Installing JMOL

Warning

JMOL requires JAVA (installation instructions)

We use the protein structure viewer JMOL in the course. This can be installed following the instructions on the JMOL website.

Download JMOL

JMOL is provided as a single JAVA application for all operating systems. To download it, click on the link below.

Clicking on the link above should download a .zip or .tar.gz file, which can be extracted, producing a directory containing the JMOL application.

Running JMOL

To start JMOL, open the parent directory in your file explorer (e.g. Finder on macOS), and double-click on the jmol.jar file.

Note

On macOS you may not be permitted to run this executable, as the program is not signed. If this is the case, open System Preferences -> Security & Privacy and click on the General tab. In the lower section of the window, you should see an option to trust the file jmol.jar. Accept this offer. As soon as you do this, JMOL should start.

Alternatively, you can start JMOL from the command-line. Navigate to the directory containing jmol.jar and issue the following command:

java -jar jmol.jar

The splash screen should appear, and the application should start.