AMBER: process and plot matrix data

From: Vlad Cojocaru <>
Date: Fri, 20 Apr 2007 11:28:12 +0200

Dear VMD and AMBER users,

I know this is not an immediate VMD or AMBER related question, and I
would like to appologize for that. However, I would still like to appeal
to your experience in processing and analyzing MD generated data and ask
you a question. I have several sets of data that look like the one
below. I would like to plot this data as matrix data in the sense of
having first column as label on Y axis, second column as label on X axis
(they can be swapped of course) and then for each (X,Y) pair create a
point (symbol) on the graph colored with a colormap according to the
value on the 3rd column. The result would be a colored square similar to
those of 2D-RMSD plots.

I have tried several programs like gnuplot, matlab or grace but none
seems to be able to do this, or maybe I did not find a way to do this.
So, if anyone of you has any idea how to generate such a plot from data
looking as the set below, I would appreciate an advice.

I also have to say that I have many such sets, so ideally I would prefer
a solution that does not involve too much " mouse work "


-----example data --------------
ILE180 LEU183 5.05514431
VAL88 LEU183 8.78831958771
LEU341 LEU183 9.41174030304
LEU176 LEU183 8.36755180359
VAL212 LEU183 6.89742231369
VAL267 LEU183 8.79418754578
ILE182 LEU183 5.07598829269
ILE188 LEU183 5.93424034119
LEU208 LEU183 3.52190303802
LEU77 LEU183 8.06875419617
LEU209 LEU183 9.38657951355
LEU18 ILE188 8.16420936584
ILE190 ILE188 7.56690168381
ILE182 ILE188 4.38945245743
LEU183 ILE188 5.93424034119
LEU208 ILE188 6.20247745514
LEU77 ILE188 8.0138130188
ILE197 ILE188 7.71743297577
ILE198 ILE188 9.86605453491
ILE188 ILE198 9.86605453491
LEU77 ILE198 3.98720002174
LEU208 ILE198 9.05824184418
LEU209 ILE198 6.56565237045
ALA78 ILE198 8.51403141022
ILE197 ILE198 5.98849058151
ILE180 LEU208 7.99722194672
LEU176 LEU208 9.70461463928
VAL212 LEU208 6.07546663284
ILE182 LEU208 3.58233737946
LEU183 LEU208 3.52190303802
ILE188 LEU208 6.20247745514
LEU77 LEU208 6.40633583069
ALA81 LEU208 8.25501441956
LEU209 LEU208 6.63098669052
ILE198 LEU208 9.05824184418
VAL212 LEU209 6.40835094452
LEU208 LEU209 6.63098669052
LEU77 LEU209 6.56077671051
ALA81 LEU209 3.44523358345
LEU183 LEU209 9.38657951355
ALA78 LEU209 9.17530822754
ILE198 LEU209 6.56565237045
ALA213 LEU209 7.63391113281
ILE74 LEU77 9.12415981293
ILE182 LEU77 9.29354667664
ILE188 LEU77 8.0138130188
LEU208 LEU77 6.40633583069
ALA81 LEU77 8.68662261963
LEU183 LEU77 8.06875419617
LEU209 LEU77 6.56077671051
ALA78 LEU77 6.04990291595
ILE197 LEU77 7.46098184586
ILE198 LEU77 3.98720002174

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
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Received on Sun Apr 22 2007 - 06:07:39 PDT
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