General Chemistry Labs

Jmol


What is Jmol?

Jmol is an open-source Java viewer for three-dimensional chemiscal structures, with features for chemicals, materials and biomolecules. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs1.

The tutorials in this course use Jmol to allow the reader to open molecules (usually pdb files) and view them interactively. Java is required on the computer that the tutorials are being viewed from and javascript must be enabled from within the browser being used.


Obtaining, Installing and Using Jmol

Two things are required to view the molecules in this tutorial; java must be installed on the computer, and javascript must be enabled in the browser used to view the tutorials. Throughout the tutorials, clicking the links labeled "View this molecule interactively" will open new browser window in which the Jmol Applet will start and display the molecule. Right-clicking (Windows/Linux PC) will open a menu that allows the user to 'interact' with the molecule.

Some tutorials require that the individual download and view pdb files of the molecules described in the tutorial. A stand-alone application of Jmol can be downloaded and installed for this purpose. The Jmol download page is located at http://jmol.sourceforge.net/download/. This page provides instructions for installing and running Jmol.


References

  1. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/