[gmx-users] ramachandran plot

[Urszula Uciechowska]

Dear Tsjerk,

Could you send me the script again? as I did not find the attachment in
your previous email.

best regards
Urszula


> 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.
> --
> Gromacs Users mailing list
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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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http://www.ug.edu.pl/