Jmol 14.28.3

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry, biochemistry, physics, and materials science. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

  • The JSmol JmolApplet is a web browser JavaScript application that can be integrated easily into web pages. Though Java-based for development and management, JSmol is completely JavaScript.
  • The Jmol application is a stand-alone Java application (Jmol.jar) that runs on the desktop. It has all the capabilities of the JSmol applet but runs approximately 3-6 times faster. In addition, it can be run in "headless" mode (JmolData.jar) in order to carry out tasks that need to be replicated.
  • Jmol.jar can be integrated into any other Java program, providing file loading, structure processing, viewing, and output capabilities.
  • Jmol is fully scriptable. For the most up-to-date scripting documentation see the Jmol/JSmol interactive scripting documentation.

Accessing the software

To load the module:

$ module load Jmol/14.28.3-iomkl-2017.01

An example command to include in your job script:

java -jar Jmol.jar inputFileName -J script_commands -s scriptFileName -j script_commands 

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the website for more information regarding this application.

There is also a wiki available for Jmol.

Last modified: 5 March 2018