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.)

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 in the Jmol Literature section of Jmol Wiki.

What Jmol can do

Samples

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

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 and Firefox (Win32, OSX, Linux, Unix)

Safari (Mac OS X)

Opera 7.5.4 (Win32 only)

Konqueror (Linux)

IceWeasel (Linux)

...

High-performance 3D rendering with no hardware requirements

File formats (see also file formats section within Jmol Wiki):

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)

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.

spinput - 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 support for unit cell and symmetry operations

Schematic shapes for secondary structures in biomolecules

Measurements

distance

angle

torsion angle

Support for RasMol/Chime scripting language

JavaScript support library

Exports to .jpg, .png, .ppm, .pdf, and PovRay

For more details, see the history of development.

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.

Learn to use Jmol

Manuals and tutorials

A handbook has been published for learning Jmol, and there are also other publications about Jmol.

There is also a list of tutorials designed to learn the use of Jmol, and more help, within Jmol Wiki.

Finally, there is a documentation section in this web site, for more technical details.

Learn by example

You can also learn by examining web pages that use Jmol: demonstration pages within this web site, and a list of websites using Jmol in Jmol Wiki.

Jmol community

Jmol Wiki

A user-maintained site collecting a lot of information about the use of Jmol. More dynamical and frequently updated than this web site! -- visit Jmol Wiki

Mailing lists

Those with interest in molecular visualization, especially the education and research communities, are encouraged to join the jmol-users mailing list or even the jmol-developers mailing list. There you can share ideas and experiences, ask for help, give us feedback, request new features or changes, discuss implementation, submit patches, or contribute code.

Without subscribing to any lists, you can also search the archives that collect all messages posted to the lists.

For more information, please visit the Project pages section.