[PyMOL] movie of diffusion of atoms/molecules

[Satya Arjunan]

Hi all,

I would like to use Pymol to visualize 3D simulation of lattice-based 
diffusion of molecules. The simulator provides the 3D coordinates (or 
the translational direction since they have fixed diffusion distance) of 
the molecules at everytime step. At the end of the simulation, I would 
like to feed the coordinates (or the translational direction) to Pymol 
using a python script and make a movie of this.

What is a good way of implementing this with Pymol with lowest 
computational cost because there are about 4000 protein molecules 
altogether? I have come across a sample script at 
http://www.rubor.de/bioinf/tips_python.html#chempy which I think I can 
use to place the atoms/molecules in pymol. I am wondering if there is 
any other cost effective way of implementing this? Is it possible just 
to provide the translational angle and distance for certain molecules 
already in the model?

Thanks in advance.
satya