# [gmx-users] DSSP secondary structure

Mon Feb 15 21:26:45 CET 2016

```Thank you Justin,
I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any way to calculate the percentage of a-helical structure of a protein during simulation? Indeed DSSP visualize it but I want to calculate it exactly.

On Monday, February 15, 2016 6:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 2/15/16 1:31 AM, mohammad r wrote:
> I changed and reduced the ratio but the xpm file was not changed at all.
>

Unfortunately there's not much I can tell you here because this is rather
cryptic.  It's illogical to get the same output with different input.  You can
calculate exactly what values to use based on the number of residues in the
protein (y-axis) and number of frames (x-axis).  Then scale xbox accordingly to
fit some nicely shaped rectangle of defined proportions.

-Justin

>
>      On Sunday, February 14, 2016 5:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 2/14/16 1:54 AM, mohammad r wrote:
>> 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):
>>
>
>> xbox = 2.0 ; x‐size of a matrix element
>> ybox = 2.0 ; y‐size of a matrix element
>
> You have a rectangular matrix, with the x-dimension being much longer than the
> y-dimension.  If you set these two values to be the same, what happens to the
> size of the rectangle?  It gets uniformly scaled.  So naturally that
> accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.
>
> -Justin
>

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

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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