Hello
Web pages with embedded JmolApplet can indeed be run from local disk 
or a CDROM, only some limitations apply on the placement of files.
This is already described (clearly enough, I hope) in the page 
mentioned by Nicolas
http://wiki.jmol.org/JmolAppletDeploymentLocal

The fundamental difference between using the standalone app and the 
applet is that
- with the app, the user decides what molecular file to open and how 
to handle it. No limitations on file access apply.
- with the applet, the person designing the webpage decides what 
molecular file to open and how it will be displayed, the user just 
plays (sorry, manipulates) the molecule. There are limitations on 
file access mentioned above.



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