You can use the command "translate" to move the individual objects in pymol. Is takes a list of 3 floating points numbers as the translational vector.
I don't know how Pymol would handle 4000 objects, but an alternative might be to load them as states within one object, and then use the "show all states" command from the "Movie" menu. The "translate" command can also move the individual states independently. (If you also need to rotate the molecules, it gets more difficult :-)
Another suggestion: If you have 4000 proteins, you may not need a very high level of detail for each molecule. You could save a lot by loading only the alpha carbon atoms and then increase their vdw-size to make them "stick" together:
pymol> alter my_object, vdw=3.0
pymol> show spheres, my_object
From: email@example.com on behalf of Satya Arjunan
Sent: Sat 2006-02-11 03:56
Subject: [PyMOL] movie of diffusion of atoms/molecules
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.
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