Juba

Jmol

Jmol is an open-source Java viewer for three-dimensional chemical structures. It is widely used in the fields of chemistry and biochemistry for visualizing molecular structures, including small molecules, proteins, nucleic acids, and crystals. Jmol is particularly popular in educational settings due to its ease of use and ability to run on multiple platforms.

Features

Jmol offers a variety of features that make it a versatile tool for molecular visualization:

• 3D Visualization: Jmol can display complex molecular structures in three dimensions, allowing users to rotate, zoom, and explore molecules interactively.
• Cross-Platform Compatibility: As a Java-based application, Jmol runs on Windows, macOS, Linux, and other operating systems that support Java.
• Scriptability: Jmol includes a scripting language that allows users to automate tasks, create custom visualizations, and perform batch processing of molecular data.
• File Format Support: Jmol supports a wide range of file formats, including PDB, CIF, MOL, and more, making it compatible with many molecular databases and software.
• Integration with Web Pages: Jmol can be embedded in web pages, allowing interactive molecular visualizations to be shared online.

Applications

Jmol is used in various applications, including:

• Education: Jmol is a valuable tool for teaching chemistry and biochemistry, providing students with a hands-on way to explore molecular structures.
• Research: Researchers use Jmol to visualize and analyze molecular data, aiding in the understanding of molecular interactions and properties.
• Drug Discovery: In the pharmaceutical industry, Jmol is used to visualize potential drug candidates and their interactions with biological targets.

History

Jmol was first released in 2002 and has since undergone continuous development. It was created to provide a free, open-source alternative to commercial molecular visualization software. Over the years, Jmol has grown in functionality and user base, becoming a staple in both academic and research settings.

Technical Details

Jmol is written in Java, which allows it to be platform-independent. It uses OpenGL for rendering 3D graphics and can be run as a standalone application or as an applet within a web browser. The Jmol project is hosted on SourceForge, where users can download the latest version and access the source code.

Also see

• Molecular modeling
• Protein structure
• Crystallography
• Java (programming language)
• Open-source software