VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
VMD provides user-editable "materials" which can be applied to molecular geometry. These material properties control the details of how VMD shades the molecular geometry, and how transparent or opaque the displayed molecular geometry is. With this feature, one can easily create nice looking transparent surfaces which allow inner structural details to be seen within a large molecular structure. The material controls can be particularly helpful when rendering molecular scenes using external ray tracers, each of which typically differ slightly.