While there is still a lot to do ( update icons, make it possible for the full UI to be rendered in the 3D window, make a stand-alone version ), it's a start.

Here's the link, where you can try it out for yourself ( PC and Mac, using Shockwave )
http://www.candointeractive.com/prototypes/molecule
Some of the changes include...
- Full-screen - the viewer will now stretch full-screen. This is very cool when used with the browsers full-screen view ( or F11 ).
- Load Random PDB button - this allows you to easily browse different structures ( those 4 letter IDs can be hard to remember! )
- Updated to work with new RCSB database format.
- The viewer is just over 100k - I'll try to ensure that this small file size is kept.
I'll try to get this updated a few times over the coming months.
I think the first major issue to look at is the creating of 3D models for each atom - if you are loading a PDB structure with 10's of thousands of atoms, I need to figure out how I can create these models faster with Shockwave 3D ( I've already implemented a number of optimisations, such as instancing a new empty model and then assigning an existing resource, rather than cloning a model ).
Enjoy!
Mal