I'm pretty close to having a fully functional 3D model kit in Jmol. It's associated with the minimization package in terms of Jar files. I don't doubt that there are still things to do -- I just quickly made up a couple of icons, and there are definitely a few bugs. One nice thing is that CTRL-Z/CTRL-Y perform undo/redo actions. I've been working with the Jmol application, not the applet for this. Two new buttons at the top on the toolbar -- [modelkit] in the center group, because really what it is is a redefinition of what picking does, and [*] on the right -- just to make it simple to see all models.
Using the model kit right now with more than one model present is problematic. Still working on that. Right now you can delete and "sprout" new atoms and change bonds in any displayed model, but that needs to be changed to allow that only for the last model in the set. That's because as atoms are added, they are always added to the last model. But this is allowing you to seemingly put bonds in between models. Still, it's a start, I think.
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900