Jmol: an open-source Java viewer for chemical structures in 3D

with features for chemicals, crystals, materials and biomolecules

Jmol is an interactive web browser applet.

This is a still image, but you can get an animated display of Jmol abilities by clicking here.

(The applet may take some seconds to load. Please, wait and do not reload the page in the meantime.)

Check out the Screenshot Gallery (still images) to see samples of what can be done with Jmol
and check out the Demonstration pages to see buttons and menus in action (interactive applet).

Overview

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

The JmolApplet is a web browser applet that can be integrated into web pages.
The Jmol application is a standalone Java application that runs on the desktop.
The JmolViewer is a development tool kit that can be integrated into other Java applications.

How to cite Jmol

The recommended way to cite Jmol is:
Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/

Remember to always use uppercase 'J', lowercase 'mol' (explanation).

If you prefer, a list of articles that describe Jmol can be found within Jmol Wiki.

What the critics are saying

Jmol v10: I can't believe it's Java!
But it's also open-source, so there's simply no question about it.
Get your copy now, before they run out of those virtual Java machine thingies.
It's just in time (JIT) for Christmas, from what I hear!

Warren L. DeLano, shell-shocked C/Python developer
Principal Scientist, DeLano Scientific, Author of PyMOL
December 2004.

Jmol features

Free, open-source software licensed under the GNU Lesser General Public License
Applet, Application, and Systems Integration Component
- The JmolApplet is a web browser applet that can be integrated into web pages. It is ideal for development of web-based courseware and web-accessible chemical databases. The JmolApplet provides an upgrade path for users of the Chime plug-in.
- The Jmol application is a standalone Java application that runs on the desktop.
- The JmolViewer can be integrated as a component into other Java applications.
Cross-platform
- Windows
- Mac OS X
- Linux/Unix
Supports all major web browsers
- Internet Explorer (Win32)
- Mozilla/Firefox (Win32, OSX, *nix)
- Safari (Mac OS X)
- Opera 7.5.4 (Win32 only)
High-performance 3D rendering with no hardware requirements
File formats
- CIF/mmCIF - Crystallographic Information File and Macromolecular Crystallographic Information File, the standards from the International Union of Crystallography
- CML - Chemical Markup Language
- CSF - Fujitsu CAChe chemical structure, now Fujitsu Sygress
- CTFile - Elsevier MDL chemical table
- GAMESS - General Atomic and Molecular Electronic Structure System output, Gordon Research Group, Iowa State University
- Gaussian 94/98/03 output - Gaussian, Inc.
- Ghemical
- HIN - HyperChem from Hypercube, Inc.
- Jaguar - Schrodinger, LLC
- MM1GP - Ghemical molecular mechanics
- MOL - Elsevier MDL structure
- MOLPRO - Molpro output
- MOPAC - MOPAC 93/97/2002 output (public domain)
  - MOPAC 2007 (v.7.101) graphf output (.mgf files) (public domain) [starting Jmol 11.1.28; reads coordinates, charges, and molecular orbitals]
- NWCHEM - NWChem output, Pacific Northwest National Laboratory
- odydata - Odyssey data, WaveFunction, Inc.
- PDB - Protein Data Bank, Research Collaboratory for Structural Bioinformatics
- QOUT - Q-Chem, Inc.
- SDF - Elsevier MDL structure
- SHELX - Structural Chemistry Department, University of Göttingen (Germany)
- SMOL - Spartan data, Wavefunction, Inc.
- xodydata - Odyssey XML data, WaveFunction, Inc.
- XYZ - Minnesota Supercomputer Institute XMol file
- XYZ+vib - XYZ format files with added vibrational vector information
- XYZ-FAH - Folding@home XYZ file
* Files which are compressed with gzip will automatically be decompressed
Animations
Vibrations
basic unit-cell support
schematic shapes for secondary structures
measurements
- distance
- angle
- torsion angle
RasMol/Chime scripting language support
JavaScript support library
Exports to .jpg, .png, .ppm, .pdf, and PovRay

Mailing Lists

Those with interest in molecular visualization, especially the education and research communities, are encouraged to join the jmol-users mailing list where you can share ideas and experiences, ask for help, and give us feedback. The jmol-users archives can be a useful reference.

Those who are seriously interested in participating should join the jmol-developers mailing list where you can request new features or changes, discuss implementation, submit patches, or contribute code. You can also browse the jmol-developers archives .