[gmx-users] xpm file

[Erik Marklund]

  You can use the m2p file to tune the size of the datapoint in the x- 
and/or y-dimension.

Erik

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 ?
>
> Thanks,
> Carla
>
> 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
>         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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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