[gmx-users] DSSP secondary structure
mohammad.r0325 at yahoo.com
Sun Feb 14 08:03:52 CET 2016
Thank you Justin,
I used xpm2ps command with below m2p file but the resolution was not changed. I've attached the xpm file, even the legend can't be seen.is there anyway to get the result file in pdf format?
m2p file (I found it in the gromacs website):
black&white = no ; Obsoletetitlefont = Times‐Roman ; A PostScript Fonttitlefontsize = 20 ; Font size (pt)legend = yes ; Show the legendlegendfont = Times‐Roman ; A PostScript Fontlegendlabel = ; Used when there is none in the .xpmlegend2label = ; Used when merging two xpm'slegendfontsize = 14 ; Font size (pt)xbox = 2.0 ; x‐size of a matrix elementybox = 2.0 ; y‐size of a matrix elementmatrixspacing = 20.0 ; Space between 2 matricesxoffset = 0.0 ; Between matrix and bounding boxyoffset = 0.0 ; Between matrix and bounding boxx‐major = 20 ; Major ticks on x axis every .. framesx‐minor = 5 ; Id. Minor ticksx‐firstmajor = 0 ; First frame for major tickx‐majorat0 = no ; Major tick at first framex‐majorticklen = 8.0 ; x‐majorticklengthx‐minorticklen = 4.0 ; x‐minorticklengthx‐label = ; Used when there is none in the .xpmx‐fontsize = 16 ; Font size (pt)x‐font = Times‐Roman ; A PostScript Fontx‐tickfontsize = 10 ; Font size (pt)x‐tickfont = Helvetica ; A PostScript Fonty‐major = 20y‐minor = 5y‐firstmajor = 0y‐majorat0 = noy‐majorticklen = 8.0y‐minorticklen = 4.0y‐label =y‐fontsize = 16y‐font = Times‐Romany‐tickfontsize = 10y‐tickfont = Helvetica
On Saturday, February 13, 2016 9:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
On 2/13/16 1:33 AM, mohammad r wrote:
> 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 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
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