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  1. MOLECULES IN MOTION …and in three dimensions A Chemist’s Theatre Paul Kiprof (pkiprof@d.umn.edu) University of Minnesota Duluth

  2. Software to Build Molecules • Builder and Molecular Mechanics • Mostly Commercial • Some Dual-Platform (Mac and PC)

  3. Commercial Software(with building capabilites) • Weblab Viewer Pro - MSI Software • www.msi.com (PC only) • Chem3D - CambridgeSoft • www.cambridgesoft.com (PC and Mac) • Free Programs from time to time • HyperChem - Hypercube • www.hyper.com (PC only) • Spartan Wave Function • www.wavefun.com (Mac and PC) • Crystaldesigner • www.crystaldesigner.no (Mac only)

  4. Software to Display Molecules • Many Packages are Free • Many are Dual-Platform • Limited Manipulation of Molecules • Rotation, Translation • Change Colors • Change Display Type • (Ball-Stick, Wire-Model, Space-Filling)

  5. Display Software • Weblab Viewer Lite - MSI Software • www.msi.com (PC and Mac) with examples • Rasmol (Academic) • http://www.umass.edu/microbio/rasmol/mostly Biochem (PC and Mac) • Chem3D Net (no save feature) • www.cambridgesoft.com (PC and Mac) • MacMolPlt (Academic) • www.msg.ameslab.gov/GAMESS/Graphics/Graphics.html

  6. Web-Based Delivery (as data files) • Plug-ins to Netscape and Internet Explorer • Chime (based on Rasmol) • www.mdli.com (PC and Mac) PC version more extensive • Chem3D Plugin CambridgeSoft • www.cambridgesoft.com (PC and Mac) • Various JAVA applets • VRML files (Cosmo Plug-in) • www.cosmosoftware.com (PC and Mac) large files

  7. Modes of Delivery - Web • Preprocessed as Movie Files • No other applications necessary for viewing on client side • Non-interactive (user has no control over viewpoint etc.) • large files • As Datafiles • Interactivity possible • smaller files (generally)

  8. Sources of Datafiles • Example Files in Program Distribution • Websites • www.webmolecules.com • Search Engines • Databases • Protein Data Bank - www.rcsb.org • Build-Them-Yourself