Hello Bruce

I will gladly take a look at your page when I have time, but here are a few 
comments in advance:

1. Using JSmol-html5 with IE is very slow, indeed. Other browsers are 
recommendable.

2. Given the current state of Java support, you'd better forget chances of 
using Jmol-Java. I agree that it is an advantage for large models or, as in 
your case, isosurface computations. But we are loosing that battle. Firefox 
just dropped support for plugins, as Chrome did before. I am switching to 
PaleMoon as my main browser (they will support plugins indefinitely), but 
Oracle will eventually abandon the offering of the Java plugin.

3. What you might try to do is to save the isosufaces to a file. Loading them 
later is very fast. I have not a clear idea to what extent your calculation is 
unique or can be done in advance and the result used repeatedly.

4. If you have the control and expertise, you culd run the calculation in the 
server (using Jmol.jar or the JmolData.jar that does not use graphics), save 
the file and then serve it to the client browser. That would be faster, running 
in Java and not in JSmol-html5.

5. Although you are fine with JSmol.min.js + Jmol2.js, if it safer to move to 
direct implementation without Jmol2.js. Probably this has no effect on 
performance, though, but it safer for the future.


I would not think you are doing anything wrong, you are just hitting the 
inherent speed limitations of JSmol.

More later, I hope.



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