[gmx-users] length of beta sheet

[Justin Lemkul]

On 12/25/14 1:43 AM, pratibha kapoor wrote:
> Hi everyone,
>
> I would like to calculate length of beta sheet. Is this any automatic tool
> to serve the purpose?
> To elaborate, I am aware that dssp can give me whether the residue is in
> beta sheet ("E") or not at each time frame but I want to know exactly how
> many hydrogen bonds are formed by each residue in E (and not just E if
> minimum criterion of two hydrogen bonds is satisfied by DSSP). From this I
> would like to calculate length of beta sheet.
>
> Any help is highly appreciated.
>

You can extract this sort of information from the .xpm file that do_dssp writes 
out.  Just parse it with whatever scripting language you like.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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