BioBlender

BioBlender allows the user to generate computer models of complex molecular structures within the Blender animation program. BioBlender allows users to visually represent the features of molecules such as proteins and enzymes and to simulate the movement of the molecules within a virtual environment.

I think this software package would also be useful for students studying nanotechnology since this software would also allow the virtual construction of nanomolecular structures in a three-dimensional setting.