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Opened 5 months ago
Closed 5 months ago
#17903 closed defect (duplicate)
Session save: Similar Structures: 'NoneType' object has no attribute 'hits'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.10.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
[deleted to fit within ticket limits]
> 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
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session save: Similar Structures: 'NoneType' object has no attribute 'hits' |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #16968