Jmol is computer

software Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work. ...

for

molecular modelling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials sci ...

chemical structure A chemical structure determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of ...

s in 3-dimensions. Jmol returns a 3D representation of a

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...

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

biochemistry Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology and ...

. It is written in the programming language

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mos ...

, so it can run on the operating systems

Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for ser ...

macOS macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac computers. Within the market of desktop and lapt ...

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, w ...

, and

Unix Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, an ...

, if Java is installed. It is free and open-source software released under a

GNU Lesser General Public License The GNU Lesser General Public License (LGPL) is a free-software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate a software component released under the LGPL into their own ...

(LGPL) version 2.0. A standalone application and a

software development kit A software development kit (SDK) is a collection of software development tools in one installable package. They facilitate the creation of applications by having a compiler, debugger and sometimes a software framework. They are normally specific ...

(SDK) exist that can be integrated into other Java applications, such as Bioclipse and

Taverna A taverna (Greek: ταβέρνα) is a small Greek restaurant that serves Greek cuisine. The taverna is an integral part of Greek culture and has become familiar to people from other countries who visit Greece, as well as through the establishme ...

. 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 model In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods ...

s, space-filling models, ribbon diagrams, etc. Jmol supports a wide range of

chemical file format A chemical file format is a type of data file which is used specifically to depicting molecular data. One of the most widely used is the chemical table file format, which is similar to ''Structure Data Format'' (SDF) files. They are text files ...

s, including

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, ...

(pdb),

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

(cif),

MDL Molfile Chemical table file (CT File) is a family of text-based chemical file formats that describe molecules and chemical reactions. One format, for example, lists each atom in a molecule, the x-y-z coordinates of that atom, and the bonds among the atoms. ...

(mol), and

Chemical Markup Language Chemical Markup Language (ChemML or 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 an XML Schema, t ...

(CML). There is also a

JavaScript JavaScript (), often abbreviated as JS, is a programming language that is one of the core technologies of the World Wide Web, alongside HTML and CSS. As of 2022, 98% of websites use JavaScript on the client side for webpage behavior, of ...

-only (

HTML5 HTML5 is a markup language used for structuring and presenting content on the World Wide Web. It is the fifth and final major HTML version that is a World Wide Web Consortium (W3C) recommendation. The current specification is known as the HTML ...

) version, ''JSmol'', that can be used on computers with no Java. The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the ''Sculpt'' mode. Chime requires plug-in installation and

Internet Explorer Internet Explorer (formerly Microsoft Internet Explorer and Windows Internet Explorer, commonly abbreviated IE or MSIE) is a series of graphical web browsers developed by Microsoft which was used in the Windows line of operating systems ( ...

6.0 or Firefox 2.0 on Microsoft Windows, or

Netscape Communicator Netscape Communicator (or ''Netscape 4'') is a discontinued Internet suite produced by Netscape Communications Corporation, and was the fourth major release in the Netscape line of browsers. It was first in beta in 1996 and was released in June ...

4.8 on Mac OS 9. Jmol requires

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

Opera Opera is a form of theatre in which music is a fundamental component and dramatic roles are taken by singers. Such a "work" (the literal translation of the Italian word "opera") is typically a collaboration between a composer and a libr ...

, Google Chrome, and Safari. __NOTOC__

Screenshots

File:Jmol screenshot 2hvy.jpg, Crystal structure of an H/ACA box RNP from ''Pyrococcus furiosus''. File:Jmol screenshot hemoglobin.png, Highlighting two salt bridges in hemoglobin tetramer (hemo group as sticks at bottom-right). File:Jmol screenshot zincfinger.png, A fragment of transcription factor TFIIIA forming three consecutive zinc finger motifs, bound to a stretch of DNA. File:Jmol screenshot thermus ribosome 1jgo and 1giy.jpg, Eubacterial 70S Ribosome from ''Thermus thermophilus''.

Screenshots

See also

References

External links