[gmx-users] analysis of the secondary structure diagram

[Nazli]

Thanks 

Sent from my iPhone

> On Feb 22, 2015, at 5:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> 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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