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.uciechow...@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.uciechow...@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 >> >> >> >> >> >> >> >> >> >> ----------------------------------------- >> >> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego >> >> http://www.ug.edu.pl/ >> >> >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >> posting! >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >> send a mail to gmx-users-requ...@gromacs.org. >> >> >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send >> > a mail to gmx-users-requ...@gromacs.org. >> > >> >> >> University of Gdansk and Medical Univesity of Gdansk >> Department of Molecular and Cellular Biology >> ul. Kladki 24 >> 80-822 Gdansk >> Poland >> >> >> ----------------------------------------- >> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego >> http://www.ug.edu.pl/ >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.