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