ChimeSquare.comTM Chime SquareTM Animations Molecular Graphics Resource

Eric C. Niederhoffer, Ph.D. Ecnhoffer@chimesquare.com Copyright 2000- , E.C. Niederhoffer. All Rights Reserved. All trademarks and copyrights are the property of their respective owners.

Welcome to Chime Square^TM, the site for three dimensional molecular graphics! The assembled collection of molecular structures are intended to facilitate your understanding of the relationship between structure and function of macromolecules. To accomplish this, the viewer (you) should have (or be developing) a foundation in biochemistry (proteins and enzymes), organic chemistry, and inorganic chemistry.

I would encourage you to use Protein Explorer (and Protein Comparator) and some of the other applications that have been developed by Eric Martz at the University of Massachusetts. Swiss-PdbViewer (Deep View) and RasMol are also very good resources for protein structure analyses. You may want to visit Gale Rhode's site for a thoughtful discussion. This is a very effective method to learn about macromolecule structure and function.

Protein structures may be obtained from the Protein Data Bank (PDB), which is hosted by the Research Collaboratory for Structural Bioinformatics.

Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The protein data bank. Nucleic Acids Research 28:235-242.

Requirements and Notes:

• Install MDL's Chemscape Chime.
• Use a compatible browser for your platform. Netscape Communicator is recommended. Mozilla and NC 7.0 appear to work well and maintains the pop-up remote control (see below) as the front window for most operations.
• Here is a review of how to use the mouse with Chime. Print this for a handy reference. Learning to use the mouse is the key to exploring Chime 3D structures!
• The files have been gzipped to reduce network traffic times. Large structures are denoted with an asterisk in the tables.
• Structures will load automatically when you open the page and there will be a series of buttons available to view selected features. PDB ID codes are listed with each structure.
• Page layouts and structures have been optimized for a monitor screen resolution of 800 x 600.
• Structures (and features) have been modified for use with a separate resizable remote control window (indicated by rc in the tables). Each pop-up remote control window automatically closes when you leave (close) its presentation page!
• If you do not have Chime installed or are using an incompatible browser, a static image (.gif) of the structure should appear.

The following animations have as an additional requirement the installation of the Macromedia Shockwave plugin.

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