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Jmol is an open-source viewer for three-dimensional chemical structures, with features for chemicals, biomolecules, crystals and materials. It runs as a stand-alone application using Java.

JSmol is a fully functional implementation of Jmol that runs in any current web browser (without Java). It also works on mobile devices, within the limits of screen dimensions and processing power. See JSmol for more details.

Features

Some prominent features that make Jmol/JSmol stand out from alternative software are:

• Possibility of embedding it in web pages, using standard JavaScript only (no plug-ins of complements need to be installed). Different elements in the page can be made to interact with the content in JSmol, providing an interactive multimedia product that offers both guided content and open exploration.
• Extensive programming capability to customize the molecular view as well as retrieve and manipulate information from the molecule, using the Jmol scripting language. This is a full programming language including variables, loops, conditionals, logical and math operations, custom functions.. in addition to understanding the identities and properties of atoms, bonds, polymeric chains... belonging to molecules.
• Localization in 24 languages.
• Multiplatform (Windows PC, MacOS, Linux, iOS, Android)
• Open source code (License).

Features include reading a variety of file types, including also PyMOL session files and output from quantum chemistry programs, file writing (including JPG, PNG, PNGJ (PNG+ZIP), and ZIP formats), and animation of multi-frame files and computed normal modes from quantum programs.

How to cite

The recommended way to cite Jmol is:

Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/

JSmol: an open-source HTML5 viewer for chemical structures in 3D. http://wiki.jmol.org/index.php/JSmol

Remember to always use uppercase 'J', uppercase 'S', lowercase 'mol' (explanation).

If you prefer, a list of articles that describe Jmol can be found in the Jmol Literature section.

About this wiki

This is the homepage for the Jmol Community Wiki. Here the community of users can discuss everything that has to do with Jmol and JSmol. You are welcome to browse around and to add new pages, extra information, comments, questions, links to useful examples of Jmol use or Jmol scripting, or whatever else you think is relevant. If you want to participate, you must become a user in the Wiki.

More official, general and static information about Jmol is available in the Jmol web site. (But content there is currently quite outdated)

Sections

About Jmol and JSmol License (terms of use) J(S)mol videos J(S)mol events Recycling Corner Recycling Corner Logos, Banners, Icons Templates for web pages Scripts you may reuse or adapt Customizing JSmol menus Jmol / JSmol Applications Websites Using J(S)mol J(S)mol in the Classroom Journals Using J(S)mol J(S)mol Literature Articles Using J(S)mol Books Using J(S)mol Wikis Using J(S)mol Blogs Using J(S)mol CMS Using J(S)mol (Moodle and others) Course Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms Applications Embedding Jmol Distributions Including Jmol Blue Obelisk Jmol/JSmol Community Community & users Communities: Crystal · Protein · Quantum Chemistry · Solid State · Folding@home List of users & their pages

Installing Jmol / JSmol Get the files from SourceForge. Support and operating systems. Users: how to install Jmol application for local, standalone use. Web page authors: how to install Jmol objects (Jmol / JSmol) embedded within your web pages. Installing and Enabling Java (Proteopedia wiki). Has step by step instructions for both Windows and Mac OS X, and for the 5 most popular web browsers. Increasing java memory for the applet. Web site administrators: How to install the application on a web server to be delivered using Java Web Start. How to configure a wiki so that it uses the Jmol applet. Developers: compile the latest Jmol source code via subversion access. Running Jmol / JSmol Jmol as a standalone application. J(S)mol as a web applet or HTML5 object. compatibility with JavaScript frameworks or libraries. J(S)mol embedded in wikis or blogs. Borrowed JSmol, or running JSmol without your own server. Running Jmol using Java Web Start. JSmol in a Jupyter notebook. Jmol in an Android tablet. Troubleshooting. Jmol / JSmol Tutorials A list of Jmol / JSmol Tutorials written by users. Using the mouse (English · Español · Français · Japanese). Scripting quickstart: rendering options · selecting atoms. How to create surfaces and isosurfaces, including cavities, pockets and tunnels. Displaying shapes, polyhedra, orbitals, dipoles, distances, forces and vibrations. Creating movies. Customizing Jmol: macros · menus. Web pages without writing code by using the Jmol "Export to Web" function.

Jmol/JSmol Development Getting Involved in J(S)mol evolution Release Procedures Important! Use the Jmol Coding Style Developing J(S)mol with Eclipse Internationalisation (status) ProgrammeerZomer / SummerOfCode MultiUser Jmol Developer mailing list (mirror) Jmol + JSmol Documentation Description of files in Jmol+JSmol distribution File formats read or written by Jmol The Jmol scripting interface Scripting as a programming language Complete reference of scripting commands: at St Olaf (primary site) at Jena3D (mirror) Loading models directly from databases Mouse manual Default colors used by Jmol Atom sets predefined in Jmol Support for bond orders · isotopes · stereochemistry · hydrogen bonds Jmol as editor Multi-touch support Copying and pasting state scripts between applets. Backward compatibility (changes of behavior across versions) Features added since version 10 Users mailing list (and a mirror)

Contributors

AngelHerraez, NicolasVervelle, Pimpim, EricMartz, Hansonr, JmolTest