What is Jmol?

Jmol is a free, open source viewer of molecular structures useful for students, educators and researchers in chemistry, biochemistry and other fields dealing with molecular structure. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

  • The Jmol application is a standalone Java application that runs on the desktop.
  • The JSmol is an object that can be integrated into web pages. It does not require Java, since it runs using just the browser's HTML5 and JavaScript engines.
  • The JmolViewer is a development tool kit that can be integrated into other Java applications.

For more details, please consult the Jmol Home page.

Usage of Jmol at LRZ

The environment modules package controls access to the software. Use "module avail jmol" to find all available versions of Jmol installed at LRZ.

To use the default version of Jmol, please type:

> module load jmol

You can either start Jmol on the login nodes of Linux-Cluster & SuperMUC-NG or by using our remote visualization service (via VNC). We however want to note that the graphics performance on the login nodes is comparatively poor. Therefore, we recommend our users to only start Jmol on the login nodes for less demanding visualisations of e.g. small molecules. To visualize larger data sets or to run more demanding Jmol extensions, please use our remote visualization service (via VNC) which will grant you entire access to the reserved "localhost" node including GPU resources.

Documentation

Please consult the Jmol Home page for documentation.

Support

If you have any questions or problems with Jmol installed at LRZ platforms, please don't hesitate to contact LRZ HPC support staff.

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