Chem 406: Biophysical Chemistry, Fall 2000
Molecular Modeling Resources

Sources for Searching and Downloading Files from the Protein Data Bank:

Protein Data Bank

Front-end for accessing structure files from the Protein Data Bank

Molecules R Us

Simple front-end for accessing structure files from the Protein Data Bank

Rasmol and Chime Manuals, Tutorials and Demonstrations:

Manuals:

Rasmole 2.7 Manual

Rasmol/Chime site

This site contains many resources for learning to use both Rasmol and Chime

Chime 2.0 - Attributes for Embed tags

(Most of the attributes described can be used with Chime 1.02.)

Chime 2.0 - Additional Chime Specific Rasmol Commands.

Tutorials:

Chime Tutorials and Demonstrations

Tutorial on Embedding Chimes and JavaScript buttons

Demonstrations:

Protein Secondary Structure

Requires Netscape and Chime

Oxymyoglobin

A demostration of using interactive scripts with Chime (Requires Netscape and Chime)

Hemoglobin Structure

An interactive tutorial on the structure of hemogolobin using Chime

Antibody Structure

An interactive tutorial on the structure of immunoglobulins using Chime

Interactive Biochemistry

Glycolysis:

Other Sites of Interest:

Folding@home

A group at Stanford University is attempting to attach the protein folding problem by doing computer simulations of the folding process. This is a very computationally demanding problem. Their approach is to have many computer processors working on the problem at the same time. They are soliciting help from the general public by asking us to run cycles on our home computers when they would otherwise be idle. The site contains a lot of good information on the protein problem along with numerous links to related sites.

Download Sites:

Netscape

Site for downloading a copy of the Netscape internet browser. Netscape Navigator is a browser only, whereas Netscape Communicator, among other things, contains a web page authoring tool. Versions are available for both MacOS and Windows.

RasMol

Site for downloading a copy of the Rasmol molelcular graphics program. Versions are available for both MacOS and Windows. This program accepts Protein Data Bank files as input for viewing biological macromolecules.

RasMol manual

An online version of the Rasmol manual. This is a good read if you wish to fully utilize the capabilities of Rasmol

Chime

This is a plug-in that allows Netscape Navigator, Netscape Communicator and Internet Explorer to display 3-dimensional models of biological macromolecules. It looks very much like Rasmol. When used, the browser must be configured to invoke the Chime plug-in when it encounters a files that is tagged with the "chemical/x-pdb" MIME type. Versions are available for both MacOS and Windows, however Version 1.0 does not work with Internet Explorer, Version 2.0 does not work with the MacOS version of Internet Explorer.