[gmx-users] analysis of the secondary structure diagram

[Justin Lemkul]

On 2/22/15 6:18 AM, nazli kashani javid wrote:
> Hi all
>
> I used do_dssp command to analyze structural changes of my protein.
> after converting to pdf format
> I realized that the Y axis of my diagram is very compress and it is not
> recognizable  ( residue axis) . I also change my ps.m2p file part y-major
>   and
> y-minor.
> y-major = 5.0
> y-minor = 1.0
>
> but it didn't work.how could I stretch my Y axis???????
>

Those keywords dealing with the frequency of tick marks, not the size of the 
axes.  What you want to adjust is the ybox/xbox ratio.

-Justin

> my protein includes 4 alpha helix (bundle) and I use do-dssp for each
> chain( 25 residue) individually.
>
> I attach my pdf file :
> https://www.dropbox.com/s/lw6ogoer7w5h07f/ssaa.pdf?dl=0
>
> any help is appreciated.
>

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

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

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