The molecule shown is a snapshot taken of the protein in the folding process your device is working on. A new snapshot is taken at least every minute or so (varies somewhat). The balls represent the amino acids, and do not show every atom. The color coding is described at: http://www.systemsbiology.org/Default.aspx?pagename=humanproteome#Aminoacid

We considered showing a 3-D stereoscopic version of the molecule which would be viewed by looking at it cross-eyed. However, we decided against this because it would double the cpu time spent on drawing the molecule and many people would have had difficulty learning the viewing technique. Drawing every atom would dramatically increase the cpu time.