Re: [gmx-users] Writing out individual coordinates

2012-04-19 Thread Tsjerk Wassenaar
Hey :) Why not just use trjconv to write a .pdb file? C-alpha atoms is offered as standard group, and the resulting file can be easily processed with sed/python. Cheers, Tsjerk On Thu, Apr 19, 2012 at 10:47 PM, Rodrigo Faccioli wrote: > I believe BioPython project can help you. It load a PDB f

Re: [gmx-users] Writing out individual coordinates

2012-04-19 Thread Rodrigo Faccioli
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

Re: [gmx-users] Writing out individual coordinates

2012-04-19 Thread Justin A. Lemkul
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 a

[gmx-users] Writing out individual coordinates

2012-04-19 Thread patrick wintrode
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 cumberso