[gmx-users] DSSP secondary structure

[Justin Lemkul]

On 2/13/16 1:33 AM, mohammad r wrote:
> Hi,
> I used the "gmx do_dssp" command to get the secondary structure of the protein during the simulation but the resolution of the resulted .xpm file is very low. how can I increase its resolution?

You can adjust the matrix proportions with an .m2p file passed to xpm2ps -di. 
These are almost always necessary as there are many more frames than residues in 
the protein, usually an order of magnitude or more.

-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

==================================================