On-line molecular structure tutorials show their molecular views in the Jmol java applet, a version of Jmol that works only within web browsers. In contrast, the Jmol application is a stand-alone program (as are RasMol, PyMol, and many other popular molecular visualization programs). Unlike the Jmol applet, it runs independently of, and has nothing to do with, web browsers. And unlike RasMol and PyMol, which need implementations (source code compilations) specific for each computer platform, a single Jmol program runs identically (with the help of java) on Windows, Apple Macs, and linux.

Optionally, the application can be used when you are developing molecular view scripts for JTAT.

Installing the application involves nothing more than putting one file, Jmol.jar, on your computer. Here are step by step instructions for installing the Jmol application.

1. Download the current Jmol .zip or .tar.gz package from jmol.org.
2. Take the one file Jmol.jar from the downloaded package. You can put it wherever you like, e.g. your desktop.
3. Windows users should also visit java.com and download the latest version of java. (Apple users who install all Apple Software Updates as they become available are guaranteed to have the current java.)
4. Double-click on the file Jmol.jar. You should see a black window, ready to load a molecule. (Continue in the next section.)

1. We'll assume that you have downloaded one or more PDB files, and placed them in your jtat/tutorialname/molecules4all directory. In the upper left corner of Jmol, click File and on that menu, select Open. Open one of your PDB files. (Hereafter, it will appear on the File, Open Recent menu.) The molecule should appear as the default ball and stick rendering, colored by element.
2. Click on the Jmol frank (lower right corner of the molecular viewport) to open Jmol's menu. Use Select, View, Style, Color to customize the molecular view.
3. File, Script... opens the Jmol Console. Here you can enter script commands, and see Jmol's responses and reports. See also scripting molecular views.
4. Once you have a molcular view that you want to put into JTAT, continue by following the instructions for installing state scripts, beginning with Display the State Script.