[gmx-users] DNA Helicoïdal Plots over time

Stéphane Téletchéa steletch at jouy.inra.fr
Mon Mar 12 13:38:55 CET 2007

Dear colleagues,

I've set up a procedure to extract and plot DNA helocoïdal parameters 
*automatically*. This etup is first intended for AMBER trajectories but 
since the main parameters are extracted from the standard Curves 
program, then i think it could be easily used by gromacs users (the 
scripts themselves do not require anything AMBER-specific).

The entire procedure is described here:

In short, this is the description i've already sent to the AMBER mailing 
I've tried to explain the whole process, but basically the main tool 
(dnaplots.pl) uses pre-filtered data extracted from individual Curves 
analysis for getting a full plot over time for the defined parameter. 
For instance, you'll easily get 23 pages of parameters using this 
procedure (namely alpha, beta, gamma, delta, ... but also intra and 
inter base paris parameters). The final plots are generated with XmGrace 
so it is easy to used in an interactive mode after the first shot to 
tweak parameters to your convenience.

The script is written in perl and can be adjusted to get more parameters 
(most of the time, it is just as easy as adding a description in one list).

This setup has been successfully used for more than 4 years by me and 
some colleagues so i tried to place a clear description of the working 
procedure on the web page for others to benefit from this work.

Feel free to ask if you need further input, and try to look inside the 
scripts (as recommended on the web page) in case you'll have some doubts 
about parameters.

Hoping this will help you analyse faster your DNA trajectories,

Stéphane Téletchéa

Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

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