From: Jérôme Hénin (
Date: Mon Mar 13 2006 - 15:22:11 CST

Actually, since we are trying to do the same thing, I thought it would be
simpler to share the whole stuff. I use a VMD script that outputs a file
containing one line per frame. It includes first the frame number, then the
list of structures for each residue:
0 C C T T T C C C H H H H H H H H H H G G H H H
1 C C C T T C C H H H H H H H H H H H G G H H T
2 ...

Then I apply the script stride2png, attached to this message. This script can
be tuned a bit, depending on the aspect ratio you want for the final picture.
I think everything inside is properly commented.

A great way to add 100% vector axes and legends around that, is to make an
empty graph with the right axes in xmgrace and export it as EPS. You can then
open it with inkscape (you need to have pstoedit installed to do that),
import the png picture and overlay it with the graph. The result can be saved
as SVG, PS or PDF to get a perfect rendering regardless of the resolution.


Le Lundi 13 Mars 2006 18:47, Nuno R. L. Ferreira a écrit :
> Hi *
> Thanks for the replies. Going to share may "experience" and my thoughts
> till 5 minutes ago ;-)
> I tryed quickly Nicolas suggestion (gnuplot) in a Ca distance matrix, and
> its reasonably simple to produce a figure. I think gnuplot won't plot
> matrices with letter entries (secondary structure information), though
> thats not a big issue since the original matrix could be converted to a
> matrix containing numbers.
> I did not yet tryed to implement a Tcl script to produce outputs formated
> as xpm/.ppm.
> The suggestion of Jerome seems to be cool (I like the pipe stuff).
> I agree with axel, since we do not need to change the relevant property
> value calculated, if I use the .xpm format. If the choice was the .ppm
> format, I have to convert the property value to a RGB code. Jerome
> surpasses this issue by an array convertion scheme.
> Jerome, did you perform any kind of convertion on your matrix prior saving
> the information to the array struct (like a descritization of the data?).
> Is your color array pre-defined, or is it defined in accordance with the
> range of values in the matrix?
> But one question arises, dealing with this .xpm/.ppm (not an issue for
> gnuplot). How am I going to incorporate the x-y tick labels/marks? By
> writing some more pixels on the first column and last row of the outputed
> file? ;-)
> Regards,
> Nuno