VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 20 2007 - 14:47:44 CDT

Vlad,
  If I understand your goal correctly, it seems that rather than
a traditional "plot", you're really just displaying a matrix, since
the keys you're using for the abscissa and ordinate are strings rather
than numeric values. Given that, you might want to have a look at
some of the VMD plugins that draw similar matrices with colored
squares, and adapt some of the code for your purposes.
Maybe you can take a look at the code in the "contact map" plugin
and use that, as it's doing something along the lines of what you
describe.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 20, 2007 at 11:28:12AM +0200, Vlad Cojocaru wrote:
> 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
> vlad
>
> -----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
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
> 

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