[PyMOL] volume approximation

[ormus c. <or...@in...>]

hi, i am looking for some advice. i would like to create a set of overlappi=
ng spheres whose combined volume approximates the=20
actual volume of a protein of interest. obviously, i am looking for a reduc=
ed representation. ideally, i am talking about no=20
more than a handful of spheres. these spheres should all be equally sized a=
nd the degree of overlap between spheres should be=20
consistent across all of them (that is, they should all overlap all neighbo=
ring spheres equally). i'm trying to construct an=20
algorithm that would take in the pdb coordinates of the protein to be appro=
ximated and output a set of points corresponding to=20
the origins of the spheres required to fill the volume of the original prot=
ein to some determined degree of accuracy (eg. >=20
90%).

i'm relatively new to pymol, but of all the molecular visualization program=
s i have looked at, it seems best suited to the=20
task at hand. has anyone done anything even remotely like this? can anyone =
offer insight as to whether i can do this within=20
pymol and, if so, where i might look (wiki, documenation, etc) to get start=
ed?

thanks in advance, ormus


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