A:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> show #67 models
> hide #75 models
> ui mousemode right select
> select #67/A:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #67/A:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #67/A:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #67 models
> show #61 models
> select #61/A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #61 models
> show #72 models
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #72/A:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #72 models
> show #73 models
> hide #73 models
> show #75 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
——— End of log from Mon Feb 24 09:50:56 2025 ———
> view name session-start
opened ChimeraX session
> select add #78
2186 atoms, 2247 bonds, 275 residues, 2 models selected
> hide #75 models
> show #75 models
> select subtract #78
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #78
2186 atoms, 2247 bonds, 275 residues, 2 models selected
> hide #75 models
> show #75 models
> select subtract #78
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #78 models
> hide #75 models
> show #75 models
> hide #75 models
> color #78 #a64e5aff
> color #78 #55ff7fff
> color #78 #4ade6dff
> color #78 #43ca63ff
> color #78 #3bb056ff
> color #78 #3eba5bff
> ui mousemode right select
> select #78/A:246
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #78/A:246
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #78/A
Alignment identifier is 78/A
> show sel atoms
> color sel red
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right select
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #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 #78/A:196
9 atoms, 8 bonds, 1 residue, 1 model selected
> 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 #78/A:189
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #78/A:183
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #78/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #78/A:163
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel blue
> ui mousemode right rotate
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right select
> select clear
> 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 #78/A:160
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> show sel atoms
[Repeated 1 time(s)]
> color sel gray
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #78/A:134
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> ui mousemode right rotate
> ui mousemode right select
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #78/A:132
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #78/A:132
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel red
> ui mousemode right translate
> show #86 models
> hide #78 models
> ui tool show "Show Sequence Viewer"
> sequence chain #86/A
Alignment identifier is 86/A
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #86/A:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> 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 #86/A:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> 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 #86/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right translate
> set bgColor white
> ui mousemode right select
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #86/A:185
9 atoms, 8 bonds, 1 residue, 1 model selected
> 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 #86/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right select
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #86/A:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #86/A:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #86/A:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #86/A:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> ui mousemode right translate
> 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 #86/A:133
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #86/A:133
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> hide #86 models
> show #93 models
> show #86 models
> hide #93 models
> show #93 models
> hide #93 models
> show #93 models
> hide #86 models
> show #86 models
> select add #86
2173 atoms, 2233 bonds, 274 residues, 1 model selected
> select subtract #86
Nothing selected
> hide #86 models
> ui tool show "Show Sequence Viewer"
> sequence chain #93/A
Alignment identifier is 93/A
> ui mousemode right select
> select #2/I:240
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:243
9 atoms, 8 bonds, 1 residue, 1 model selected
> 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 #93/A:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #2/I:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:193
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/I:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/I:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> 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 #93/A:160
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:160
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #2/I:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #93/A:157
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> ui mousemode right translate
> ui mousemode right select
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel blue
> select #2/I:128
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/I:126
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #93/A:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> rainbow sel
> ui mousemode right translate
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
——— End of log from Tue Feb 25 17:51:14 2025 ———
> view name session-start
opened ChimeraX session
> hide #93 models
> select add #93
2151 atoms, 2207 bonds, 270 residues, 1 model selected
> select subtract #93
Nothing selected
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> A/fold_2025_05_21_ancestor_a_model_2.cif"
Chain information for fold_2025_05_21_ancestor_a_model_2.cif #94
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #94 to #2
Computing secondary structure
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 fold_2025_05_21_ancestor_a_model_2.cif,
chain A (#94), sequence alignment score = 669.5
RMSD between 149 pruned atom pairs is 0.647 angstroms; (across all 149 pairs:
0.647)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> B/fold_2025_05_21_ancestorb_model_0.cif"
Chain information for fold_2025_05_21_ancestorb_model_0.cif #95
---
Chain | Description
A | .
Computing secondary structure
> hide #94 models
> ui tool show Matchmaker
> matchmaker #95 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorb_model_0.cif,
chain A (#95), sequence alignment score = 679.9
RMSD between 149 pruned atom pairs is 0.634 angstroms; (across all 149 pairs:
0.634)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> B/fold_2025_05_21_ancestorb_model_1.cif"
Chain information for fold_2025_05_21_ancestorb_model_1.cif #96
---
Chain | Description
A | .
Computing secondary structure
> hide #95 models
> ui tool show Matchmaker
> matchmaker #96 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorb_model_1.cif,
chain A (#96), sequence alignment score = 700.9
RMSD between 148 pruned atom pairs is 0.586 angstroms; (across all 149 pairs:
0.617)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> B/fold_2025_05_21_ancestorb_model_2.cif"
Chain information for fold_2025_05_21_ancestorb_model_2.cif #97
---
Chain | Description
A | .
Computing secondary structure
> hide #96 models
> ui tool show Matchmaker
> matchmaker #97 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorb_model_2.cif,
chain A (#97), sequence alignment score = 685.9
RMSD between 148 pruned atom pairs is 0.611 angstroms; (across all 149 pairs:
0.649)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> B/fold_2025_05_21_ancestorb_full_data_3.json"
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
UASLP/Lab Virología/AlphaFold3/Ancestor
B/fold_2025_05_21_ancestorb_full_data_3.json structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> B/fold_2025_05_21_ancestorb_model_3.cif"
Chain information for fold_2025_05_21_ancestorb_model_3.cif #98
---
Chain | Description
A | .
Computing secondary structure
> hide #97 models
> ui tool show Matchmaker
> matchmaker #98 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorb_model_3.cif,
chain A (#98), sequence alignment score = 682.9
RMSD between 148 pruned atom pairs is 0.628 angstroms; (across all 149 pairs:
0.663)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> B/fold_2025_05_21_ancestorb_model_4.cif"
Chain information for fold_2025_05_21_ancestorb_model_4.cif #99
---
Chain | Description
A | .
Computing secondary structure
> hide #98 models
> ui tool show Matchmaker
> matchmaker #99 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorb_model_4.cif,
chain A (#99), sequence alignment score = 672.1
RMSD between 149 pruned atom pairs is 0.667 angstroms; (across all 149 pairs:
0.667)
> hide #99 models
> color #95 #878a91ff
> color #95 #d3d9e3ff
> color #95 #edf3ffff
> color #97 #c5f7cbff
> color #97 #d7f7dcff
> color #98 #daeafaff
> color #98 #e5ebfaff
> color #97 #e8f7ecff
> color #99 #b9c2bfff
> color #99 #bac2baff
> color #99 #e4eee4ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
——— End of log from Thu May 22 13:21:18 2025 ———
> view name session-start
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> C/fold_2025_05_21_ancestorc_model_0.cif"
Chain information for fold_2025_05_21_ancestorc_model_0.cif #100
---
Chain | Description
A | .
Computing secondary structure
> color #100 #a58ca2ff
> color #100 #caacc6ff
> color #100 #c3a6bfff
> ui tool show Matchmaker
> matchmaker #100 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorc_model_0.cif,
chain A (#100), sequence alignment score = 700.7
RMSD between 148 pruned atom pairs is 0.639 angstroms; (across all 149 pairs:
0.681)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> D/fold_2025_05_21_ancestord_model_0.cif"
Chain information for fold_2025_05_21_ancestord_model_0.cif #101
---
Chain | Description
A | .
Computing secondary structure
> hide #100 models
> ui tool show Matchmaker
> matchmaker #101 to #2
Computing secondary structure
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 fold_2025_05_21_ancestord_model_0.cif,
chain A (#101), sequence alignment score = 607.9
RMSD between 148 pruned atom pairs is 0.654 angstroms; (across all 149 pairs:
0.710)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> D/fold_2025_05_21_ancestord_model_1.cif"
Chain information for fold_2025_05_21_ancestord_model_1.cif #102
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #102 to #2
Computing secondary structure
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 fold_2025_05_21_ancestord_model_1.cif,
chain A (#102), sequence alignment score = 607.9
RMSD between 148 pruned atom pairs is 0.656 angstroms; (across all 149 pairs:
0.708)
> hide #101 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
——— End of log from Thu May 22 13:36:48 2025 ———
> view name session-start
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> D/fold_2025_05_21_ancestord_model_2.cif"
Chain information for fold_2025_05_21_ancestord_model_2.cif #103
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #103 to #2
Computing secondary structure
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 fold_2025_05_21_ancestord_model_2.cif,
chain A (#103), sequence alignment score = 607.9
RMSD between 148 pruned atom pairs is 0.636 angstroms; (across all 149 pairs:
0.690)
> hide #102 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> D/fold_2025_05_21_ancestord_model_3.cif"
Chain information for fold_2025_05_21_ancestord_model_3.cif #104
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #104 to #2
Computing secondary structure
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 fold_2025_05_21_ancestord_model_3.cif,
chain A (#104), sequence alignment score = 604.9
RMSD between 148 pruned atom pairs is 0.628 angstroms; (across all 149 pairs:
0.690)
> hide #103 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> D/fold_2025_05_21_ancestord_model_4.cif"
Chain information for fold_2025_05_21_ancestord_model_4.cif #105
---
Chain | Description
A | .
Computing secondary structure
> hide #104 models
> ui tool show Matchmaker
> matchmaker #105 to #2
Computing secondary structure
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 fold_2025_05_21_ancestord_model_4.cif,
chain A (#105), sequence alignment score = 607.9
RMSD between 148 pruned atom pairs is 0.624 angstroms; (across all 149 pairs:
0.671)
> color #101 #878876ff
> color #101 #ebeecfff
> color #102 #aba9a1ff
> color #102 #efede1ff
> color #103 #b8bbb0ff
> color #103 #e1e5d8ff
> color #104 #948c7dff
> color #104 #f7ead0ff
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
——— End of log from Mon Jun 2 19:21:36 2025 ———
> view name session-start
opened ChimeraX session
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> E/fold_2025_05_21_ancestore_model_0.cif"
Chain information for fold_2025_05_21_ancestore_model_0.cif #106
---
Chain | Description
A | .
Computing secondary structure
> hide #105 models
> ui tool show Matchmaker
> matchmaker #106 to #2
Computing secondary structure
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 fold_2025_05_21_ancestore_model_0.cif,
chain A (#106), sequence alignment score = 557
RMSD between 149 pruned atom pairs is 0.689 angstroms; (across all 149 pairs:
0.689)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> E/fold_2025_05_21_ancestore_model_1.cif"
Chain information for fold_2025_05_21_ancestore_model_1.cif #107
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #107 to #2
Computing secondary structure
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 fold_2025_05_21_ancestore_model_1.cif,
chain A (#107), sequence alignment score = 554
RMSD between 149 pruned atom pairs is 0.658 angstroms; (across all 149 pairs:
0.658)
> hide #106 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> E/fold_2025_05_21_ancestore_model_2.cif"
Chain information for fold_2025_05_21_ancestore_model_2.cif #108
---
Chain | Description
A | .
Computing secondary structure
> hide #107 models
> ui tool show Matchmaker
> matchmaker #108 to #2
Computing secondary structure
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 fold_2025_05_21_ancestore_model_2.cif,
chain A (#108), sequence alignment score = 557
RMSD between 149 pruned atom pairs is 0.698 angstroms; (across all 149 pairs:
0.698)
> hide #108 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> E/fold_2025_05_21_ancestore_model_3.cif"
Chain information for fold_2025_05_21_ancestore_model_3.cif #109
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #109 to #2
Computing secondary structure
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 fold_2025_05_21_ancestore_model_3.cif,
chain A (#109), sequence alignment score = 554
RMSD between 149 pruned atom pairs is 0.671 angstroms; (across all 149 pairs:
0.671)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> E/fold_2025_05_21_ancestore_model_4.cif"
Chain information for fold_2025_05_21_ancestore_model_4.cif #110
---
Chain | Description
A | .
Computing secondary structure
> hide #109 models
> ui tool show Matchmaker
> matchmaker #110 to #2
Computing secondary structure
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 fold_2025_05_21_ancestore_model_4.cif,
chain A (#110), sequence alignment score = 554
RMSD between 149 pruned atom pairs is 0.664 angstroms; (across all 149 pairs:
0.664)
> color #107 #1eff25ff
> color #107 #0c6a10ff
> color #106 #78717dff
> color #106 #efe0f8ff
> color #106 #f8e5f5ff
> color #106 #e0f8e2ff
> color #106 #f6f6f8ff
> color #104 #f7f7f7ff
> color #108 #606261ff
> color #108 #eff3f0ff
> color #109 #8c8c85ff
> color #109 #f3f2e8ff
> color #110 #787b7aff
> color #110 #f9fffdff
> show #107 models
> hide #110 models
> show #110 models
> hide #107 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> F/fold_2025_05_21_ancestorf_model_0.cif"
Chain information for fold_2025_05_21_ancestorf_model_0.cif #111
---
Chain | Description
A | .
Computing secondary structure
> hide #110 models
> ui tool show Matchmaker
> matchmaker #111 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorf_model_0.cif,
chain A (#111), sequence alignment score = 526.6
RMSD between 148 pruned atom pairs is 0.665 angstroms; (across all 149 pairs:
0.692)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> F/fold_2025_05_21_ancestorf_model_1.cif"
Chain information for fold_2025_05_21_ancestorf_model_1.cif #112
---
Chain | Description
A | .
Computing secondary structure
> hide #111 models
> ui tool show Matchmaker
> matchmaker #112 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorf_model_1.cif,
chain A (#112), sequence alignment score = 537.4
RMSD between 148 pruned atom pairs is 0.683 angstroms; (across all 149 pairs:
0.708)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> F/fold_2025_05_21_ancestorf_model_2.cif"
Chain information for fold_2025_05_21_ancestorf_model_2.cif #113
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #113 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorf_model_2.cif,
chain A (#113), sequence alignment score = 537.4
RMSD between 148 pruned atom pairs is 0.680 angstroms; (across all 149 pairs:
0.717)
> hide #112 models
> hide #113 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> F/fold_2025_05_21_ancestorf_model_3.cif"
Chain information for fold_2025_05_21_ancestorf_model_3.cif #114
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #114 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorf_model_3.cif,
chain A (#114), sequence alignment score = 534.4
RMSD between 148 pruned atom pairs is 0.688 angstroms; (across all 149 pairs:
0.720)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> F/fold_2025_05_21_ancestorf_model_4.cif"
Chain information for fold_2025_05_21_ancestorf_model_4.cif #115
---
Chain | Description
A | .
Computing secondary structure
> hide #114 models
> ui tool show Foldseek
> ui tool show Matchmaker
> matchmaker #115 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorf_model_4.cif,
chain A (#115), sequence alignment score = 526.6
RMSD between 148 pruned atom pairs is 0.653 angstroms; (across all 149 pairs:
0.690)
> color #111 #6c6b69ff
> color #111 #fffdf8ff
> color #112 #747371ff
> color #112 #faf7f3ff
> color #113 #ddd6c8ff
> color #113 #f3ebdcff
> color #113 #f1f3f0ff
> color #114 #9e9f9aff
> color #114 #f2f3ebff
> color #115 #ce7cddff
> color #115 #bb80ddff
> color #115 #a781ddff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> G/fold_2025_05_21_ancestorg_model_0.cif"
Chain information for fold_2025_05_21_ancestorg_model_0.cif #116
---
Chain | Description
A | .
Computing secondary structure
> hide #115 models
> ui tool show Matchmaker
> matchmaker #116 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorg_model_0.cif,
chain A (#116), sequence alignment score = 550.2
RMSD between 148 pruned atom pairs is 0.710 angstroms; (across all 149 pairs:
0.762)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> G/fold_2025_05_21_ancestorg_model_1.cif"
Chain information for fold_2025_05_21_ancestorg_model_1.cif #117
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #117 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorg_model_1.cif,
chain A (#117), sequence alignment score = 550.2
RMSD between 148 pruned atom pairs is 0.691 angstroms; (across all 149 pairs:
0.740)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> G/fold_2025_05_21_ancestorg_model_2.cif"
Chain information for fold_2025_05_21_ancestorg_model_2.cif #118
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #118 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorg_model_2.cif,
chain A (#118), sequence alignment score = 550.2
RMSD between 148 pruned atom pairs is 0.699 angstroms; (across all 149 pairs:
0.748)
> hide #116 models
> hide #117 models
> color #116 #7a7b7aff
> color #116 #f6f7f4ff
> color #117 #616864ff
> color #118 #b5b4b3ff
> color #118 #fffdfcff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> G/fold_2025_05_21_ancestorg_model_3.cif"
Chain information for fold_2025_05_21_ancestorg_model_3.cif #119
---
Chain | Description
A | .
Computing secondary structure
> hide #118 models
> ui tool show Matchmaker
> matchmaker #119 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorg_model_3.cif,
chain A (#119), sequence alignment score = 550.2
RMSD between 148 pruned atom pairs is 0.693 angstroms; (across all 149 pairs:
0.746)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Ancestor
> G/fold_2025_05_21_ancestorg_model_4.cif"
Chain information for fold_2025_05_21_ancestorg_model_4.cif #120
---
Chain | Description
A | .
Computing secondary structure
> hide #119 models
> ui tool show Matchmaker
> matchmaker #120 to #2
Computing secondary structure
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 fold_2025_05_21_ancestorg_model_4.cif,
chain A (#120), sequence alignment score = 550.2
RMSD between 148 pruned atom pairs is 0.703 angstroms; (across all 149 pairs:
0.756)
> color #119 #696c6eff
> color #119 #d8dfe3ff
> color #120 #747c82ff
> color #120 #797e82ff
> color #120 #dce5ecff
> color #117 #5e5868ff
> color #117 #5b6568ff
> color #117 #9eb0b5ff
> color #117 #aec2c8ff
> color #117 #839196ff
> color #117 #718996ff
> hide #120 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Secuencia
> ancestral/fold_2025_05_21_sec_ancestral_model_0.cif"
Chain information for fold_2025_05_21_sec_ancestral_model_0.cif #121
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #121 to #2
Computing secondary structure
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
fold_2025_05_21_sec_ancestral_model_0.cif, chain A (#121), sequence alignment
score = 580.6
RMSD between 148 pruned atom pairs is 0.651 angstroms; (across all 149 pairs:
0.702)
> hide #121 models
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Secuencia
> ancestral/fold_2025_05_21_sec_ancestral_model_1.cif"
Chain information for fold_2025_05_21_sec_ancestral_model_1.cif #122
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #122 to #2
Computing secondary structure
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
fold_2025_05_21_sec_ancestral_model_1.cif, chain A (#122), sequence alignment
score = 569.8
RMSD between 148 pruned atom pairs is 0.640 angstroms; (across all 149 pairs:
0.691)
> color #121 #e4efe9ff
> color #121 #ebf7f1ff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Secuencia
> ancestral/fold_2025_05_21_sec_ancestral_model_2.cif"
Chain information for fold_2025_05_21_sec_ancestral_model_2.cif #123
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #123 to #2
Computing secondary structure
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
fold_2025_05_21_sec_ancestral_model_2.cif, chain A (#123), sequence alignment
score = 569.8
RMSD between 148 pruned atom pairs is 0.655 angstroms; (across all 149 pairs:
0.709)
> hide #122 models
> ui tool show Matchmaker
> matchmaker #123 to #2
Computing secondary structure
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
fold_2025_05_21_sec_ancestral_model_2.cif, chain A (#123), sequence alignment
score = 569.8
RMSD between 148 pruned atom pairs is 0.655 angstroms; (across all 149 pairs:
0.709)
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Secuencia
> ancestral/fold_2025_05_21_sec_ancestral_model_3.cif"
Chain information for fold_2025_05_21_sec_ancestral_model_3.cif #124
---
Chain | Description
A | .
Computing secondary structure
> hide #123 models
> color #123 #544f56ff
> color #123 #535456ff
> color #123 #e7e8eeff
> ui tool show Matchmaker
> matchmaker #124 to #2
Computing secondary structure
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
fold_2025_05_21_sec_ancestral_model_3.cif, chain A (#124), sequence alignment
score = 569.8
RMSD between 148 pruned atom pairs is 0.652 angstroms; (across all 149 pairs:
0.715)
> color #124 #6d6c6dff
> color #124 #f3f1f3ff
> open "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/Secuencia
> ancestral/fold_2025_05_21_sec_ancestral_model_4.cif"
Chain information for fold_2025_05_21_sec_ancestral_model_4.cif #125
---
Chain | Description
A | .
Computing secondary structure
> hide #124 models
> ui tool show Matchmaker
> matchmaker #125 to #2
Computing secondary structure
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
fold_2025_05_21_sec_ancestral_model_4.cif, chain A (#125), sequence alignment
score = 569.8
RMSD between 148 pruned atom pairs is 0.650 angstroms; (across all 149 pairs:
0.696)
> color #125 #7b7d7bff
> color #125 #e8ebe7ff
> hide #125 models
> show #94 models
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\tools.py", line 281, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001EE8AD35A10>,
<chimerax.similarstructures.gui.SimilarStructuresPanel object at
0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 1053, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x000001EE8AD35A10>, <chimerax.similarstructures.gui.SimilarStructuresPanel
object at 0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001EE8AD35A10>,
<chimerax.similarstructures.gui.SimilarStructuresPanel object at
0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]
ValueError: error processing: 'tools' -> [, , , , ]: Error while saving
session data for 'tools' -> [, , , , ]
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\tools.py", line 281, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001EE8AD35A10>,
<chimerax.similarstructures.gui.SimilarStructuresPanel object at
0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 170, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 1053, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x000001EE8AD35A10>, <chimerax.similarstructures.gui.SimilarStructuresPanel
object at 0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001EE8AD35A10>,
<chimerax.similarstructures.gui.SimilarStructuresPanel object at
0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]
ValueError: error processing: 'tools' -> [, , , , ]: Error while saving
session data for 'tools' -> [, , , , ]
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save "C:/Users/Carolina/OneDrive - Universidad Autonoma de San Luis Potosi -
> UASLP/Lab Virología/AlphaFold3/CHIKVaaint.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\tools.py", line 281, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001EE8AD35A10>,
<chimerax.similarstructures.gui.SimilarStructuresPanel object at
0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 1053, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x000001EE8AD35A10>, <chimerax.similarstructures.gui.SimilarStructuresPanel
object at 0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001EE8AD35A10>,
<chimerax.similarstructures.gui.SimilarStructuresPanel object at
0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]
ValueError: error processing: 'tools' -> [, , , , ]: Error while saving
session data for 'tools' -> [, , , , ]
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\tools.py", line 281, in take_snapshot
if not tool_inst.SESSION_SAVE:
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 395, in SESSION_SAVE
return len(self.hits) > 0
^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\similarstructures\gui.py", line 101, in hits
return self.results.hits
^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'hits'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001EE8AD35A10>,
<chimerax.similarstructures.gui.SimilarStructuresPanel object at
0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 170, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 1053, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x000001EE8AD35A10>, <chimerax.similarstructures.gui.SimilarStructuresPanel
object at 0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x000001EE8AD35A10>,
<chimerax.similarstructures.gui.SimilarStructuresPanel object at
0x000001EEC6FAFC10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001EEA6F20310>, <chimerax.model_panel.tool.ModelPanel object at
0x000001EE8AA84790>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001EEA6F651D0>]
ValueError: error processing: 'tools' -> [, , , , ]: Error while saving
session data for 'tools' -> [, , , , ]
File "C:\Program Files\ChimeraX\ChimeraX 1.10.dev202501160116\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
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: 3.11.4
Locale: es_MX.cp1252
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
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: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.12.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202501160116
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.43
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.11
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.0
PyQt6-Qt6: 6.8.1
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.1
PyQt6_sip: 13.9.1
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
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