[gmx-users] about using do_dssp for a few residues

[Justin Lemkul]

On 11/18/13 4:08 PM, jianqing wrote:
> Will appreciate if anyone could provide any suggestions!
>

The only secondary structure that should be affected would be beta-sheets, since 
their hydrogen bonding patterns are based on non-local interactions.  Helices, 
bends, and turns should show up independently of any other residues.

Your initial conclusion was correct - do_dssp, like any other program, only 
considers atoms within the index file provided.

If you only care to visualize those residues of interest, manually modify the 
.xpm file.  You can make sensible figures by providing an .m2p file on the 
original .xpm so that it renders better.  The default representation is usually 
unintelligible, but proper manipulation of the x- and y-axis ratio can yield a 
very nice figure.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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