Jmol in the Classroom

From Jmol
Jump to navigation Jump to search

The idea behind this page is that you enter "teachable moments" when you have used Jmol in an effective way during class.

FirstGlance in Jmol

  • FirstGlance in Jmol offers a guided tour of any macromolecule (PDB code or uploaded model). Information in the PDB file header is presented in readable form with links to extensive help. Technical language is minimized; for example, "Reliability" offers an objective assessment of free-R (e. g. "Better than average at this resolution") with explanations in minimally-technical language. Secondary structure, hydrophobic cores, charge distribution, "local uncertainty" (B factor/temperature factor) are available at a single click. Find any residue or sequence motif in the 3D structure. Find the non-covalent interactions with any moiety. You don't need to learn any Jmol commands. Used more than 1,000,000 times. Suitable for high school up to investigators in biochemical research teams. More.
  • To find it, google firstglance as a single word, no space.
  • Lesson plans with syllabi and assessments for students at various levels, using FirstGlance: Introduction to Structural Bioinformatics.


Proteopedia.Org is a JSmol-based protein structure wiki that makes it easy to create customized molecular scenes. While reading about the molecule, you click green links that change the interactive 3D molecular scene in JSmol.

Functional Groups: getting structures by name

On day 5 of first-semester organic chemistry (textbook Smith, 3rd ed., Chapter 3, topic "Functional Groups"). Bob Hanson.

I thought it would be fun to get students to suggest examples, so I fired up This page has a button on the right that uses the prompt command and taps into the NIH CACTUS service using load $chemicalName (Jmol 12.1).

I just clicked on "Load MOL by NAME" and then asked the students to give me a name of something they knew, like a medication.

We ended up looking at diphenylhydramine, morphine, THC, heroin, hydrocodone, adderall, and tetracycline, writing out several of these structures on the board based on the 3D models. This lead to discussions of reactivity, hints about the connections between names (even these trade names) and functional groups, a little about the blood/brain barrier issue, hints about synthesis (it's amazing how simple many of these drugs are).

Great fun!

Integrating Jmol in virtual learning environments

Using Java applets to enhance online teaching and assessment in Blackboard. Tim Wallace (2011), in Symposium on the Benefits of eLearning Technologies. University of Manchester.

Molecular visualization in STEM education: Leveraging Jmol in an integrated assessment platform. G. Rule, D. Bajzek & A. Kessler (2010), in J. Sanchez & K. Zhang (eds.), Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2010, pp. 304-309. Chesapeake, VA: AACE.

Jmol in Wiki

I use the Wiki-Extension to show molecules in a Wiki that is hosted by the german ZUM (Zentrale für Unterrichts-Medien = Central for Teaching with Media).


--BLachner 14:04, 2 April 2013 (CEST)