Henry,

There is Jmol-JSO, which is the method to insert Jmol objects of any variant 
into the web page (replacing the old Jmol.js method).

That may insert
a) a Java applet
b) an HTML5 object (JSmol)
c) a WebGL object

So WebGL is an alternative, it is not attached to either Jmol/Java or JSmol. 
As I understand, it uses hardware? to accelerate graphical computation, 
that's why the behaviour (rotation) is smoother than JSmol. I do not know 
about surface computation but I bet it is accelerated too --or maybe not, it is 
just rendering that gets improved.
I don't have the time now for a test, but I have an old page with side-by-side 
Jmol modalities of variants, maybe you can time the surface in those (it's a 
small molecule). I see now that although the page is old, it's now using a 
recent version of Jmol.
http://biomodel.uah.es/Jmol/export-image/index_new.htm

Ah, it seems that isosurfaces are not implemented.





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