Oh, I almost forgot to mention. This page

http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/buttons.htm

also demonstrates animated molecular surfaces and cavities.

There are constraints on this, for sure. Some browsers will crash if too 
many isosurfaces are loaded. This small system with just 14 frames is 
probably about the limit one can expect. Anything much larger would have 
to be created using an AVI movie from JPEGs that Jmol would write.

Notice that the buttons are linked to each other, turning each other on 
and off so that only one button is active at any given time. This is 
important.

Bob


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