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
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