Yes, indeed, TwirlyMol now uses proper spherical shading for the atoms. In addition, if you are using any of the 5 or so browsers that are not Internet Explorer (shame on you, IE), you will see that distant atoms are now wreathed in a fog (really it's a representation of the uniform electron gas). Through the magic of the internets, any TwirlyMol using the Chemical Identifier Resolver will suddenly look a whole lot better.
We've also addressed some minor bugs: shadows in wrong place, loading issues with multiple molecules, slow loading, issues with Opera.
Markus has also been doing some work on caching. To take advantage of this new work (and shave several seconds off load times), use the following new HTML:
<div id="DIVNAME" height="200" width="200"></div>Here's an example of it in action, where the CHEMICAL_IDENTIFIER is restasis and the DIVNAME is foggymol: