Molecular Graphics

Molecular graphics will be used extensively in Bioc 460.

• 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.
  
• What is Jmol?   
  • Jmol is a free, open source molecule viewer for students, educators, and researchers in  chemistry and biochemistry. Jmol is a successor to such legacy products as XMol, Rasmol, and  the Chime plugin.   
  • Because Jmol’s core rendering engine was written in Java, it is cross-platform, running on  Windows, Mac OS X, and Linux/Unix systems. However, v1.4.2 (or higher) of Sun Java must be  installed. See below for installation instructions.   
  • The class will use the JmolApplet implementation; the applet is  generally stored on a remote web server (e.g., Protein Data Bank) and downloaded whenever a  user visits a web page that integrates Jmol. At this point in time, the applet is unsigned or  “untrusted”, meaning that it runs in a protected environment and cannot affect your machine.   
  • The Jmol application is an optional download from the Jmol development web site. It is a Javabased “wrapper” around the Jmol rendering engine that can be run locally from the desktop.  
       
• How do I install what I need to use Jmol? 
  (If you think you already have the latest version of Java software, you can try Step 2 first.)   
  • Step 1: 
    • Make sure that the latest version of Sun Java is installed on your operating system.   
    • The easiest way to check is to visit http://www.java.com, click on the link to “download the latest  Java software”, and follow the instructions. If you already have the latest version, the installation  will terminate. If not, make sure that you install Java, including extensions for the browser(s) you  plan on using to view molecules.   
  • Step 2:    
    • Visit http://www.jmol.org to test your Java installation and the Jmol applet. 
    • If the main graphic on the front page is displayed, installation was successful. That’s it!  Remember, Jmol doesn’t actually exist on your machine as an application, so there is nothing  else to install or configure.
• How do I use Jmol?   
  • When you visit a website that contains the JmolApplet, the molecule will load within a square  viewing area. 
  • Clicking and dragging the mouse will rotate the molecule, while Shift + Drag will  zoom in and out.   
  • Jmol has several simple commands coded into right-click context menus -- you can play with the menus and see what happens; you can always "reset" at the top of the routine to return to the original view of the molecule. 
  • 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 Biochemistry 460 and 462a here. Not all the conversions from the original Chime routines have been completed, so some of the structures may not yet be live links.