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.