In order to use either RasMol or Chime you need the atomic coordinates of the molecule you wish to view. Experimentally, coordinates are obtained by an array of techniques including X-ray crystallography and NMR spectrometry. They can also be obtained using computational chemistry programs. For large biological molecules the coordinates of molecules whose structure has been determined can be obtained for free over the web from the Protein Data Bank. There is a similar web-based database for small molecule structures called the Cambridge Crystallographic Data Centre, but you must subscribe (give them money) to obtain coordinates from this source. Below you will learn how to obtain coordinate files from the Protein Data Bank and how to generate them using the computational chemistry program Spartan.

There are several different file formats that can be used by RasMol and Chime. All are plain text files that in someway list each atom along with their corresponding x, y and z coordinates. We will focus on the "pdb" format.

pdb Files

The "pdb" format was originally developed for storing protein structures in the Protein Data Bank but is now used to provide the atomic coordinates for just about any molecule.

bullet View a pdb file for the structure of the protein hen eggwhite lysozyme.

bullet View a pdb file for the structure of aspartame (Nutrasweet).

Protein Data Bank

The Protein Data Bank is resource that provides a vast wealth of information on the three-dimensional structures of biological macromolecules. The first three-dimensional structure of a protein was reported in 1958. In 1990 the Protein Data Bank contained approximately 300 structures. Today (2/8/02) it is the home for over 17,000 structures and its inventory is updated weekly. The Data Bank contains not only the coordinates for proteins, but also nucleic acids and virus particles. Access to Data Bank is free over the Web. The web site provides extensive searching tools and direct links to several visualization tools including RasMol and Chime.

bullet The Protein Data Bank's Website

Spartan

Spartan is a computational chemistry program that allows the user to build three dimensional models of molecules, determine their optimal geometry, do molecular orbital calculations, and to predict various molecular properties. The application is developed and marketed by Wavefunction, Inc, and is probably the most accessible computational chemistry program for the casual user. The people at Wavefunction have put a lot of effort into making the program easy to use, and have developed a host of resources for using the application in an educational setting. In addition to being a very powerful educational tool, it is at the same time a serious tool for researchers.

Spartan is available for both the Macintosh (MacSpartan), Windows (PC Spartan), and Unix platforms. There are a couple of version, which vary in the features and price. They offer discounts for educational institutions. The Macintosh and Unix versions are capable of exporting high resolution images that can be incorporated into web sites.
Images of aspartame (Nutrasweet) produced by MacSpartan:
a. Ball-and-Stick model
b. Ball-and-Stick model overlaid with a transparent Electron Density Surface
c. The Electrostatic Potential mapped onto the Electron Density Surface
d. Tube model with surfaces showing the Highest Energy Molecular Orbital that is Occupied (HOMO

bullet Visit Wavefunction, Inc. Web Site

bullet Obtain demo versions of Spartan to tour some of Spartan's capabilities

[UWEC Web] [Chemistry Dept.]

Warren Gallagher
Department of Chemistry
(715) 836-5388
wgallagh@uwec.edu

updated: Saturday, January 22, 2005