[gmx-users] xpm file
erikm at xray.bmc.uu.se
Tue Oct 5 13:25:43 CEST 2010
You can use the m2p file to tune the size of the datapoint in the x-
Carla Jamous skrev 2010-10-05 13.21:
> 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 out.
> 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
> <mailto: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
> And the legend of my axis: x axis=time(ps)
> y axis=Hydrogen Bond
> 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
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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