hi, i am looking for some advice. i would like to create a set of overlapping spheres whose combined volume approximates the actual volume of a protein of interest. obviously, i am looking for a reduced representation. ideally, i am talking about no more than a handful of spheres. these spheres should all be equally sized and the degree of overlap between spheres should be consistent across all of them (that is, they should all overlap all neighboring spheres equally). i'm trying to construct an algorithm that would take in the pdb coordinates of the protein to be approximated and output a set of points corresponding to the origins of the spheres required to fill the volume of the original protein to some determined degree of accuracy (eg. > 90%).
i'm relatively new to pymol, but of all the molecular visualization programs i have looked at, it seems best suited to the task at hand. has anyone done anything even remotely like this? can anyone offer insight as to whether i can do this within pymol and, if so, where i might look (wiki, documenation, etc) to get started? thanks in advance, ormus -- India.com free e-mail - www.india.com. Check out our value-added Premium features, such as an extra 20MB for mail storage, POP3, e-mail forwarding, and ads-free mailboxes!
