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Molecular Graphics

Molecular graphics will be used extensively in Bioc 462a.

• Most of the molecular graphics will use Jmol, a molecular graphics program which runs as part of the web page and works on either a PC or a Mac on most browsers (but NOT with Internet Explorer in Mac OS X -- see below). Jmol requires no installation.
• To use the Jmol applets, your browser must have Java and Javascript enabled.
• Make sure that you have the latest versions of Java installed. If in doubt, visit http://www.java.com.
  Note that on Mac OS X, Internet Explorer is not supported because it does not provide LiveConnect communications between JavaScript and Java applets. Also note that the Mozilla family of browsers (including FireFox and Camino) must be configured to use at least Java 1.4.2 using http://javaplugin.sourceforge.net.
• Atom selection is an inherent function of Jmol. At its most basic, clicking on an atom will bring up its identifying information in the “status” bar of your browser, so make sure that the status bar is visible (under "view" options). Bond distances are displayed by double-clicking on first one atom and then floating your mouse over another atom; distances can be displayed permanently by double clicking on the second atom. Similarly, bond angles are observed by selecting 3 atoms.

• You can access a list of Jmol structures and animations used in class here. All the conversions from the original Chime routines have been completed, so the structures should all be live links, but some of the animations at the bottom are still in Chime, requiring a plug-in. 
  
• Instructions for browser requirements and downloading software for the old list of Chime routines are shown here, and you can still access the old list of Chime routines and animations.