> for figures. Also, in general, I was not sure whether JSmol would 
> spin large proteins smoothly.

Important to distinguish between Jmol-JSO-Java and Jmol-JSO-HTML5 
(JSmol proper).
My impressions so far are:
- if you go for Java, responsiveness will be the same (as the applet 
is the same)
- if you have a page or template, I see no point in moving away from 
Jmol.js  (I know Bob advocates the change, but I can only agree for 
new development of pages)
- if you go for HTML5 JSmol, responsiveness is acceptable only in 
computers, but still slower. Loading of the page and libraries is 
much slower than for the Java + Jmol.js version. Proteins in tablets 
behave somewhat sluggish (not that I have much direct experience). Of 
course if Java is not available, JSmol is the only way.


> Any links to pages with tips about how to switch over would be very 
> appreciated.

http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Converting_pages_from_Jmol_to_JSmol

not much, but...

Please read also "Installation" and "Initialization" in that same 
page for file details




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