Nexus is an experimental collaborative 3D Semantic Web visualization tool being built with (WebGL/OpenSimulator) to test various ideas and design concepts in visualizations, software design, and algorithms.  Collaboration is one of the key design ideas and which is why this is not being done as a stand-alone application.

Some key paradigms and principals are being following in Nexus's design:
1) Must be collaborative - all visualizations must be sharable in real-time accross multiple clients regardless of location.
2) All-RDF - rather than use any custom formats or internal data representations, RDF is used throughout Nexus's architecture.  Nexus consumes, internalizes, and exports everythying as RDF - Client/server communications are in RDF, user and client sessions are in RDF, cursor postion and directional vectors are in RDF, even the visualizations themselves are in RDF which allows them to be tightly coupled with the original data itself.
3) Explore 3D - many graph layout programs use 2D layout but 3D is being explored in Nexus including 4D (time-based)
4) If a best-practice dogma is encountered, thumb your nose at it and try to come up with something better.  If you can't, try again later. ;-)

Molecular visualization is achievable in Nexus because it's visuals are tied to the back-end data using RDF data modelling.  The added benefit in doing it this way is that other semantic data sources can be semantically linked and reference while searching for/or working with a particular structure(s).  In addition, since Nexus is driven by a SPARQL query engine (Jena ARQ), molecular selection criteria become more flexible by allowing a SPARQL query to be used to pick which parts of a structure are acted upon for display or modification.  Nexus is not limited to just molecular visualization but will be able to visualize various semantic datatypes (FOAF, DOAC, etc) from multiple data sources.