Course Syllabus

Course Schedule

Lecture Notes

Problem Sets

Lab Assignments

Modeling Resources

Answer Keys

Web Termpapers

[UWEC Web]

[Chemistry Dept.]

Warren Gallagher
Department of
(715) 836-5388

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

Protein Data Bank
This site provides an array of ways for accessing and viewing the structure files from the Protein Data Bank
IMB Jena Image Library of Biological Macromoleucles
It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available. This site provides examples of using both Chime and Jmol to visualize biological macromolecules.

Structural Classification Databases

SCOP: Structural Classification of Protein
A hierarchical key for proteins that is arranged according to secondary structure content and arrangement
CATH: Protein Structural Classification
A hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H)


Jmol is an open source Java-bases applet for molecular modeling. It be run as either a stand-alone application or embedding into web pages. It's functionality supercedes those of Rasmol and Chime but keeps the same scripting language as these two older applications.

Home Sites:

Jmol homepage
To run Jmol as a standalone application, download Jmol from the Jmol homepage. Double-click on the "Jmol.jar" file that will be in the folder that will be downloaded. Your computer will need to have the Java Runtime Environment installed for this to work.


Jmol Guide
Jmol Applet Guide
Jmol Interactive Scripting Language
Jmol.js Javascript Library
Rasmol Manual (Jmol can use Rasmol Commands)


Jmol tutorial
Embedding Jmol into webpages using a simple text editor
Embedding Jmol into webages using GoLive
An Introduction to Jmol Scripting


Jmol Wiki
Jmol Demonstrations Page
Online Macromolecular Museum

Rasmol, DeepView, and Chime Manuals


RasMol 2.7 Manual
DeepView (SwissPDBViewer) User Guide
Rasmol/Chime site
This site contains many resources for learning to use both Rasmol and Chime
Chime 2.6 - Attributes for Embed tags
Chime 2.6 - Additional Chime Specific Rasmol Commands.


Chime Tutorials and Demonstrations
Tutorial on Embedding Chimes and JavaScript buttons
RasMol tutorial
DeepView (SwissPDBViewer tutorial)


Protein Secondary Structure
Requires Netscape and Chime
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
These are Chime based tutorials on Protein Structures that accompanies Garret & Grisham's Biochemsitry 2nd Ed. This link requires a password.

Other Sites of Interest:

Crystallography Made Crystal Clear
This is the companion web site for Gale Rhodes' textbook of the same name.
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:

Site for downloading a copy of the Jmol package. The Jmol package contains both a standalone version of Jmol (Jmol.jar) and the components you need for serving Jmol applets from web pages. It also contains a Javascript library file (Jmol.js), which can simplify the embedding of Jmol applets into web pages.
Site for downloading a copy of the Netscape internet browser. The Chime plug-in works reliably only with the Netscape 4.x version browsers. 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.
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.
DeepView (SwissPDBViewer)
Site for downloading a copy of the DeepView application. DeepView (formally known as SwissPDBViewer) is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
This is a plug-in that allows Netscape Navigator and Netscape Communicator 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. The current version is 2.6. It does not work reliably with Microsoft's Internet Explorer.