I have updated Dan Stowell’s Jmol Resource type so that it now works with Moodle 1.8.
It uses the new Moodle forms library (lib/formslib.php) for the resource type configuration interface, and I have also transferred ‘hard-coded’ text to lang files to facilitate internationalization.
Jmol 11.0.2, the latest stable release, is bundled with the updated resource type. Recent Jmol versions have a number of new useful features including translucent display, polygons, orbital cartoons, and enhanced crystallographic capabilities.
I have added a few more options, which I hope have pedagogic value:
- You can now add a control which will toggle hydrogen atoms on and off. This should be useful for demonstrating the relationship between full structural formulae (with hydrogens on) and skeletal structural formulae (with hydrogens off) for organic molecules.
- You can also add a control which will show/hide a unit cell. This does require a data structure file (e.g. PDB) with crystallographic data (e.g. CRYST1 record) but is useful for displaying, for example, ionic or metallic lattices.
- For protein and nucleic acid molecules (e.g. in PDB files), there are additional ‘Advanced’ menus to render the structure in various schematic representations (cartoon, rockets ribbon etc), and to colour the structure in various ways (by atom, residue, chain direction etc).
- Perspective depth is now turned off by default, as although it can help in 3-D visualization, the processing required is rather resource intensive and can impact performance on lower specification clients.
- As before, you can also enter additional Jmolscript code to control the initial display of the applet.
- The full-range of built-in menus can still be accessed by right-clicking the applet, or selecting the Jmol logo.
The aim is to allow simple access to basic Jmol functions for novice or time-constrained users, but also allow access to more advanced Jmol features for more experienced users. The new forms library in Moodle 1.8 makes it fairly straightforward to add new features, so I’m open to further suggestions, as long as they don’t overcomplicate things.
You can download the new Jmol Resource type from here, where you can also see examples of the Jmol Resource type (old version) and Jmol Filter ‘in action’. Just [Login as a guest], initial display may be a little slow. If feedback is positive, I’ll add it to the Moodle Modules and Plugins database.
Installation is much the same as before, and the detailed instructions are bundled as readme.txt in the .zip file. Of course, do test and complete a backup before deploying on a ‘production’ server – though it seems to be working fine for us.
Note that if you are using Moodle 1.6 or (I think – not actually tested) Moodle 1.7, you will have to stick with the original version in the Modules and Plugins database, and not this update.
Enjoy!
Geoff
