VMD-L Mailing List

From: Nicolas Sapay (n.sapay_at_ibcp.fr)
Date: Mon Mar 13 2006 - 04:34:22 CST

Hello,
You should try Gnuplot. It is very easy to plot matrices with this
software. If I remember, the commands are :
set pm3d map
set palette gray
splot "yourfile.txt"

Nicolas

Le sam 11/03/2006 à 20:05, Nuno R. L. Ferreira a écrit :
    Hi *
    
    I'm calculating some properties on a trajectory, using VMD in batch mode.
    Some of these properties are ascii matrices, like a Calpha distance map
    (matrix has real numbers) or secondary structure vs time (matrix contains
    stride code letters; nº rows == nº residues).
    
    How do I convert this plain matrices to an image?
    I though that the best way was to produce a raster file (like .ppm or .xpm),
    and then use ImageMagick or NetPBM programs to convert the text file to a
    more appropriate image format, like .png.
    
    To do that, I need some scripting.
    If I want to get a .ppm (or netpbm like) file, I need to convert each matrix
    entry to an RGB code. In the .xpm case, I need to convert the matrix entries
    to a code, which is then coupled to a color via a code on the header of the
    file.
    
    Do you guys ever tryed to do that? Is this a good approach?
    
    Best regards,
    N.
    
    
    
    ######################################
    Nuno Ricardo Santos Loureiro da Silva Ferreira
    Departamento de Química
    Faculdade de Ciências e Tecnologia
    Universidade de Coimbra
    3004-535 Coimbra - Portugal
    Fax: +351 239 827703 - www.biolchem.qui.uc.pt
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-- 
[ Dr Nicolas Sapay ]
Institut de Biologie et Chimie des Proteines
CNRS - Claude Bernard University, IFR128 Bioscience Lyon-Gerland
Phone: +33 (0)4 72 72 26 46 - Fax: +33 (0)4 72 72 26 04
Address: 7 passage du Vercors,  69367-F Lyon cedex 07, France