The ability to run Jmol using local data is useful for testing (and in my case from giving demos/talks from the laptop). Finding out how to allow this is getting more fun with each release of both Java and the OS; I here offer my recipe for OS X Mavericks:
1. Open a local file using Safari (a file which say invokes the Jmol applet) 2. In Safari/Preferences/Security/Internet plug-ins, check allow, and then manage Website settings 3. Select Java as the plug-in, and "currently open website" should declare “Local documents”. You should select "Allow always". If you do not have a local document open at the time, this option will not appear. This should do the trick and allow Jmol to open up in local mode. I would mention that these various policies depend very much on the browser being used. Thus Firefox is different (and Chrome, being 32-bit, does not run 64-bit Java applets).
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