Getting a message from Cathal Garvey reminded me I haven't played with OpenSCAD for a while. OpenSCAD is a simple but powerful scripting language for making 3D models. I've been wondering for a while about converting PDB files into spacefill models of molecules in a format I could print them from, so I wrote a little Perl script to convert PDB to SCAD. Nothing clever.
This might look like a bear investigating a big flower, but it's actually aspirin rendered in OpenSCAD from this PDB file.