AP Classroom Management

SOFTWARE REVIEW: A MOLECULAR MODELING PROGRAM

If you are struggling with teaching advanced molecular concepts, this might be the freeware program for you. It was developed in 1995 by Roger Sayle.

The program gives a student the opportunity to view a molecule, and take it apart piece by piece. It allows the visualization and separation of; hydrophobic groups, individual amino acids, alpha helices, beta sheets, dimer interactions, and unique binding phenomena. The three-dimensional capabilities of RASMOL and the vivid color capability of the program allow any student to explore the world of micro- and macromolecules. The program uses a command line window where the desired operations are entered. The commands are simple one word requests and can be highly specific, down to the amino acid or even specific atom number. Magnification, separation and color labeling are a few examples of the capabilities of the program. A separate window holds the structure of choice where rotation around all axes is possible. The colors are clear and a variety of choices are offered for the viewing of the molecule- strands, ribbons, wireframe, backbone and the conventional ball and stick.

RASMOL is downloaded form the RASMOL homepage on the web. The URL is http://www.umass.edu/microbio/rasmol/

The homepage offers additional information on the program as well as the necessary instructions for downloading. A copy of the instruction manual for the program is available at this site, and will give you the commands necessary to manipulate the molecule in whatever way you or the student chooses.

The molecules used for viewing and analysis come from a variety of sites on the internet and can be quickly and conveniently downloaded to your copy of RASMOL. These sites have been created with the intention to serve as a library of common micro- and macromolecules for students and educators.

The macromolecule site that I have used most extensively is the Protein Data Bank of Brookhaven National Laboratory. To download molecular data to use in RASMOL follow these instructions:

1. Visit the web site of the data bank
2. CHOOSE the Searching and Browsing option
3. Then chose the 3DB Browser,
4. At the full text query prompt, simply enter the type of molecule you wish to view. (EG: DNA polymerase or HIV protease) The data bank will come up with a list of specific entries that correlate with the query that you provided. Simply select the specific molecule you wish to view by clicking and therefore highlighting the entry.
5. Click on the Retrieve Data option to bring up the particular molecule.
6. If after reading the header, you decide that this is a molecule that you wish to view, click on complete with coordinates, which brings up all necessary information for creation of the molecule on RASMOL.
7. Now SAVE the pdb file to your own disk or hard drive so the molecule can be brought up in RASMOL.

There are two additional sites for micromolecules that I have used as well -

1. 1. The data bank created by Dave Woodcock of Okanga University College
2. 2. The KLOTHO database from Washington University St Louis

Both offer complete listings of molecules which are broken down into a classification scheme of families and groups. and can be downloaded for use in RASMOL.

I have had success using this program in the past and plan to implementit into our high school and advanced placement biology curriculum during this coming year. If you try this program or have any questions, please write or call me. My E mail is not functioning at the moment, but you can reach me snail mail, fax or phone. As soon as the E mail is fucntioning, I will rpovide my E mail address.

Jeremy Osterstock
Archmere Academy
3600 Philadelphia Pike
Clamont, DE 19703
302-798-6632 xt 762
fax 302-798-7290

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