[gmx-users] Query regarding dssp plot

[Aditya Padhi]

Dear Justin,
        Thank you for the reply. I was using my 50 ns trajectory for
generating the .xpm and .eps files. But when I tried the first 200 ps
trajectory, I can see a clear image with helical content. I was wondering
how to solve this because I have to use the whole 50 ns .tpr and .trr
files. Please suggest me.

Thanking you,
Regards
Aditya.


On Wed, May 21, 2014 at 5:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/21/14, 7:56 AM, Aditya Padhi wrote:
>
>> Dear Gromacs users,
>>          When I am using the DSSP program to generate the secondary
>> structure changes of my protein (23 amino acids) and its mainchain, I am
>> getting the results in the form of .eps file and using Ghostview, I
>> visualized and saved in .jpeg format. But the figure looks blurred and I
>> can not clearly see any secondary structure changes. Can anyone suggest me
>> what and where I am doing the mistake and the possible solutions for this.
>>           I am attaching the figure with this mail for your reference.
>>
>>
> The list does not accept attachments.  If you want to supply an image,
> upload it to a file-sharing server.
>
> If the image is simply distorted, that's where .m2p files are useful to
> alter the size properties of the matrix.
>
> -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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-- 
********************************************
Aditya Kumar Padhi
Ph.D Scholar
School of Biological Sciences (SBS)
Indian Institute of Technology Delhi
New Delhi-110016, India
Contact no:+91-9711539958
********************************************