Original URL: http://www.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html

Molecular Models for Biochemistry at CMU

The linked pages described here have tutorials and quizzes that are based on Chime and RasMol images of the molecules and macromolecules found in biochemistry. They are intended to complement standard biochemistry texts where more explanation is provided, but where interactive 3-D images of the molecules are not available.

Please see viewing suggestions below before choosing a topic.


SMALL MOLECULE GALLERY
Introduction & Index to Chime displays of some textbook examples used in the Modern Biology (03-121) and Cell Biology (03-240) courses at CMU.
Also shown are some protein and lipid bilayer structures.
Quizzes (T-F and Chime) on functional groups are linked from the page.

Practice Quizzes: A separate listing of the Chime and GIF-based quizzes at this site.
AMINO ACID STRUCTURES
Amino Acid & Peptide Structures are viewed as Chime-generated images.

Take an Amino Acid Structure Quiz based on GIFs from the above tutorial.

Structures are shown as a collection of Amino Acid GIF images.

Amino Acid Identification Quizzes
The names, abbreviations, and one-letter codes are tested in three formats:
  1. Chime images.
  2. Ball & Stick GIF images.
  3. Spacefill GIF images.
PROTEIN STRUCTURES
Protein Architecture using Chime-generated images of Protein G.

Take a Protein Structure Quiz using GIFs from the Protein Architecture tutorial.

Selected Chime Displays of proteins & nucleic acids from CMU biochemistry courses.

Chime Displays with a RasMol Command Line of Crambin and BPTI.
NUCLEOTIDE   & NUCLEIC ACID STRUCTURES

Overview of DNA & RNA Structure.

A Tour of tRNA Structure: A Chime-based tutorial on Yeast tRNAPhe structure; and
An "animated" RasMol tour of the crystal structure.
Nucleotide Identification Quizzes
The names and abbreviations are tested in two formats:
  1. Chime images.
  2. Ball & Stick GIF images.
STRUCTURES FOR MOLECULAR BIOLOGY
Introduction and links to these molecular models:
  B-Form DNA helix
  A-Form RNA helix
  cAMP Receptor Protein (CRP)
  Human hnRNP A1
  snRNP U1A
  EF-Tu, tRNAPhe, and GTP
  Zif268 Zinc Finger
  EcoRI Restriction Endonuclease
  HhaI Restriction Methylase
  Nucleosome
METABOLIC PATHWAYS
Glycolysis. Chime-generated intermediates on the glycolytic pathway.

TCA cycle. Chime-generated intermediates in the tricarboxylic acid cycle.
ADDITIONAL TOPICS from CMU biochemistry courses.
Advanced Biochemistry (03-740) Fall Term, 1998.

Physical Biochemistry (03-438) Spring Term, 1999.


Biochemistry I (03-231) Spring Term, 1999.


Periodic Table of Elements. Chime display that illustrates the RasMol CPK coloring scheme.
LINKS to other sites with graphics displays related to biochemistry.
Please note the following for optimal viewing:
These pages all require a frames-enabled browser, such as Netscape Navigator 3.01 or Navigator 4.05. See Netscape's home page for current information. (Microsoft Internet Explorer 4 (still) does not handle the Chime plug-in displays adequately, but may work on some of the GIF-based quizzes.)
In addition, JavaScript must be enabled.
Navigator 3: Select Network Preferences... under the Netscape Options menu; then Languages.
Navigator 4: Select Preferences... under the Netscape Edit menu; then Advanced.

The following plug-in is required for viewing most of these pages unless "GIF" appears in the link or description. (All of the CMU cluster Macs and PCs have Chime installed):

Chemscape Chime Plug-in v2.0.
 
Get the Chime plug-in from the MDL Inc. software download page. It is now available for the Mac, Windows, and SGI IRIX computers (v0.9z, only). Internet Explorer 5, on a Windows platform, appears to function well; see the MDL page, Release Notes v2.0 for details. After installing this plug-in, try out the moving images at the MDL Inc. site.
Their Sample Sites page lists many other sites where the Chime plug-in is being used to display molecules.

RasMol v2.6 by Roger Sayle.
 
The RasMol Home Page maintained by Dr. Eric Martz, provides RasMol in versions for several operating systems, with installation instructions, and extensive supplementary resources. Included are Frequently Asked Questions (FAQ), tutorials on how to use RasMol, and several documents on how to create "movie" scripts.
This site also has several different kinds of Chime-based tutorials and detailed instructions for creating Chime images on WWW pages. See the Chime Resources page for these offerings.
The RasMol Manual (160K) has been updated to v2.6 and converted to HTML format. It can be read (or downloaded) at the above site.

The RasMol Manual: Frames added some new features to the v2.6 HTML Manual and permits faster navigation between topics.

The CMU RasMol Tutorial is an on-line version of the tutorial written by Dr. David Hackney for use in our biochemistry courses.

Are you an experienced RasMol user?
The interactive RasMol Quiz will test your mastery of RasMol commands.

You should also look at the CMU Chime Features page, for a short demonstration on how this plug-in is used with the molecular models shown here.

Unless otherwise noted, the small molecule atomic coordinates are from Klotho: Biochemical Compounds Declarative Database.

Adjust your Netscape window to a width of about 9-10 inches (640-700).

Interactive Displays of Molecular Structures on WWW Pages outlines some of our goals and plans for this site. It was the basis for a CMU TELFair presentation on October 2, 1998.


Some of the topics on this page can be downloaded as StuffIt files for individual or local server use. For information, please contact:
Dr. William McClure
wm0p@andrew.cmu.edu.
Department of Biological Sciences
Carnegie Mellon University
Pittsburgh, PA 15213

5.10.99


contents of this CD