[gmx-users] xpm file

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 1 14:34:12 CEST 2010

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.


> 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


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