BioMolecular Explorer 3D: A Guide to These Resources

Software for interactive molecular exploration in High School Biology courses.


A Guide to These Resources

The Explore the Molecules page of BioMolecular Explorer 3D presents a list of molecules that can be viewed and/or explored in 3D in a browser such as Internet Explorer, Firefox or Safari. Each molecule in the list is in one or both of the following formats: Guided Tutorial, FirstGlance in Jmol, Biomodel Presentation, and Animation. In addition, all molecules on the list have links to online background information suitable for lesson planning, and some molecules have links to lesson plans and/or questions for students.

Guided Tutorials are presentations that use animations and text to explain the structure and function of a specific molecule. The author of the tutorial has made choices about what to show and how to show it, and provides a guided tour of the structure.

FirstGlance in Jmol allows you to view a molecule and explore it using a variety of pre-set views that appear with a click of your mouse. For example, pre-set views include displays of secondary structure, cartoon backbone display, polar vs. non-polar amino acids, and others. Every pre-set view updates an information panel that explains the view's colors and style of depiction. In addition, FirstGlance in Jmol offers options such as "Find..." that allow you to search for and display a specific part of a molecule. In summary, FirstGlance in Jmol is software that displays a molecular structure in 3D and helps you to explore it; it is not a tutorial with a prepared presentation for you to follow.

Biomodel presents an overview of several important classes of biomolecules, such as carbohydrates, lipids, nucleic acids, and proteins. Examples of each are displayed and discussed briefly. Each section offers access to two control panels for Tools and Color Schemes, as well as help with using the mouse to control the structure. Biomodel is available in Spanish as well as English. (See the Explore the Molecules page for links to both versions).

Animations are movies that highlight one or more specific aspects of a molecular structure. The structure can be manipulated in 3d using the mouse at any time during the movie.

We welcome your comments and questions. In addition, if you have lesson plans for these materials that you would like to receive comments on or are willing to share, please contact us. We would be happy to review your materials and can make them available through this web site to other interested teachers.

Next section: Explore the Molecules