Jmol filter

An example of the Jmol filter in action

Jmol is open-source Java software for interactive 3D viewing of molecular structures. It can easily be embedded into a webpage... including a Moodle page.

The Moodle Jmol filter is recently developed but comes as a single download and is easy to use and install.

• Download the Jmol filter'

The Jmol filter is very useful for including a molecule viewer in a variety of situations - e.g. in a Label, a Forum discussion, or a Quiz question. If you wish to load a molecule data file as a "resource", you should also consider installing the Jmol resource module.

It requires no additional capability on your web server, but is a Java applet, added to the page with JavaScript controls, so requires both Java and a JavaScript-enabled browser for the user.

• See it in action in this course (Log in as guest)

How to use

1. Upload a molecule data file to the Moodle server. (This is important - Jmol refuses to display data files held on other servers, so you can't just link to a file that exists somewhere else on the web.)
2. Simply create a link to the molecule file, wherever you want the molecule viewer to appear.

• Parameters can be added to the end of the URL to specify certain display options. Add "?c=0" to hide the controls, or "?s=150" to set the viewer's size at 150 pixels. Or "?c=0&s=150" to do both.

1. If you wish to run extra Jmol script upon intialisation, include this immediately after the link, and enclose it in JMOLSCRIPT{}. For example:

Water molecules JMOLSCRIPT{rotate x 15; zoom 50; set axes on;}