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

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

The latest stable version is Jmol 13.0

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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 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 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 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 theChime 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.
• Multi-language
  • Translated into multiple languages: Catalan (ca), Chinese (both zh_CN and zh_TW) Czech (cs), Dutch (nl), Finnish (fi) French (fr), German (de), Hungarian (hu), Indonesian (id), Italian (it), Korean (ko), Malay (ms), Portuguese - Brazil (pt_BR), Spanish (es), 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: Internet Explorer, Mozilla and Firefox, Safari, Google Chrome, Opera, Konqueror, IceWeasel, ...
• High-performance 3D rendering with no hardware requirements
• File formats (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
  CRYSTAL	Output files from CRYSTAL, a computational tool for solid state chemistry and physics. Theoretical Chemistry Group, Univ. Torino, Italy.

  * Files which are compressed with gzip will automatically be decompressed
• 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 (Jmol.js)
• Exports to jpg, png, gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, 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

Jmol v. 13.0 is the latest official, stable version. 
There are also prerelease versions that are being developed for enhanced functionality (odd-numbered versions like 11.7, 11.9, 12.1, 12.3). 

You can get the latest stable version from this direct download link. Or, if you are interested in other versions or the prereleases, read details in 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.