VMD-L Mailing List

From: Nuno R. L. Ferreira (nunolf_at_ci.uc.pt)
Date: Mon Mar 13 2006 - 11:47:04 CST

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 

-- 
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Nuno Ricardo Santos Loureiro da Silva Ferreira
Ph.D student
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal
www.biolchem.qui.uc.pt
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\" Do not worry about your dificulties in mathematics.
   I can assure you that mine are still greater.\"
                                       e=mc2
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