VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 26 2005 - 10:04:26 CDT

Hey Scott,
  Yes, the secondary structure is determined based on the initial
frame, and is not usually recalculated since for a large structure it can
take STRIDE quite a while to do the work. You can force VMD to recalculate
the secondary structure by issuing the command:
  mol ssrecalc top

If you want VMD to calculate the secondary structure for each frame, you
can use the sscache script in the VMD script library:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/

Let me know if you have more questions on this.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 26, 2005 at 10:55:10AM -0400, Scott Thibault wrote:
> Hi,
>
> Is it true that the identification of secondary structures like helix
> are determined on the first frame of a trajectory? Is there a way to
> have it recomputed for each frame?
>
> Thanks,
> --Scott Thibault 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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