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Blender! I wrote a python plugin (I think it's sitting in a broken state right now), that can bring in pdb files in various forms. Blender can also take in vrml 1.0 directly. But you can do fun stuff like these: http://www.geeta.ca/gallery2/v/mdraw/maneeshcoveridea.png.html http://www.geeta.ca/gallery2/v/mdraw/1g11small.png.html and animating is easy once you get the hang of it; plenty of good on-line tutorials out there from the blender community.
