VMD-L Mailing List

From: griadi_at_utalca.cl
Date: Wed Jun 21 2006 - 11:28:33 CDT

Dear all VMD users,

I'd like to share with the comunity a little script for calculating the average
position of all atoms in a selection (of atoms and frames) in a .dcd file. The
program is in attachment and has two parts. The first, taken from
someone else in the VMD list, aligns the chosen selection along the .dcd. The
second part calculates the average along the chosen frames for all the atoms in
the selection and saves it in a file called average.pdb in the working
directory. Additionally, it calculates the RMSD respect to the aligned
frame 0(taken from someone else in the VMD-list). That part can be modified to
calculate the RMSD respect the average structure.

The system variables can be changed in the first lines of the script.

Important: If the simulation is large, the calculations will take a WHILE. Also,
it's important to be careful in using the program because if you make a
selection including more than one conected structure, the average structure will
be the average of the whole selection AND NOT the average of the independent
conected structures.

Next step would be to develop a tk interface for it.

Best regards to all,
Gonzalo Riadi
Center for Bioinformatics and Molecular Simulation.
University of Talca.

-------------------------------------------------
Este mensaje fue enviado por: http://webmail.utalca.cl