More Moodle Molecules 2007

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Jmol Moodle

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More Moodle Molecules 2007

  1. 1. Geoff Rowland geoff.rowland@yeovil.ac.uk Yeovil College http://moodle.yeovil.ac.uk University Centre Yeovil http://www.ucy.ac.uk
  2. 2. Teaching molecular structure • 2D representations
  3. 3. Physical models
  4. 4. Stereoscopic display
  5. 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. 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. 7. Jmol examples • Aspirin: jmol.sourceforge.net/demo/bonds • Nanotech: jmol.sourceforge.net/demo/nanotech • Protein backbone: jmol.sourceforge.net/demo/ribbons
  8. 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. 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. 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. 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. 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. 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. 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. 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. 16. Jmol-based IMS Content Package
  17. 17. Molecular Learning Resource Repositories? From: http://docs.moodle.org/en/Community_hub
  18. 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. 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. 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. 21. Geoff Rowland geoff.rowland@yeovil.ac.uk Yeovil College http://moodle.yeovil.ac.uk University Centre Yeovil http://www.ucy.ac.uk

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