Copyright 1995, Richard B. Hallick. All rights reserved
This is an experimental project begun at the University of Arizona to use computer graphics still images, movies, and interactive molecular graphics to enhance the teaching of molecular structure to undergraduate students of biology, biochemistry, and molecular biology.
The beginning biology student, normally armed with only a high school chemistry course as preparation, is confronted with detailed concepts about the structure of biological molecules, often in the first few weeks of the freshman year. Most begin their study of biology with little or no knowledge of organic chemistry, and at best a concurrent course in introductory chemistry. Beginning chapters in the typical introductory biology textbook deal with amino acids, sugars, fats, nucleotides, stereochemistry, assymetric carbon atoms, isomers, functional groups, and polarity of molecules.This is immediately followed by an introduction to proteins and nucleic acids.
In our experience, students learn about structure from models, either physical models or through computer graphics modeling. Through models, students begin to appreciate that understanding chemistry is fundamental to a study of biology, and learn to think about the question of "How does it really work?"
Our vision is to make static, single view textbook images come alive on the computer screen, to allow students to view graphic images, rotate them in 3D on the computer screen, and switch between different molecular representations, such as wire-frame, ball-and-stick, space-filling, and protein secondary structure (ribbon) diagram.
A number of computer resources were used to create the molecular models described in this project. Most are readily available for non-commercial use.
MacMolecule is a 3D-molecular graphics rendering program for Macintosh computers. Image files containing X,Y,Z atomic coordinates and covalent bond data can be rendered in ball-stick, wire frame, and space-filling models. The program is distributed as freeware for non-commercial, educational use, but all rights are reserved. (Copywrite 1991-94 Arizona Board of Regents). Hardware requirements are a Macintosh with a 680X0 CPU and a math co-processor.
If you are online, you can click Here to download macmolecule1.7.sea.hqx
If you are online, you can click Here to download macmolecule-images1.5.sea.hqx
Translate is a freeware utility for conversion of Brookhaven PDB files to MacMolecule format. It supports both complete, and residue by residue file conversion, and stripping of water molecules.
If you are online, you can click Here to download Translate.sea.hqx
MacBable, and the related Bable, will interconvert various file formats used in molecular modeling, determine connectivity, and add Hydrogen atoms. It is available for various platforms including MS-DOS, Mac OS, and UNIX.
Linus will be the successor to MacMolelcule. Both the rendering engine and interface have been completely re-written. Image quality, speed, and functionality have all been improved, and the requirement for a math co-processor has been eliminated. Working prototypes running on the PowerPC Macintosh are being tested during the Winter 1994-95. Many of the images shown in this project were created with Linus.
The X, Y, and Z coordinates of atoms in a molecule are normally determined by means of x-ray crystallographic analysis. The Brookhaven Protein Data Bank, Chemistry Department, Brookhaven National Laboratory, Upton, New York, USA is the source of X, Y, Z coordinates for proteins and nucleic acids.
If you are online, Click Brookhaven PDB Gopher Siteto access this site.
Dr. Hallick is Professor of Biochemistry at the University of Arizona. He has authored the HTML documents, molecular graphics image files, and tutorials. Photo of Rickhallick@arizona.edu
Dr. Myers is Professor of Computer Science at the University of Arizona. He has written the molecular graphics rendering algorithms that underlie this project. Photo of Genegene@cs.arizona.edu