[gmx-users] question

[Justin Lemkul]

On 5/14/14, 11:11 AM, Andrew Bostick wrote:
> Dear Gromacs users
>
> After I calculated the secondary structure of residues from 1 to 59 using
> do_dssp during 20 ns MD simulation, I used xpm2ps to show the picture with
> ps.m2p.
>
> y-axis is true but x- axis is very long.
>
> My ps.m2p file is as follows:
>
> ; Command line options of xpm2ps override the parameters in this file
> black&white              = no           ; Obsolete
> titlefont                = Times-Roman  ; A PostScript Font
> titlefontsize            = 20           ; Font size (pt)
> legend                   = yes          ; Show the legend
> legendfont               = Times-Roman  ; A PostScript Font
> legendlabel              =              ; Used when there is none in the
> .xpm
> legend2label             =              ; Used when merging two xpm's
> legendfontsize           = 14           ; Font size (pt)
> xbox                     = 2.0          ; x-size of a matrix element
> ybox                     = 2.0          ; y-size of a matrix element
> matrixspacing            = 20.0         ; Space between 2 matrices
> xoffset                  = 0.0          ; Between matrix and bounding box
> yoffset                  = 0.0          ; Between matrix and bounding box
> x-major                  = 5           ; Major ticks on x axis every ..
> frames
> x-minor                  = 1            ; Id. Minor ticks
> x-firstmajor             = 0            ; First frame for major tick
> x-majorat0               = no           ; Major tick at first frame
> x-majorticklen           = 8.0          ; x-majorticklength
> x-minorticklen           = 4.0          ; x-minorticklength
> x-label                  =              ; Used when there is none in the
> .xpm
> x-fontsize               = 16           ; Font size (pt)
> x-font                   = Times-Roman  ; A PostScript Font
> x-tickfontsize           = 10           ; Font size (pt)
> x-tickfont               = Helvetica    ; A PostScript Font
> y-major                  = 10
> y-minor                  = 5
> y-firstmajor             = 0
> y-majorat0               = no
> y-majorticklen           = 8.0
> y-minorticklen           = 4.0
> y-label                  =
> y-fontsize               = 16
> y-font                   = Times-Roman
> y-tickfontsize           = 10
> y-tickfont               = Helvetica
>
> How to solve this problem?
>

Increase the ratio of ybox/xbox.  Setting them equal means the dimensions of 
your rectangle will be (# of residues)/(# of frames), with the denominator being 
massively larger than the numerator, hence the badly skewed output.

-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

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