This document discusses using molecular visualization software like RasMol, Chime, and Jmol to display and interact with 3D molecular structures in online courses. It provides a history of these tools and how they have evolved from requiring expensive computers to run to being accessible through web browsers using Java applets. The document also describes integrating Jmol into Moodle courses through filters and custom resources, and outlines ideas for sharing structured molecular data and learning objects between courses.

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