# Re: AMBER: process and plot matrix data

From: Patrick McCarren <mccarren.chem.ucla.edu>
Date: Fri, 20 Apr 2007 03:02:15 -0700 (PDT)

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
UCLA

>
> 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 "
>
> Thanks
>
> -----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
>
>
>
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Received on Sun Apr 22 2007 - 06:07:40 PDT
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