Jonathan, definitely keep working on #9238. Jason can just put those things in the new notebook. Having something working completely is a very good idea, and we can continue to test it on the old notebook, which is still the current notebook, after all.
I do think we need to also add the piece of #9238 that changes the lighting. Currently I have good lighting in the command line and bad lighting in the notebook, even without the new jmol - someone the new jmol is called from the notebook, even though I didn't install it in this version!!! I even checked this in the advanced menu. Mystifying.
I'm just testing quick, and then I'll post patches. Since they aren't mine, I feel free to give positive review.
