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.
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 pymol> sort Cheers, Esben -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net on behalf of Satya Arjunan Sent: Sat 2006-02-11 03:56 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] movie of diffusion of atoms/molecules 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 ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
