Re: AMBER: process and plot matrix data

From: Vlad Cojocaru <>
Date: Fri, 20 Apr 2007 15:18:46 +0200

Dear Patrick,

Well, I could do that for sure, but I wanted to avoid that and
especially I wanted to avoid any manual work since its a bunch of graphs
I need to generate. Somebody else gave me a nice recipe for doing it in
matlab ... I am working on that

Thanks a lot anyhow for answering


Patrick McCarren wrote:

>Could you assign a unique number for each amino acid you are looking at so
>that you have a numerical x,y,z? Almost all of the programs that do
>contour plots Mathematica, Maple, and even Excel should work for that.
>Then, you could use the text for the labels on the axes. I've done this
>for 2-D plots in Excel, I think (I may have done it manually with text
>boxes), and I'm pretty sure Mathematica could use text labels instead.
>Patrick McCarren
>>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
>>The AMBER Mail Reflector
>>To post, send mail to
>>To unsubscribe, send "unsubscribe amber" to
>The AMBER Mail Reflector
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>To unsubscribe, send "unsubscribe amber" to

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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Apr 22 2007 - 06:07:43 PDT
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