Jmol Moodle

1. Geoff Rowland geoff.rowland@yeovil.ac.uk
Yeovil College http://moodle.yeovil.ac.uk
University Centre Yeovil http://www.ucy.ac.uk

2. Teaching molecular structure
• 2D representations

3. Physical models

4. Stereoscopic display

5. Computer-based Molecular Display
1985 Molecular display typically required Evans & Sutherland computer
• $250,000
1990s RasMol: Roger Sayle
• Visualise and manipulate 3D structures on an ordinary desktop computer
(Linux/Windows/Mac)
• Free
• Powerful RasMol Scripting language
– Display
– Animations
MDL Chime Plug-in
• Ported RasMol code to Netscape browser plug-in
• Extended Chime Script & Controls
• Some small drawbacks:
– Installation required
– Proprietary
– Limited platforms (No Internet Explorer or Mac OSX support)

6. Java Applet
• Similar to RasMol/MDL Chime
• Most RasMol/Chime capabilities + New bug fixes & features
• Enhanced Jmol Scripting language
• Standalone application or applet (embed in Web pages)
• Open Source
• Platform neutral (Java)
• No installation required
• Well managed project. Active and responsive developer/user community
http://jmol.sf.net
But
• Java issues (Version? Installed? Performance? Applet download delays?)
• Java & JavaScript security in Moodle

7. Jmol examples
• Aspirin:
jmol.sourceforge.net/demo/bonds
• Nanotech:
jmol.sourceforge.net/demo/nanotech
• Protein backbone:
jmol.sourceforge.net/demo/ribbons

8. Jmol-Moodle integrations
Use Moodle’s modular structure
2005 Initial development by Dan Stowell (UCL)
• Jmol filter
– Analogous to media filter
– Simply link to a molecular data file (e.g. .mol, .xyz, .pdb) that exists on your
server
– Use anywhere – labels, quizzes, HTML blocks, databases, glossaries,
forum discussions…
– Some customisation and scripting is possible
• Jmol resource type
– Easier to use/customise, more flexible
– Use to add a single item to your course
• See moodle.org “Modules and Plugins Database” for download

9. 2006 Moodle Jmol-resources in action
• Further Education Post-16 context:
– AS/A2 Chemistry & Biology
• But also appropriate for:
– Physics, Geology etc
• FE vocational science
– GCSE science
– HE science
– Post-graduate courses
http://moodle.yeovil.ac.uk/course/view.php?id=795
[Login as a guest]

10. Jmol filter & resource: default controls
• Atoms off, 20%, 100%
– Switch stick, ball & stick, and space fill displays
– Helps emphasise these are models (atoms are not really
coloured spheres!)
• Spin
– Helps 3D visualisation
• Download file
– For local scrutiny, manipulation, display etc
• Jmol help
– Atom colour key and basic applet instructions

11. Jmol resource & filter: customisable controls
Jmol filter: c=0, c=1, c=2 etc
Jmol resource type: GUI
• Unit cell
– crystalline and metallic structures
• Show H atoms
– organic chemistry: relationship
between full structures and skeletal
formulae
• Jmol menu
– left-click Jmol logo
– right-click applet
• Jmol console
– ultimate configurability
– prototyping Jmol scripts

12. Jmol resource & filter: additional scripting
Jmol filter: JMOLSCRIPT{} extension
Jmol resource: additional script text box
or Jmol Console
• wireframe - adjust thickness of bonds
• spacefill - adjust radii (metallic, ionic, van der Waals’)
• set scale3d - display different molecules at same scale
• set frank off - hide Jmol logo (small applets)
• color - change colour of bonds atoms etc
• label - add labels
• icosahedra - molecular geometry, complex crystal structures,
aluminosilicates, zeolites etc
Full Jmol Interactive Scripting documentation
http://www.stolaf.edu/people/hansonr/jmol/docs/

13. Problems with initial implementation
• Usability & performance issues
– Slow page load with multiple applets
– Sluggish editing
– Cross-talk between multiple applets and controls
• Jmol resource type broken in Moodle 1.8
– new formslib
• Did not exploit many Jmol features and new capabilities
– Protein structure cartoons
– Molecular orbitals
– Shapes/polyhedra
– Extended crystallographic arrays
– Animations
– Jmol more Web-standards compliant and JavaScript-aware
• Easier for user to resize

14. 2007 Jmol resource type 4 Moodle 1.8
• Option (recommended) to initially display image (JPEG) rather than
applet
– Faster page load
– Show 2D formula then 3D display
• Formslib-based configuration interfaces
– Wider range of default options and controls
– Advanced options and controls
• Pedagogic groupings of controls
• (Potential) Internationalisation
– Interface text transferred to lang strings
• End user control (CSS, DOM, JavaScript. No Frames!)
– Toggle image and applet
– Resize applet
– Scroll text keeping applet fixed
http://moodledev.yeovil.ac.uk/moodle/course/view.php?id=3

15. To Do
• Port new features (esp. initial image display) to
Jmol Filter
• User (teacher & student) feedback and feature
requests
• Other ways to build Jmol resources
– How to bundle structure data, scripts and controls
– IMS/SCORM packages (RELOAD, eXe)
– Jmol export of web pages
• Sharing Jmol resources
– Moodle Network?
– Repositories?

16. Jmol-based IMS Content Package

17. Molecular Learning Resource Repositories?
From: http://docs.moodle.org/en/Community_hub

18. Potential Pitfalls…
Structure files are widely available but consider:
• ownership/copyright/citation issues
• origin/provenance (experimentally determined, X-
ray crystallography, spectroscopy, model building?)
• appropriateness for pedagogical purpose
But
• Chemical structure databases have given
provisional permission for the distribution of
structures based on their data.

19. Molecule Repositories ?
Elgg Files: Jmol Gallery Plugin
• Sophisticated access control
• Searchable metadata (Tags)
• Thumbnail & gallery views
http://moodle.yeovil.ac.uk/elgg/admin/files/47
Moodle Repositories
• DOOR
• Moodle Repository API?

20. Acknowledgements & Sources
Molecular Visualisation Software
• History of Molecular Visualisation http://www.umass.edu/microbio/rasmol/history.htm
• RasMol http://www.openrasmol.org/
• Chime http://www.mdl.com/products/framework/chime/
• Jmol http://jmol.sf.net
• Java JRE http://java.com/en/download/index.jsp the JRE or full JDK is essential to run Jmol
applets!
Molecule Databases
• CDS http://cds.dl.ac.uk/ inorganic, metallic, and small molecular structures
• PDB www.rcsb.org/pdb/ biological macromolecules
Other sources of molecules
http://www.umass.edu/microbio/rasmol/whereget.htm
http://www.wsu.edu/~wherland/wwwlist03.htm
Tools
• Open Babel http://openbabel.sourceforge.net for inter-converting molecular data formats
• RELOAD http://www.reload.ac.uk/ for building IMS Content Packages
Learning Object Repositories
• Elgg http://elgg.org
• DOOR http://door.sourceforge.net

21. Geoff Rowland geoff.rowland@yeovil.ac.uk
Yeovil College http://moodle.yeovil.ac.uk
University Centre Yeovil http://www.ucy.ac.uk