VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 20 2005 - 10:14:22 CDT
- Next message: Dan Strahs: "problem with coloring surface by electrostatic potential"
- Previous message: Michel Espinoza-Fonseca: "secondary structure assingnment"
- In reply to: Michel Espinoza-Fonseca: "secondary structure assingnment"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi,
The "timeline" plugin calls STRIDE to compute the secondary structure for
each timestep:
http://bioweb.pasteur.fr/docs/man/doc/stride.1
You'll have to read the STRIDE documentation and papers to decide if it's
accurate enough for your purposes. One could conceivably call DSSP or another
secondary structure program instead if you knew that they'd give better
results.
John Stone
vmd_at_ks.uiuc.edu
On Tue, Sep 20, 2005 at 07:22:07AM -0500, Michel Espinoza-Fonseca wrote:
> Hi all,
>
> I would like to know if any of you know which algorithm is the timeline plug in (included in VMD) using for the assignment of the secondary structure? Is it accurate enough to assign it?
> Thank you,
> Michel
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
- Next message: Dan Strahs: "problem with coloring surface by electrostatic potential"
- Previous message: Michel Espinoza-Fonseca: "secondary structure assingnment"
- In reply to: Michel Espinoza-Fonseca: "secondary structure assingnment"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]