Jmol is an open-source Java viewer

File viewer

A file viewer is application software that presents the data stored in a computer file in a human-friendly form. The file contents are generally displayed on the screen, or they may be printed...

 for chemical structures in 3D

3D computer graphics

3D computer graphics are graphics that use a three-dimensional representation of geometric data that is stored in the computer for the purposes of performing calculations and rendering 2D images...

,
that does not require 3D acceleration plugins.
Jmol returns a 3D representation of a molecule

Molecule

A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

 that may be used as a teaching tool, or for research e.g. in chemistry

Chemistry

Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds....

 and biochemistry

Biochemistry

Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...

.
It is free and open source software

Free and open source software

Free and open-source software or free/libre/open-source software is software that is liberally licensed to grant users the right to use, study, change, and improve its design through the availability of its source code...

, written in Java

Java (programming language)

Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

 and so it runs on Windows

Microsoft Windows

Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...

, Mac OS X

Mac OS X

Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Linux

Linux

Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

 and Unix

Unix

Unix is a multitasking, multi-user computer operating system originally developed in 1969 by a group of AT&T employees at Bell Labs, including Ken Thompson, Dennis Ritchie, Brian Kernighan, Douglas McIlroy, and Joe Ossanna...

 systems.
There is a standalone application and a development tool kit that can be integrated into other Java applications, such as Bioclipse

Bioclipse

The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform...

 and Taverna

Taverna workbench

Taverna Workbench is an open source software tool for designing and executing workflows, created by the myGrid project and funded through the OMII-UK...

.

A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways.
For example, molecules can be displayed as "ball and stick" models, "space filling" models, "ribbon" models, etc.
Jmol supports a wide range of molecular file formats

Chemical file format

This article discusses some common molecular file formats, including usage and converting between them.-Distinguishing formats:Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format can be found by three...

, including Protein Data Bank

Protein Data Bank (file format)

The Protein Data Bank file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed...

 (pdb), Crystallographic Information File

Crystallographic Information File

Crystallographic Information File is a standard text file format for representing crystallographic information, promulgated by the International Union of Crystallography . CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on...

 (cif), MDL Molfile (mol), and Chemical Markup Language

Chemical Markup Language

CML is an approach to managing molecular information using tools such as XML and Java. It was the first domain specific implementation based strictly on XML, first based on a DTD and later on XML Schema, the most robust and widely used system for precise information management in many areas...

 (CML).

The Jmol applet, among other capabilities, offers an alternative to the Chime

MDL Chime

MDL Chime is a free plugin used by web browsers to display the three dimensional structures of molecules. It is part of the ISIS product line acquired by Symyx Technologies from scientific publisher Elsevier in October 2007. It is based on the RasMol code.Chime is used by a wide range of...

 plugin, which is no longer under active development. While Jmol has many features that are not available in Chime, it does not claim to reproduce all Chime functionality (most notably, Chime's Sculpt mode). Chime requires plug-in installation and Internet Explorer

Internet Explorer

Windows Internet Explorer is a series of graphical web browsers developed by Microsoft and included as part of the Microsoft Windows line of operating systems, starting in 1995. It was first released as part of the add-on package Plus! for Windows 95 that year...

 6.0 or Firefox 2.0

Mozilla Firefox 2

Mozilla Firefox 2 was a version of Firefox, a web browser released on October 24, 2006 by the Mozilla Corporation.Firefox 2 uses version 1.8 of the Gecko layout engine for displaying web pages...

 on Microsoft Windows

Microsoft Windows

Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...

, or OS 9/Netscape Communicator

Netscape Communicator

Netscape Communicator was an Internet suite produced by Netscape Communications Corporation. Initially released in June 1997, Netscape Communicator 4.0 was the successor to Netscape Navigator 3.x and included more groupware features intended to appeal to enterprises.- Editions :Netscape...

 4.8 on the Macintosh

Macintosh

The Macintosh , or Mac, is a series of several lines of personal computers designed, developed, and marketed by Apple Inc. The first Macintosh was introduced by Apple's then-chairman Steve Jobs on January 24, 1984; it was the first commercially successful personal computer to feature a mouse and a...

. Jmol requires Java

Java (programming language)

Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

 installation and operates on a wide variety of platforms. For example, Jmol is fully functional in Mozilla Firefox

Mozilla Firefox

Mozilla Firefox is a free and open source web browser descended from the Mozilla Application Suite and managed by Mozilla Corporation. , Firefox is the second most widely used browser, with approximately 25% of worldwide usage share of web browsers...

, Internet Explorer

Internet Explorer

Windows Internet Explorer is a series of graphical web browsers developed by Microsoft and included as part of the Microsoft Windows line of operating systems, starting in 1995. It was first released as part of the add-on package Plus! for Windows 95 that year...

, Opera

Opera (web browser)

Opera is a web browser and Internet suite developed by Opera Software with over 200 million users worldwide. The browser handles common Internet-related tasks such as displaying web sites, sending and receiving e-mail messages, managing contacts, chatting on IRC, downloading files via BitTorrent,...

 and Google Chrome on Microsoft Windows

Microsoft Windows

Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...

, in Mozilla Firefox

Mozilla Firefox

Mozilla Firefox is a free and open source web browser descended from the Mozilla Application Suite and managed by Mozilla Corporation. , Firefox is the second most widely used browser, with approximately 25% of worldwide usage share of web browsers...

 and Google Chrome on Linux

Linux

Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, and in Safari

Safari (web browser)

Safari is a web browser developed by Apple Inc. and included with the Mac OS X and iOS operating systems. First released as a public beta on January 7, 2003 on the company's Mac OS X operating system, it became Apple's default browser beginning with Mac OS X v10.3 "Panther". Safari is also the...

 on Mac OS X

Mac OS X

Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

.

__notoc__

See also

• List of molecular graphics systems
• List of software for molecular mechanics modeling
• Chemistry Development Kit
  Chemistry Development Kit
  The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS...
  
   (CDK)
• Molecular graphics
  Molecular graphics
  Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device"...
  
  
• Proteopedia
  Proteopedia
  Proteopedia is a wiki, 3D encyclopedia of proteins and other molecules..The site contains a page for every entry in the Protein Data Bank , as well as pages that are more descriptive of protein structures in general such as acetylcholinesterase, hemoglobin, and the photosystem II with a Jmol view...
  
  
• PyMOL
  PyMOL
  PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities...
  
  
• Jmol extension for MediaWiki

External links

• Jmol official web site
• Jmol wiki where a list of Websites, Wikis, Moodles, ... using Jmol is available