PovChem is a powerful tool to generate a POV format file from a PDB entry.
It supports CPK, Ball-n-Stick and Cylinder model. You could adjust a lot
of parameters to get a good molecuar graphic.

The document could be found at 
    http://cherubino.med.jhmi.edu/~paul/Manual.html

WWW: http://grserv.med.jhmi.edu/~paul/PovChem.html