I believe BioPython project can help you. It load a PDB file and you have methods which help you selecting atoms.
Please see [1]... [1] http://biopython.org/wiki/Main_Page Best regards, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Thu, Apr 19, 2012 at 5:25 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > patrick wintrode wrote: > >> Hi. >> >> For each alpha carbon in my protein, I want to write out the x, y and z >> coordinates as separate time series. >> >> If I use g_traj with the flags -oxt -x (or y orz) and -n along with an >> index file selecting the appropriate alpha carbon, will that do the trick? >> Does anyone know of a less cumbersome way of doing this? >> >> > You don't necessarily have to do each alpha carbon separately (though you > could script all of it, which is relatively easy). If you use the default > C-alpha group, all of the chosen x/y/z coordinates are printed in order of > the atom number, which can then be parsed with something like awk or perl. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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