I want to calculate center of mass of a protein. I know there are many tools servers out there to do this job but I've something more to do with it. I've gone through several sites to know about this. At last I've got to know something. Here (http://pipe.ibibiosolutions.com/Com.html) they have shown something. What made me to come here are
1 ) While calculating do I need to consider every atom in the protein or just backbone is enough?
2) If I need to take all atoms how can I assign mass to every atom should I keep the mass constant? (be cause in this script they kept all atoms mass equal https://code.google.com/p/pdb-tools/source/browse/trunk/pdbTools/pdb_centermass.py). Even if backbone is enough, should I assign the individual molecular mass to each amino acid in protein?
3) At last after solving the equation, how can I get the coordinates of the center of mass?
I just want to know whats going on beyond the equation which solves it.