This is the way to do it with Pymol for one frame: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08154.html
I guess with a little bit of python scripting you could read through all the frames of your trajectory. Thomas 2011/1/4 ahmet yıldırım <ahmedo...@gmail.com> > I get the residue versus time ( secondary structure graph) using do_dssp > tool. I want to get the percentage value(alpha helix, beta sheet, coil ...) > of secondary structure. For example: > > Secondary structure percentage (%): > Helix:51.6 > B-sheet:0 > Random coil:24.0 > Turn:24.4 > > 04 Ocak 2011 14:59 tarihinde Mark Abraham <mark.abra...@anu.edu.au> yazdı: > >> On 4/01/2011 11:38 PM, ahmet yıldırım wrote: >> >> Dear Mark, >> >> I will do by using the g_analyze tool but I do not know how to use it. >> >> >> There's a section in Appendix D of the manual for each tool, or you can >> use the -h argument to the tool to get the same information. >> >> Either way, you haven't got the right tool. Hint: it's a "protein specific >> analysis" >> >> Mark >> >> >> >> Thanks >> >> 2011/1/4 Mark Abraham <mark.abra...@anu.edu.au> >> >>> On 4/01/2011 8:33 PM, ahmet yıldırım wrote: >>> >>>> Hi, >>>> >>>> How can I calculate the percentages (alpha helix, beta sheet, coil ...) >>>> of secondary structure? >>>> >>> >>> Look in manual section 7.4 for a suitable tool. >>> >>> Mark >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> Ahmet YILDIRIM >> >> >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Ahmet YILDIRIM > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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