more moodle molecules 2007
DESCRIPTION
Jmol MoodleTRANSCRIPT
Geoff Rowland [email protected]
Yeovil College http://moodle.yeovil.ac.ukUniversity Centre Yeovil http://www.ucy.ac.uk
Computer-based Molecular Display1985 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)
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
Jmol examples
• Aspirin: jmol.sourceforge.net/demo/bonds
• Nanotech:jmol.sourceforge.net/demo/nanotech
• Protein backbone:jmol.sourceforge.net/demo/ribbons
Jmol-Moodle integrationsUse 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
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]
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
Jmol resource & filter: customisable controlsJmol 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
Jmol resource & filter: additional scriptingJmol filter: JMOLSCRIPT{} extensionJmol resource: additional script text boxor 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 documentationhttp://www.stolaf.edu/people/hansonr/jmol/docs/
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
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
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?
Molecular Learning Resource Repositories?
From: http://docs.moodle.org/en/Community_hub
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.
Molecule Repositories ?Elgg Files: Jmol Gallery Plugin• Sophisticated access control• Searchable metadata (Tags)• Thumbnail & gallery viewshttp://moodle.yeovil.ac.uk/
elgg/admin/files/47
Moodle Repositories• DOOR• Moodle Repository API?
Acknowledgements & SourcesMolecular 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
Geoff Rowland [email protected]
Yeovil College http://moodle.yeovil.ac.ukUniversity Centre Yeovil http://www.ucy.ac.uk
