VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 20 2005 - 10:14:22 CDT

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
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