Hi 

Once Pymol allow python scripts, you can write a little script to do this. Or, You can use VMD software and use TKinter programming to obtain and plot this data. There is some tutorials at web which you can try.

There is a python script  available for PyMOL:

http://www.pymolwiki.org/index.php/Center_of_mass

Once you have the coordinates, you can place a pseudo atom at the center of mass and use this to mark the centre in visualisation and to measure distances and angles