Dear Hussein,
Great to hear from you! (Hope things are wonderful in Claremont - it’s been ages since I’ve visited.)
If you haven’t built Avogadro v2, that’s probably the first place to start. There are build instructions here:
http://wiki.openchemistry.org/Build
The next step would be to submit a small bug-fix patch, e.g., something from the avogadrolibs issues:
https://github.com/openchemistry/avogadrolibs/issues
A key component of the project would be to port the existing 3Dmol.js code to Avogadro2. I’m sure there are more components for “reach” goals, since the biological tracking/visualization code in Avogadro v2 is pretty much in its infancy. (And there’s nothing saying that you need to restrict yourself to the 3Dmol.js code, only that it exists, and I’ve heard comments that people like it better than PyMOL.)
https://github.com/3dmol/3Dmol.js/blob/master/3Dmol/glcartoon.js
Beyond that, I’d be happy to talk more as you start to put together a proposal draft.
Thanks and best regards,
-Geoff