RE: [PyMOL] movie of diffusion of atoms/molecules

[EPF \(E. P. Friis\) <EP...@no...>]

Hi Satya

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.=20

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=3D3.0
pymol> show spheres, my_object
pymol> sort


Cheers,

Esben


-----Original Message-----
From: pym...@li... on behalf of Satya Arjunan
Sent: Sat 2006-02-11 03:56
To: pym...@li...
Subject: [PyMOL] movie of diffusion of atoms/molecules
=20
Hi all,

I would like to use Pymol to visualize 3D simulation of lattice-based=20
diffusion of molecules. The simulator provides the 3D coordinates (or=20
the translational direction since they have fixed diffusion distance) of =

the molecules at everytime step. At the end of the simulation, I would=20
like to feed the coordinates (or the translational direction) to Pymol=20
using a python script and make a movie of this.

What is a good way of implementing this with Pymol with lowest=20
computational cost because there are about 4000 protein molecules=20
altogether? I have come across a sample script at=20
http://www.rubor.de/bioinf/tips_python.html#chempy which I think I can=20
use to place the atoms/molecules in pymol. I am wondering if there is=20
any other cost effective way of implementing this? Is it possible just=20
to provide the translational angle and distance for certain molecules=20
already in the model?

Thanks in advance.
satya


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