Jmol: an open-source browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D

with features for molecules, crystals, materials, and biomolecules

Jmol/JSmol Download Page (jsmol.zip is contained within Jmol-xx.xx.xx-binary.zip)

Main Jmol/JSmol project page

Jmol/JSmol scripting documentation

Overview

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

• The JSmol JmolApplet is a web browser JavaScript application that can be integrated easily into web pages. Though Java-based for development and management, JSmol is completely JavaScript.
• The Jmol application is a stand-alone Java application (Jmol.jar) that runs on the desktop. It has all the capabilities of the JSmol applet but runs approximately 3-6 times faster. In addition, it can be run in "headless" mode (JmolData.jar) in order to carry out tasks that need to be replicated.
• Jmol.jar can be integrated into any other Java program, providing file loading, structure processing, viewing, and output capabilities.
• Jmol is fully scriptable. For the most up-to-date scripting documentation see the Jmol/JSmol interactive scripting documentation.

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 especially jsmol.htm simple.htm simple2.htm jsmetest2.htm jsv_predict2.htm 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.
• 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
• See the scripting documentation and also the Jmol Wiki file format page for complete details on file types that Jmol can read. Note that files which are compressed using gzip will automatically be decompressed.
• Animations
• Vibrations
• Surfaces
• Orbitals
• Support for unit cell and symmetry operations
• Schematic shapes for secondary structures in biomolecules, including DSSR for investigating the secondary structure of nucleic acids.
• Measurements
  • distance
  • angle
  • torsion angle
• Support for RasMol/Chime scripting language
• Exports to jpg, png, pngj (a png image that can be dragged back into Jmol to reproduce the exact model state the image was created from) gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, idtf, web page.

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.

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