Chem 110L: Macromolecular Visualization Laboratory Exercise: Start Page


Virtual Reality with Molecules!

This assignment will introduce you to the basics of visualizing and analyzing biological macromolecules using computer programs. Being able to successfully use computers to study molecules involves at least two different sets of skills.

  1. First, you must be able to ask some meaningful scientific questions about the object you are studying, and understand the meaning of the answers. For example, if you want to know if an α-helix of a DNA-binding protein fits into the small or the large groove, you may ask what are the dimensions of the two grooves of a double-stranded DNA. Or, if your goal is to design a novel AIDS drug that targets HIV protease, you may ask what amino acids are lining the active site of this enzyme.
  2. Second, you must be skilled in using computer programs to answer such questions. There is a large number of molecular visualization programs available, and most of them are constantly evolving to be more powerful and user-friendly. The list of some freely available visualization programs is provided at the end of the tutorial. It is important for you to know the general capabilities of such programs, but you are not expected to memorize how a particular program operates. You will be asked to use computer visualization throughout the lab series, but it is largely your choice which program you use. The following tutorial focuses on the programs SYBYL and PyMOL because these are installed in the Laboratory for Computational Chemistry and Biochemistry. The tutorial assumes no prior knowledge of these programs.

Learning Objectives

The following tutorial illustrates the kind of questions one can answer with the help of computer modeling, and shows how to create images that help to illustrate important features of macromolecules. You will also learn that biological macromolecules come in very different shapes and sizes.

The tutorial also teaches a few technical skills that are commonly used while working with computer visualization programs. First, it shows some typical capabilities of the visualization programs SYBYL and PyMOL. It also teaches about image capture and manipulation programs on Linux workstations, and shows how you can send images created on an Unix computer to other people. After completing this session you should have learned the following:

Tutorial Assignments

As you work through this tutorial, you will answer various questions presented in the tutorial. Some questions can be answered immediately, for example, by measuring certain distances. Other questions may require more research and may appear difficult if this is your first time learning biochemistry. The tutorial is accessible from your home or campus computers, so you can answer the more difficult questions later after you have done your research. Most questions in this tutorial do not require more than a short (4-6 sentences) sentence paragraph with optional schemes. Answers to the tutorial questions and the homework assignments constitute the first lab report. You can recognize the questions in the tutorial easily because they are italicized.

Optional Further Reading

Tutorial includes links to a few external JMol or Chime-based tutorials. It is recommended that you visit these tutorials from your personal computer after the class and learn more about each of the topics discussed. You should install the Chime Plugin which works with Firefox, and Internet Explorer. A good place to start with the Chime is the Molecular Visualization Resources page at the University of Massachusetts Amherst.


Tutorial by Dr. Kalju Kahn, Department of Chemistry and Biochemistry, UC Santa Barbara. ©2003-2010