I wrote some scripts that let you create 3D models of molecules in SL (using balls, sticks, or both), starting with a list of the atoms, their coordinates, and the bonds. You could get that data from a PDB file (Protein Data Bank file), for example. The scripts are all open-source, licensed under a GNU GPL 2.0 license. If you’d like a copy of the scripts, along with instructions and some sample data, then just send me an IM inworld (at Troy McLuhan) and I’ll send them to you (all nicely packaged inside one notecard).
A C60 Buckyball (above) and a caffeine molecule (below)
Rez Tone (his SL name) from IBM made some modifications to my scripts so that they can handle huge molecules with thousands of atoms. Below is an example of a molecule he made with those scripts (rhodopsin - a protein found in the retina used for night vision).
