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
MILES-IGERT Trainee
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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