[gmx-users] xpm file

Carla Jamous carlajamous at gmail.com
Tue Oct 5 13:21:21 CEST 2010

Thank you Justin,

I used an .m2p file to change the properties of my .xpm.
I got an .eps file that I opened with Gimp. In order to visualize this .eps
file, I have to put 200% in Gimp.
But my problem is that my graph is too large, so I can't seem to print it
I really  to print the .eps file, so please is there a way to do it or do I
have to split my trajectory and generate many .eps ?


On Fri, Oct 1, 2010 at 2:34 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Carla Jamous wrote:
>> Hi everyone,
>> Please I need some help visualizing an .xpm file.
>> I tried to open my .xpm file (g_hbond matrix) with Gimp but It gives me
>> red lines that I don't understand.
>> So I converted my .xpm file into an .eps file with xpm2ps. When I try to
>> open my .eps file, I get the legend:
>> Hydrogen bonds
>> white=none
>> red=Present
>> And the legend of my axis: x axis=time(ps)
>>                                          y axis=Hydrogen Bond index
>> But I can't see the values: It means I see that there is an axis but it's
>> a black bold line instead of values of time or number of atoms in hydrogen
>> bonds.
> You're not going to get any numbers in this plot (aside from hydrogen bond
> indices).  The matrix you're trying to plot is an existence matrix, a red
> pixel if the hydrogen bond is present, a white one if none is present.  You
> can map which hydrogen bond is which from the hbond.ndx file.  That is, once
> you get it rendered properly (see below).
>  Please how can I visualize correctly my matrix?
> You can alter its properties (proportions, x/y spacing) with a .m2p file.
>  There is an example in the online manual.  If the plot is simply a straight
> line, you'll probably want to decrease the x-spacing and increase the
> y-spacing to make it look normal.
> -Justin
>  Thank you
>> Carla
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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