Jmol Tutorials

Physical models and computer visualization tools are highly synergistic. When students are introduced to protein structure through the use of physical models, they will often have additional questions that can be productively addressed using computer-generated images. The Jmol tutorials listed below have been created to complement and enhance the use of the physical models produced by the CBM.

These tutorials are constantly under development. Therefore, check back often to see the latest iterations. If you have suggestions for changing the tutorials or creating new tutorials, contact the CBM.

Jumbled Jmols

These Jmols are designed to show two structures: one correct and one incorrect due to amino acids being switched around, or "jumbled". Based on observations of where polar and hydrophobic residues, the user must then attempt to figure out which of the two is the real structure.

Other Jmols

Acetylcholinesterase - Shows the active site of the enzyme and its substrate.
Amino Acids - Switches among the 20 amino acids, highlighting the sidechains of each.
Basic Principles of Chemistry that Drive Protein Folding - The Amino Acid Starter Kit Tutorial.
Basic Principles of Chemistry that Drive Protein Folding, Part 2 - Allows the commands of Part 1 on five additional proteins.
GFP Peptide - Starts out with a peptide, then zooms out to the whole GFP protein.
Hemoglobin - Highlights various sections of the protein, including hydrophobic, polar, acidic, and basic sections.
Modeling an Alpha Helix - Shows an alpha helix and its sidechains.
Modeling a Beta Sheet - Shows a beta sheet of the protein GFP and its sidechains. Also shows the alpha helices and beta sheets of the entire protein.
Zinc Finger - Shows the zinc ion as well as a few select sidechains.

Jmols used specifically in the Tactile Learning Curriculum Modules can be found on a separate page.