Satya, Hmm...for maximum performance, I'd recommend creating a fake PDB file with a single HETATM entry for each protein/sphere.
You'll get much better load performance than with CGOs, you can stick a radius value in the B or Q column if you need it, you can defer builds (set defer_builds_mode,1) or if you have a nice graphics card you can use "sphere_mode,5" for pixel-perfect spheres. Cheers, Warren PS. No there isn't a CGO callback...just for PyOpenGL. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Satya Arjunan > Sent: Thursday, February 16, 2006 6:11 PM > To: EPF (Esben Peter Friis); pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] movie of diffusion of atoms/molecules > > Hi Esben and List, > > Thank you for your answering my questions. I realize now that > it would be better to just represent a molecule as a sphere > with diameter corresponding to the protein's diameter because > like you said, with 4000 molecules, I don't need atomistic detail. > > Here is my situation: I now have a file with 100 frames, each > frame has the 3D coordinates of 4000 spheres obtained from my > simulator. Right now I have found a way to load the > coordinates as cgo objects for each frame as shown in the > script below. The problem is that Pymol needs to load all the > frames before it can start playing the movie, which requires > a lot of memory when considering 4000 spheres * 100 frames. > Is there any callback function that is called when Pymol > wants to move to the next frame? With such a function, I can > clear the previous frames in the memory using cmd.delete and > load a new frame from the file. > > I appreciate if there is any other solution for the above > problem. Thanks! > > satya > > > > > import string > import random > from pymol.cgo import * > from pymol import cmd > > axes = [ > LINEWIDTH, 3.0, > BEGIN, LINES, > COLOR, 0.2, 1.0, 0.2, > > VERTEX, 0.0, 0.0, 0.0, > VERTEX, 100.0, 0.0, 0.0, > > COLOR, 1.0, 0.2, 0.2, > VERTEX, 0.0, 0.0, 0.0, > VERTEX, 0.0, 100.0, 0.0, > > COLOR, 0.2, 0.2, 1.0, > VERTEX, 0.0, 0.0, 0.0, > VERTEX, 00, 0.0, 100.0, > END > ] > > > > c=0 > for a in xrange(0,100): > balls = [] > for i in xrange(0,40): > balls.extend([COLOR, > random.randrange(0,10,1)/10.0, > random.randrange(0,10,1)/10.0, > random.randrange(0,10,1)/10.0, > SPHERE, > random.randint(0,100), > random.randint(0,100), > random.randint(0,100), > 1,]) > obj = axes + balls > cmd.load_cgo(obj,'cgo01',c) > c = c + 1 > > pdb_list = [ > "HETATM 1 X UNK 1 %8.3f%8.3f%8.3f 1.00 > 10.00\n"%(3.2,0,0), > "HETATM 2 Y UNK 2 %8.3f%8.3f%8.3f 1.00 > 10.00\n"%(0,3.2,0), > "HETATM 3 Z UNK 3 %8.3f%8.3f%8.3f 1.00 > 10.00\n"%(0,0,3.2), > ] > cmd.read_pdbstr(string.join(pdb_list,''),'lab2') > cmd.hide('(lab2)') > cmd.label('lab2','name') > cmd.color('white','lab2') > cmd.zoom('cgo01') > cmd.clip('far',-5) > > > > > 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=1216 > > 42 > > > <http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121 > > 642> _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > ------------------------------------------------------- > 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 > > > >
