Hello;

I have weighted point masses, actually a peptide molecule, in 3d space. I execute a molecular dynamic program to find out different confomations of this molecule. And wanted to orient second and other conformers with respect to first one. First I adjust center of masses of each conformer as origin. Later calculate moment of inertia and its eigenvalues and vector. After that I do not know how to orient the molecules. The only things that I know is transformation matrix should be calculated and applied to get new coordinates of molecule being oriented.

Thanks.