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

with features for chemicals, crystals, materials and biomolecules

• Overview
• How to cite Jmol
• What Jmol can do
  • Samples
  • Features
  • What the critics are saying
• Obtain Jmol
• Learn to use Jmol
  • Manuals and tutorials
  • Learn by example
  • Jmol community

Overview

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.

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 the 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 object within the webpage).

Features

• Free, open-source software licensed under the GNU Lesser General Public License
• HTML5 object, application, and systems integration component
  • JSmol is a web browser object that can be integrated into web pages. It is ideal for development of web-based courseware and web-accessible chemical databases. .
  • 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.
• Multi-language
  • Translated into multiple languages: Basque (eu), Brazilian Portuguese (pt_BR), Catalan (ca), Chinese (both zh_CN and zh_TW), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Hungarian (hu), Indonesian (id), Italian (it), Japanese (jp), Korean (ko), Malayan (ms), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk), in addition to the native American English (en-US) and British English (en-GB).
  • Automatically adopts the language of the user's operating system, if it is among the translations available. You can change to another language if desired.
  • For up-to-date details or instructions for adding your language, see the Wiki.
• Cross-platform
  • Windows
  • Mac OS X
  • Linux / Unix
• Supports all major web browsers: Firefox, Safari, Chrome, Opera, Edge...
• High-performance 3D rendering with no hardware requirements
• Many file formats are supported
  Files which are compressed with gzip will automatically be decompressed
  See also the file formats section within Jmol Wiki.
  MOL MDL / Elsevier / Symyx structure (classic version V2000)
  V3000 MDL / Elsevier / Symyx structure (new version V3000)
  SDF MDL / Elsevier / Symyx structure (multiple models)
  CTFile MDL / Elsevier / Symyx chemical table (generic)
  CIF Crystallographic Information File - standard from the International Union of Crystallography
  mmCIF Macromolecular Crystallographic Information File - standard from the International Union of Crystallography
  CML Chemical Markup Language
  PDB Protein Data Bank - Research Collaboratory for Structural Bioinformatics
  XYZ XYZ format, XMol file - Minnesota Supercomputer Institute
  XYZ+vib XYZ format with added vibrational vector information
  XYZ-FAH XYZ format for Folding@home
  MOL2 Sybyl, Tripos
  Alchemy Tripos
  CSF Fujitsu CAChe chemical structure, now Fujitsu Sygress
  GAMESS General Atomic and Molecular Electronic Structure System output (both US and UK variants) - Gordon Research Group, Iowa State University
  Gaussian Gaussian 94/98/03 output - Gaussian, Inc.
  Cube Gaussian, Inc.
  Ghemical The Ghemical computational chemistry package
  MM1GP Ghemical molecular mechanics file
  HIN HIN / HIV files from HyperChem - Hypercube, Inc.
  Jaguar Schrodinger, LLC
  MOLPRO Molpro output
  MOPAC MOPAC 93/97/2002 output (public domain)
  MGF MOPAC 2007 (v.7.101) graphf output (public domain)
  NWCHEM NWChem output - Pacific Northwest National Laboratory
  odydata Odyssey data - WaveFunction, Inc.
  xodydata Odyssey XML data - WaveFunction, Inc.
  QOUT Q-Chem, Inc.
  SHELX Structural Chemistry Department, University of Göttingen (Germany)
  SMOL Spartan data - Wavefunction, Inc.
  spinput Spartan data - Wavefunction, Inc.
  GRO Gromos87 format from GROMACS
  PQR Modified pdb format including charge and radius
  Amber The Amber package of molecular simulation programs
  JME Java Molecular Editor - Peter Ertl
  CASTEP The CASTEP software package, uses density functional theory
  FHI-aims Full-potential / all-electron electronic structure theory with local orbitals - Fritz-Haber-Institut der Max-Planck-Gesellschaft
  VASP VASP / VAMP / Vienna ab-initio simulation package
  DGrid Miroslav Kohout, Max-Planck Institute
  ADF ADF output - Amsterdam Density Functional
  XSD Accelrys Materials Studio
  AGL ArgusLab
  DFT Wien2k
  AMPAC AMPAC output - Semichem, Inc.
  WebMO WebMO interface to computational chemistry packages
  Molden Electron density / molecular orbitals
  PSI3 Output files from the PSI3 suite of quantum chemical programs
• Animations
• Vibrations
• Surfaces
• Orbitals
• 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 (JSmol.min.js)
• Exports to jpg, png, gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, stl, idtf, web page.
• 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.

Obtain Jmol

You can get the latest version of Jmol from the download page.

Being a .jar file, the Jmol application will be displayed as a Java icon. If you want a Jmol icon to be shown instead, you can get it from the Jmol Wiki.

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.