VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 28 2004 - 12:26:09 CDT

Scott,
  VMD doesn't calculate this for itself, it uses the program STRIDE
to do these calculations:
  http://wolf.bi.umist.ac.uk/unix/stride.html
  http://www.rfcgr.mrc.ac.uk/Registered/Help/stride/

Stride determines the secondary structure and VMD uses this to
perform its drawing tasks.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 28, 2004 at 11:18:11AM -0600, Scott Pendley wrote:
> Hello all,
>
> I was wondering if any of you could tell me the algorithm by which VMD
> calculated whether a given residue is an alpha helix. Does it use the
> phi/psi angles? If it does, what is the area that is compares them
> against to determine helicity? Any help would be appreciated.
>
> Sincerely,
>
> Scott 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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