Teachers' Molecular Visualization Resources

Molecular Visualization Freeware -- Resources for Teachers

This document provides an overview of free molecular visualization resources of interest to teachers, all of which are available at:

http://www.umass.edu/microbio/rasmol

If you are reading this document from paper, you may prefer to read it from the web so you can click on the links below. Start at http://www.umass.edu/microbio/rasmol/teachers.htm

RasMol Quick Start: tells beginners how to use RasMol, also where and how to download any molecule of interest (large or small) for viewing in RasMol. http://www.umass.edu/microbio/rasmol/rasquick.htm

What questions can you answer about a protein/DNA molecule with RasMol? http://www.umass.edu/microbio/rasmol/raswhat.htm Walks beginners step by step thru methods for answering questions including:

Supported by the National Science Foundation and MDL Information Systems.

How many chains are there?
Is there anything besides the protein/DNA chains (such as bound substrate, metal ions, or water)?
Where are the main chain hydrogen bonds?
Where are the disulfide bonds?
Where are the alpha helices and beta strands?
Where are the hydrophobic amino acids?
What atoms contact (anything of interest)? (Examples: metal ions, or protein-DNA contacts.)
How do I find the distance between two atoms?
How do I label an atom?
How do I see the molecule in stereo?
How do I save this view?
How do I restore the view later for my class?

How to save selected views of molecules for use in your teaching. This document explains how to use RasMol's powerful save script filename command, and provides troubleshooting if needed. http://www.umass.edu/microbio/chime/prsswc/prssft.htm This document also explains how to create a master script which plays back your RasMol-saved scripts smoothly, in the desired order.

Putting your teaching presentation on the web. Explains how to incorporate your RasMol-saved scripts into a Chime-based presentation on the web. A downloadable Chime template is provided. You need merely change a few lines in it with a text editor -- no programming is involved! An example of such a teaching presentation, showing the gal4 transcriptional regulator complexed to DNA, is provided. http://www.umass.edu/microbio/chime/prsswc/template.htm

A ready-to-use tutorial on basic DNA structure is designed for self-directed (nonlinear) exploration by students, with an easy-to-use, fun, push-button interface. http://www.umass.edu/microbio/chime/dna/index.htm Downloadable for local installation.

A 10-minute lecture segment on protein secondary structure (using lysozyme as an example, matched to Campbell's Biology textbook) can be illustrated with a ready-to-run (linear) presentation viewable, then downloadable (for projection from a computer without an Internet connection) from http://www.umass.edu/microbio/chime/protsecs/index.htm

Web-based visualization tutorials on over 30 other molecules are indexed at the World Index of Animated Tutorials on Biomolecular Structures at http://www.umass.edu/microbio/rasmol/tutbymol.htm

Quelques scripts RasMol ont été traduits en Français par l'Institut National de Recherche Pédagogique de la France. Thèmes d'étude: Structure du tétramère de l'hémoglobine, de ADN, de CMH, et de antigène-anticorps. http://www.umass.edu/microbio/rasmol/nonengli.htm

Español. Contactar con José Miguel Fernández-Fernández, en la Universidad de Granada, España (jmfernan@goliat.ugr.es). El manual del "RasMol" y otros guías ("scripts") están actualmente siendo traducidos.