[gmx-users] do_dssp result over written on the one line

[Justin Lemkul]

On 8/16/14, 7:30 AM, Batdorj Batsaikhan wrote:
> Dear gmx users,
>
> I done secondary structure analysis using do_dssp. then I converted xpm file to eps. following commands:
>
> $ gmx do_dssp -s md3.tpr -f md.xtc -o ss.xpm -tu ns -sss -xvg
> $ xpm2ps -f ss.xpm -o ss.eps
>
> but result of ss.eps is written on the one line. How to fix it?
>

You need to increase the size of the y-axis relative to x by using an .m2p file 
with a suitable ybox/xbox ratio.  The default output is generally very distorted 
because there are orders of magnitudes more frames (x-axis) than there are 
protein residues (y-axis) in most simulations.

http://manual.gromacs.org/online/m2p.html

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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