We posted a while back about a script for bringing in chemical structures that are in the standard pdb (protein data bank) format into Blender. After several months Malte Reimold (intermalte) has updated the script.
From the site:
Pdb2blend is a python script for the open source 3d modeling software blender. Pdb2blend converts 3d structural molecular data in pdb file format to typical models such as Overlapping Spheres, Sticks or Sticks and Balls in the blender environment.
The new version, now at version 1.2 fixes some problems with pdb file conventions. It's inside a .blend file, so to access the importer use alt+p the script to run it. You could also take the script out of the .blend file and use it as a regular script (which is what I do). You can find the new version (zip) on intermalte's site and you can find the BA thread for discussion here. And if you are looking for some .pdb's to start simulating angstrom sized worlds, you can find some here and here.
And on a side note, when at the molecular visualization birds of a feather at Siggraph I was asked numerous times if Blender could import real molecular data. Luckily, Malte's script was well known to me, so I could point them right to it!