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Hi! It is precisely for such reasons that we (thanks to a lot of good work by Jonathan Gutow and Volker Braun) have jsmol as the default 3d viewer for Sage 6.4. Try it out!

That said, it probably depends on your Java if you do plan to use Java applets for better rotation of dense plots and such; this is the first I've seen of a security issue of this kind (as opposed to problems with IcedTea or certain browsers) where it isn't allowed at all, but Java is in principle allowed.

Finally, the jmol jar files are in the Sage tree, shouldn't be in /usr/lib ... ? Maybe that is a different jmol instance?