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RE: [PyMOL] movie of diffusion of atoms/molecules
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From: Warren D. <wa...@de...> - 2006-02-17 02:58:53
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Satya,
Hmm...for maximum performance, I'd recommend creating a fake PDB file
with a single HETATM entry for each protein/sphere. =20
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. =20
Principal Scientist
. DeLano Scientific LLC =20
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. South San Francisco, CA 94080 USA =20
. Biz:(650)-872-0942 Tech:(650)-872-0834 =20
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:wa...@de... =20
=20
> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Satya Arjunan
> Sent: Thursday, February 16, 2006 6:11 PM
> To: EPF (Esben Peter Friis); pym...@li...
> Subject: Re: [PyMOL] movie of diffusion of atoms/molecules
>=20
> Hi Esben and List,
>=20
> Thank you for your answering my questions. I realize now that=20
> it would be better to just represent a molecule as a sphere=20
> with diameter corresponding to the protein's diameter because=20
> like you said, with 4000 molecules, I don't need atomistic detail.
>=20
> Here is my situation: I now have a file with 100 frames, each=20
> frame has the 3D coordinates of 4000 spheres obtained from my=20
> simulator. Right now I have found a way to load the=20
> coordinates as cgo objects for each frame as shown in the=20
> script below. The problem is that Pymol needs to load all the=20
> frames before it can start playing the movie, which requires=20
> a lot of memory when considering 4000 spheres * 100 frames.=20
> Is there any callback function that is called when Pymol=20
> wants to move to the next frame? With such a function, I can=20
> clear the previous frames in the memory using cmd.delete and=20
> load a new frame from the file.
>=20
> I appreciate if there is any other solution for the above=20
> problem. Thanks!
>=20
> satya
>=20
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> import string
> import random
> from pymol.cgo import *
> from pymol import cmd
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> axes =3D [
> LINEWIDTH, 3.0,
> BEGIN, LINES,
> COLOR, 0.2, 1.0, 0.2,
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> VERTEX, 0.0, 0.0, 0.0,
> VERTEX, 100.0, 0.0, 0.0,
>=20
> COLOR, 1.0, 0.2, 0.2,
> VERTEX, 0.0, 0.0, 0.0,
> VERTEX, 0.0, 100.0, 0.0,
> =20
> COLOR, 0.2, 0.2, 1.0, =20
> VERTEX, 0.0, 0.0, 0.0,
> VERTEX, 00, 0.0, 100.0,
> END
> ]
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> c=3D0
> for a in xrange(0,100):
> balls =3D []
> 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 =3D axes + balls
> cmd.load_cgo(obj,'cgo01',c)
> c =3D c + 1
>=20
> pdb_list =3D [
> "HETATM 1 X UNK 1 %8.3f%8.3f%8.3f 1.00=20
> 10.00\n"%(3.2,0,0),
> "HETATM 2 Y UNK 2 %8.3f%8.3f%8.3f 1.00=20
> 10.00\n"%(0,3.2,0),
> "HETATM 3 Z UNK 3 %8.3f%8.3f%8.3f 1.00=20
> 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)
>=20
> >
> > Hi Satya
> >
> > You can use the command "translate" to move the individual=20
> objects in=20
> > pymol. Is takes a list of 3 floating points numbers as the=20
> > translational vector.
> >
> > I don't know how Pymol would handle 4000 objects, but an=20
> alternative=20
> > might be to load them as states within one object, and then use the=20
> > "show all states" command from the "Movie" menu. The "translate"
> > command can also move the individual states independently. (If you=20
> > also need to rotate the molecules, it gets more difficult :-)
> >
> > Another suggestion: If you have 4000 proteins, you may not=20
> need a very=20
> > high level of detail for each molecule. You could save a lot by=20
> > loading only the alpha carbon atoms and then increase their=20
> vdw-size=20
> > 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=20
> > Arjunan
> > Sent: Sat 2006-02-11 03:56
> > To: pym...@li...
> > Subject: [PyMOL] movie of diffusion of atoms/molecules
> >
> > Hi all,
> >
> > I would like to use Pymol to visualize 3D simulation of=20
> lattice-based=20
> > diffusion of molecules. The simulator provides the 3D=20
> coordinates (or=20
> > the translational direction since they have fixed diffusion=20
> distance)=20
> > of the molecules at everytime step. At the end of the simulation, I=20
> > would like to feed the coordinates (or the translational=20
> direction) to=20
> > Pymol 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=20
> think I can=20
> > use to place the atoms/molecules in pymol. I am wondering=20
> if there is=20
> > any other cost effective way of implementing this? Is it=20
> possible just=20
> > to provide the translational angle and distance for certain=20
> molecules=20
> > already in the model?
> >
> > Thanks in advance.
> > satya
> >
> >
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