Here's Jmol, an open-source Java viewer for chemical structures in 3D, on the NetBeans Platform, benefiting from its module system, extensibility, loose coupling, windowing management, and ecosystem (e.g., now you can install space invaders from plugins.netbeans.org into Jmol). And I imagine that other NetBeans Platform applications, such as Instant JChem, might find it interesting to have Jmol plugged into their application too, which is now completely possible.
The left hand side, i.e., the list of proteins, is obtained live from the Protein Data Bank, which is what we did during the recent NetBeans Platform course in Amsterdam. Then I continued working on it via the old POV-Ray tutorial, which I am updating to NetBeans Platform 7.1. (It is still currently on Sang Shin's Javapassion.com page, but will eventually be removed from there once it has been updated on netbeans.org). Then I ended up abandoning that approach since Jmol has embedded POV-Ray, so that the whole process of downloading POV-Ray and running it externally isn't necessary at all. So then it was a question of embedding the JMolPanel in a TopComponent and passing the name of the Node to the Jmol script.
Still a lot of cleaning up to do. Once the architecture is reasonably stable, I'll set up a hacking session in an Amsterdam pub, where all the participants can each work (or in pairs) on various features which can all be contributed via independent modules. For example, Jmol has heaps of export formats and renderers, so each of those could be developed independently once a general architecture has been set up.