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Jmol is computer
software Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital comput ...
for molecular modelling of
chemical structure A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target m ...
s in 3 dimensions. It is an
open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...
Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the mol file format. JSmol is an implementation in JavaScript of the functionality of Jmol. It can hence be embedded in web pages to display interactive 3D models of molecules and other structures without the need for any software apart from the web browser (''it does not use Java''). Both Jmol and JSmol render an interactive 3D representation of a
molecule A molecule is a group of two or more atoms that are held together by Force, attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemi ...
or other structure that may be used as a teaching tool, or for research, in several fields, e.g.
chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a physical science within the natural sciences that studies the chemical elements that make up matter and chemical compound, compounds made of atoms, molecules a ...
,
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, a ...
,
materials science Materials science is an interdisciplinary field of researching and discovering materials. Materials engineering is an engineering field of finding uses for materials in other fields and industries. The intellectual origins of materials sci ...
,
crystallography Crystallography is the branch of science devoted to the study of molecular and crystalline structure and properties. The word ''crystallography'' is derived from the Ancient Greek word (; "clear ice, rock-crystal"), and (; "to write"). In J ...
,
symmetry Symmetry () in everyday life refers to a sense of harmonious and beautiful proportion and balance. In mathematics, the term has a more precise definition and is usually used to refer to an object that is Invariant (mathematics), invariant und ...
or
nanotechnology Nanotechnology is the manipulation of matter with at least one dimension sized from 1 to 100 nanometers (nm). At this scale, commonly known as the nanoscale, surface area and quantum mechanical effects become important in describing propertie ...
.


Software

Jmol is written in the programming language
Java Java is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea (a part of Pacific Ocean) to the north. With a population of 156.9 million people (including Madura) in mid 2024, proje ...
, so it can run on different operating systems:
Windows Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...
,
macOS macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...
,
Linux Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...
, and
Unix Unix (, ; trademarked as UNIX) is a family of multitasking, multi-user 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, a ...
, as long as they have Java installed. It is
free and open-source software Free and open-source software (FOSS) is software available under a license that grants users the right to use, modify, and distribute the software modified or not to everyone free of charge. FOSS is an inclusive umbrella term encompassing free ...
released under the
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. The interface is translated into more than 20 languages. There are several products implemented: * A standalone application (the ''Jmol application''), composed of a single Jmol.jar file that can be used without installation, requiring only that the computer has Java installed. * A software development kit (SDK), i.e. a component that can be integrated into other Java applications, such as Bioclipse and
Taverna A taverna (; ) 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 establishment of tavernes ...
. * ''JSmol'', a JavaScript library that allows integration of the 3D models in web pages and wikis. Molecules can be displayed in different styles of rendering, like
ball-and-stick model In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the Molecular geometry, three-dimensional position of the atoms and the chemical bond, bonds between them. The atoms are typically represente ...
s, space-filling models,
ribbon diagram Ribbon diagrams, also known as Richardson diagrams, are three-dimensional space, 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and o ...
s, molecular surfaces, etc. Jmol supports a wide range of
chemical file format A chemical file format is a type of data file which is used specifically for 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, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...
(pdb), Crystallographic Information File (cif and mmcif), MDL Molfile (mol and sdf), and Chemical Markup Language (CML). It can also display other types of files for structures with 3D data. JSmol replaced the Jmol Java applet, which in turn had been previously developed as an alternative to the Chime plug-in, both of which became unsupported by web browsers. Jmol was initiated to reproduce functions present in Chime (with the exception of the ''Sculpt'' mode) and has been continuously growing in features, surpassing the simple display of molecular structures. Most notably, it has a large set of commands and a thorough scripting language (''JmolScript'') that includes many characteristics of a programming language, such as variables, arrays, mathematical and Boolean operators, SQL-like queries, functions, loops, conditionals, try-catch, switch...


Screenshots

File:Jmol screenshot symmetry.png, Two translucent planes illustrating symmetry planes for the water molecule. File:Jmol screenshot electrostatic potential.png, The electrostatic potential of allene mapped onto a translucent surface. File:Jmol screenshot measurements-1.png, A shaded rendering of caffeine, with some measurements shown (distance, angle, dihedral) File:Jmol screenshot animated SN2.gif, An SN2 reaction animated displaying the distance measured between the chlorine and carbon atoms. File:Jmol screenshot crystal.png, Display of quartz crystal structure, filling 2×2×2 unit cells. The unit cell boundbox is drawn and the unit cell data are shown on upper left. File:Jmol screenshot orbitals.png, Cartoon p-orbitals of benzene together with the corresponding translucent molecular orbital. File:Jmol screenshot 2hvy.jpg, Crystal structure of an H/ACA box RNP from '' Pyrococcus furiosus'' File:Jmol screenshot hemoglobin.png, Highlighting two
salt bridge In electrochemistry, a salt bridge or ion bridge is an essential laboratory device discovered over 100 years ago. It contains an electrolyte solution, typically an inert solution, used to connect the Redox, oxidation and reduction Half cell, ...
s in
hemoglobin Hemoglobin (haemoglobin, Hb or Hgb) is a protein containing iron that facilitates the transportation of oxygen in red blood cells. Almost all vertebrates contain hemoglobin, with the sole exception of the fish family Channichthyidae. Hemoglobin ...
tetramer (hemo group as sticks at bottom-right) File:Jmol screenshot zincfinger.png, A fragment of
transcription factor In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription (genetics), transcription of genetics, genetic information from DNA to messenger RNA, by binding t ...
TFIIIA forming three consecutive zinc finger motifs, bound to a stretch of
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
File:Jmol screenshot thermus ribosome 1jgo and 1giy.jpg, Eubacterial 70S Ribosome from '' Thermus thermophilus''


See also

* Chemistry Development Kit (CDK) *
Comparison of software for molecular mechanics modeling This is a list of computer programs that are predominantly used for molecular mechanics calculations. See also *Car–Parrinello molecular dynamics *Comparison of force-field implementations *Comparison of nucleic acid simulation software * ...
*
List of free and open-source software packages This is a list of free and open-source software (FOSS) packages, computer software licensed under free software licenses and open-source licenses. Software that fits the Free Software Definition may be more appropriately called free software; ...
* List of molecular graphics systems * Molecular graphics * Molecule editor * Proteopedia * PyMOL * SAMSON * SMILES


References


External links


Demonstration of JSmol capabilities
A simple page with interactive demonstrations of several features of JSmol embedded in the page.
Jmol website
(Official website, though not fully up to date)
Jmol Wiki
(active and updated) with, among other information, listings o
websiteswikis
an
moodles
* * Jmol extension at MediaWiki.
Jmol extension for MediaWiki
at SourceForge.
Jmol extension for MediaWiki
at JmolWiki.
Proteopedia - Life in 3D
a collaborative and free 3D-encyclopedia of proteins and other biomolecules. ''(Uses Jmol Extension as a core component)''
Biomodel
Complements for learning biochemistry and molecular biology.
Molview
Chemistry software for Linux Free chemistry software Free software programmed in Java (programming language) Molecular modelling software {{Chemistry software