<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
You can use the m2p file to tune the size of the datapoint in the x-
and/or y-dimension.<br>
<br>
Erik<br>
<br>
Carla Jamous skrev 2010-10-05 13.21:
<blockquote
cite="mid:AANLkTimzDY=E5q=WXeODJUZogm-YuNF9wg64T11aziTh@mail.gmail.com"
type="cite"><br>
Thank you Justin,<br>
<br>
I used an .m2p file to change the properties of my .xpm.<br>
I got an .eps file that I opened with Gimp. In order to visualize
this .eps file, I have to put 200% in Gimp.<br>
But my problem is that my graph is too large, so I can't seem to
print it out.<br>
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 ?<br>
<br>
Thanks,<br>
Carla<br>
<br>
<div class="gmail_quote">On Fri, Oct 1, 2010 at 2:34 PM, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im"><br>
<br>
Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi everyone,<br>
<br>
Please I need some help visualizing an .xpm file.<br>
I tried to open my .xpm file (g_hbond matrix) with Gimp
but It gives me red lines that I don't understand.<br>
So I converted my .xpm file into an .eps file with xpm2ps.
When I try to open my .eps file, I get the legend:<br>
Hydrogen bonds<br>
white=none<br>
red=Present<br>
<br>
And the legend of my axis: x axis=time(ps)<br>
y axis=Hydrogen
Bond index<br>
<br>
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.<br>
<br>
</blockquote>
<br>
</div>
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).
<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Please how can I visualize correctly my matrix?<br>
<br>
</blockquote>
<br>
</div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Thank you<br>
<br>
Carla<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<font color="#888888">
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote>
</div>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
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
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
</pre>
</body>
</html>