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

with features for chemicals, crystals, materials and biomolecules

JSmol is the HTML5 modality of Jmol, able to be embedded into web pages. All the functionality of Jmol (as a standalone application) is also present in JSmol. JSmol is an interactive web browser object. This is a still image, but you can see several animated displays of Jmol abilities by clicking here or on the image itself. (The JSmol library may take some seconds to load. Please, wait and do not reload the page in the meantime.) Here you can see the JSmol object in action, running a script written in the Jmol scripting language. It is not a movie, slide show, or animated image file ... JSmol is an interactive web browser object. Please, choose among the following demos: a display of assorted capabilities of Jmol. (3 min) a more specific display, illustrated with the ethane molecule. (1.5 min) a display of some features suitable for macromolecules. (1.5 min)

Quick links: Download Jmol+JSmol. The complete package is named Jmol-xx.xx.xx-binary.zip ; inside it you will find: Jmol.jar , the Jmol application (runs without installation, even from a portable disk, but needs Java installed) jsmol.zip , the package needed for implementing JSmol in web pages (does not need Java) Main project page (source code) for Jmol+JSmol at SourceForge. J(S)mol scripting documentation

SourceForge awards for the Jmol project (March 2022):

• 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.