Course Information Lecture Notes Homework Exams Gradebook Extra Problems Molecular Graphics Software Sites Useful Links 462a Home

Molecular Graphics

Molecular graphics will be used extensively in Bioc 462a.

• The molecular graphics/structures are being translated into a new program called Jmol, which runs on both PCs and Macs in most browsers; requirements are listed on the Molecular Graphics link at left.
• All the older molecular graphics on this website used Chime, a molecular graphics plugin which runs as part of the web page and works on either a PC or a Mac (but NOT with Mac OS X).
• The version of Chime used in these graphics requires Netscape Navigator 4.08, or Netscape Communicator 4.7x or 4.8x; Netscape 6 and later do NOT work with this version of Chime, nor does Internet Explorer. You can download Netscape 4.7, for example, and just open that version for these notes; you can have more than one version of Netscape on your computer, and indeed you can be running more than one browser simultaneously.) 
•  If you do not already have the older version of Netscape, or the Chime 2.0.3 or 2.3 plugin, you can follow the links below, choose the appropriate folder that describes your computer and download the programs.  Then install the program on your computer. Be sure that the Chime plugin is installed in the plugin folder of the correct version of Netscape (4.7 or 4.8).
• Obtaining and Installing the Latest Version of Chime
• Obtaining and Installing the Latest Version of Netscape (You need Netscape Communicator 4.7x, or 4.8x, hidden on Netscape homepage under Browser Central, Resources and Tools, Product Archive, on left.)

Exercises using Chime

• It is strongly urged that you go through these exercises to familiarize yourself with Chime and molecular graphics.
• For an explanation of how to navigate the Chime graphics page used in this course go here.
• A good place to learn the basics of using Chime can be found here. Go through the entire tutorial! This site was developed by Dr. Harry Ungar, Cabrillo College and is used with permission.
• Visit the Protein Data Bank to explore further the use use of Chime here.
• Go here to explore the full range of Chime commands.
• An excellent tutorial using Chime to explore protein structure has been developed by Dr. William McClure at Carnegie Mellon University, which is reproduced with permission here.
• In addition, Dr. McClure has developed a self-test on protein structure using Chime, which is reproduced with permission here.
• There is also a self-test over amino acids using Chime, which is reproduced with permission here.
• The textbook authors have several nice Chime tutorials here.
• You can access the original list of chime routines and animations used in class here.
• You can access a list of chime routines used at Carnegie Mellon University here.