1) Thank you for posting the videos.
2) I hope to have some time to get onto the Chat tomorrow, (probably afternoon).
3) Those of you working on the notebook please check out the status of enhancements to Jmol that are ready to go into the flask notebook. See trac #12299 (
http://trac.sagemath.org/sage_trac/ticket/12299) and an example server running at
http://gutow.no-ip.org:8080/ . Just create an account and try it. I still think there may be some problems with the switching to a signed applet to download the 3-D data, but I haven't been able to reproduce it. Anybody who does find problems please report them.
4) As to switching to pure js for the 3-D rendering, I think that may work for images of limited size, but somebody needs to write the code to handle what you want to do. The Jmol project is working on pure js alternatives for web pages. It is working OK for object based images (collections of spheres) without too many objects, but there is no effective implementation of surfaces yet. I would guess something workable is 1-3 years out.
Jonathan