Jmol – molecular structure viewer

Jmol is a molecular visualization application for examining three-dimensional chemical structures, crystals, materials, and biomolecules. It provides tools for exploring atomic arrangements, analysing molecular geometry, and presenting structural information in chemistry and related scientific disciplines.

Jmol can operate as a standalone desktop application or as a component within other applications. Its companion HTML5 implementation, JSmol, brings interactive molecular visualization to web browsers without requiring Java browser plugins. Both implementations share the underlying molecular visualization capabilities and scripting language, making it possible to construct interactive educational material and web-based chemical databases.

The application supports an extensive range of molecular and crystallographic file formats, including output from computational chemistry programs. Structures can be displayed using different representations, with tools for measuring distances and angles, examining molecular orbitals, and visualising vibrational motion. The scripting system provides precise control over molecular scenes, animations, and user interactions, allowing complex presentations to be reproduced consistently.

This is free and open source software.

Key Features

• Interactive three-dimensional visualization of molecular and crystal structures.
• Standalone desktop viewer and embeddable visualization component.
• HTML5 molecular viewing through JSmol without requiring Java browser plugins.
• Support for PDB, mmCIF, CIF, MOL, SDF, MOL2, XYZ, CML, and other molecular formats.
• Read data from Gaussian, GAMESS, MOPAC, VASP, CASTEP, CRYSTAL, and other computational chemistry programs.
• Ball-and-stick, space-filling, wireframe, and other molecular representations.
• Cartoon and secondary-structure representations for biomolecules.
• Visualisation of molecular orbitals, surfaces, and isosurfaces.
• Display crystal unit cells, symmetry operations, and periodic structures.
• Measure interatomic distances, bond angles, and torsion angles.
• Animate molecular vibrations and changes between structural models.
• Display dipoles, forces, vectors, and other molecular properties.
• Load molecular structures from supported online chemical databases.
• Compare multiple structures and molecular models.
• Extensive scripting language derived from RasMol and Chime commands.
• JavaScript controls for building interactive molecular web pages.
• Integration with JSpecView for displaying molecular spectra.
• Export molecular images, animations, and three-dimensional graphics.
• Internationalised user interface with multiple translations.
• Cross-platform support – runs on Linux, macOS, and Windows.

Website: jmol.sourceforge.net
Support:
Developer: Jmol Development Team
License: GNU Lesser General Public License v2.1

Jmol is written in Java. Learn Java with our recommended free books and free tutorials.

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