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Hmmm... embedding in quizzes makes things harder.

The easiest way to do is to use HTML in your Quiz questions manually. I'll give you the steps with all file references to your moodle root directory.

Download the jmol library from http://jmol.sf.net/ and put it in your Moodle directory somewhere (I put it in lib/jmol/).

Next, open javascript.php and find the lines that look like this:

<script src="<?php
echo $CFG->httpswwwroot ?>/lib/cookies.js" type="text/javascript" language="JavaScript"></script>

After them, add another line referencing your jmol like so:

<script src="<?php
echo $CFG->httpswwwroot ?>/lib/jmol/Jmol.js" type="text/javascript" language="JavaScript"></script>

Make sure you get the capitolization of your files right!

Now you can upload a mol file (or similar) to your course resource files. Make a note of the URL cause we'll need that in a sec.

Make your quiz and when you've finished editing a question make sure you're in HTML mode (ie click the [<>] button on the wysiwyg editor, if you use it) and, where you want the simulation to appear, enter code along the following lines:

<script type="text/javascript">
jmolApplet(300, "load http://URL/to/file.mol");
script>

Replacing 300 with the (square) size you want it to be (in pixels) and http://URL/to/file.mol to the URL you noted earlier pointing to your file.

I'm not sure if the Moodle filters will let you put a script in there, so if it doesn't let me know and we'll figure out and alternative (which may involve some serious hacking).

I've just uploaded a Moodle "Filter" to integrate Jmol. It's not the same as having Jmol files as a "Resource" but it may help you.

http://moodle.org/mod/forum/discuss.php?d=36973

Thanks for that Kathy, Yep I've done that and it works great
Unfortunately for my teaching (University) where students use campus and off campus computers i need a method where they don't have to download plugins, thus I can't go the chime route. I'm going to go the Jmol route that stands independent!

Thank you!