[gmx-users] ramachandran plot

[Tsjerk Wassenaar]

Hi Urszula,

Attached is an R script for drawing 2D circular or combined circular/linear
KDEs. It works as a command line script, taking as arguments a file with
2-column data, and an output image file name (./kde2d.r input.dat
output.png). It's pretty easy to adapt to suit your needs, even if you
don't know R specifically. I wrote the routine for a manuscript we just
submitted, where the method is explained in some detail, and if you like
the images and care to use it for publications, I would be obliged if you
could reference that paper ("High-Throughput Simulations of Dimer and
Trimer Assembly of Membrane Proteins. The DAFT approach."). If you run into
problems or have further questions, please let me know.

Cheers,

Tsjerk

On Fri, Nov 14, 2014 at 4:31 PM, Urszula Uciechowska <
urszula.uciechowska at biotech.ug.edu.pl> wrote:

> Could you please send me the code? It can be on my private email.
>
> Thanks a lot
>
> Ursuzla
>
> > Hi Urszula,
> >
> > It's a while ago that I made that one, and I don't have the code at hand.
> > But it's a combination of a density plot (kde2d) with the points laid
> > over,
> > and a polygon to highlight the forbidden region. These days I'm doing
> > circular 2D KDEs, whic is more correct. I can send the R code for thay if
> > you want.
> >
> > Best,
> >
> > Tsjerk
> > On Nov 14, 2014 12:34 PM, "Urszula Uciechowska" <
> > urszula.uciechowska at biotech.ug.edu.pl> wrote:
> >
> >> Dear Gromacs users,
> >>
> >> I generated the ramachandran plot and would like to colour it in xmgrace
> >> as it was shown in tutorial:
> >>  http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
> >>
> >> Does anyone know how to do it?
> >>
> >> Best regards
> >> Urszula Uciechowska
> >>
> >>
> >>
> >>
> >> -----------------------------------------
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>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.