Molecule is a utility MaxScript for 3DS Max 8/9 to create and render molecular models.
(It may work for previous versions but I have not checked it on those.)
It allows you to import either Protein Data Bank Molecule data files. Or MOL data files.
The Molecule package also includes a material editor application with which you can assign specific colors to each atom substance in your molecules so the relationship of the different compounds are evident in the resulting model.