Thanks Nick, for the excellent instructions! I had been beating my head against the wall for awhile trying to get .pdbs into Blender (I'm haven't had much luck with some of the .pdb importers, such as ePMV (they feel sluggish and buggy on my mid-2013 MacBook Pro).
However, I did want to mention of couple of things that I thought might be helpful to anyone who runs across this post (by now, you probably already know this, I certainly didn't when I started!):
1) When exporting the Wavefront object, I have found that I need the ribbons (New Cartoon) to have a resolution of at least 25 and licorice should be higher still. Otherwise, when you import into Blender, it won't look smooth. However, don't crank it up crazy high (like 50+), or your object/mtl files will be insanely huge (2-30 Gb--unmanageable!). Still trying to find just the right balance. :)
2) Once imported, make sure you remove duplicate vertices (select object, click "Tab" to go into edit mode, and under "Tools" (on the left) click "Remove Doubles". After that, click "Tab" again to go back to Object mode and click "Smooth" under shading. It is important to remove duplicate vertices--if you don't, you get weird and ugly results if you try to use the modifier "Subdivision Surface" (which can make renders look better).
Hope this is helpful!