VMD is a molecular visualization program. VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring molecule. VMD can be used to animate and analyze the trajectory
of molecular dynamics (MD) simulations, and can interactively manipulate molecules being simulated on remote computers (Interactive MD).
I found on my disk the PDB file of a caffeine molecule:
You can export the scene to external rendering formats including POV-Ray, Raster3D, RenderMan, Gelato, Tachyon, Wavefront, as well as STL or VRML2 files for 3-D printing.
Image rendered by the Tachyon ray-tracer.
WMD is available for Windows, Linux and MacOS. Source code is alos provided.