Jmol

Jmol is written in the programming language Java, so it can run on different operating systems: Windows, macOS, Linux, and Unix, as long as they have Java installed. It is free and open-source software released under the GNU Lesser General Public License (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.
• 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 models, space-filling models, ribbon diagrams, molecular surfaces, etc.{{cite book

|last= Herráez |first= A

|year= 2007

|title= How to Use Jmol to Study and Present Molecular Structures, Volume 1

|isbn= 978-1-84799-259-8

|publisher= Lulu Enterprises: Morrisville, NC, USA

|page= 21

|url= https://books.google.com/books?id=59kQFyfbsJMC&q=jmol+applet+web&pg=PA21

}}

Jmol supports a wide range of chemical file formats, including Protein Data Bank (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{{citation

|last1= Willighagen |first1= Egon

|last2= Howard |first2= Miguel

|year= 2007

|title= Fast and scriptable molecular graphics in web browsers without Java3D

|journal= Nature Precedings

|doi= 10.1038/npre.2007.50.1

|url= http://precedings.nature.com/documents/50/version/1

|doi-access= free

}}

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){{cite web |url= https://chemapps.stolaf.edu/jmol/docs/ |title=Jmol/JSmol Scripting Documentation}} 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...

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 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

{{Portal|Free and open-source software}}

• Chemistry Development Kit (CDK)
• Comparison of software for molecular mechanics modeling
• List of free and open-source software packages
• List of molecular graphics systems
• Molecular graphics
• Molecule editor
• Proteopedia
• PyMOL
• SAMSON
• SMILES

{{Reflist}}

{{Commons category|Jmol}}

• [https://jmol.sourceforge.net/demo/ Demonstration of JSmol capabilities]. A simple page with interactive demonstrations of several features of JSmol embedded in the page.
• [https://jmol.sourceforge.net/ Jmol website] (Official website, though not fully up to date)
• [http://wiki.jmol.org/ Jmol Wiki] (active and updated) with, among other information, listings of [http://wiki.jmol.org/index.php/Websites_Using_Jmol websites], [http://wiki.jmol.org/index.php/Wikis_Using_Jmol wikis], and [http://wiki.jmol.org/index.php/Moodles_Using_Jmol moodles]

• {{cite journal |url=https://doi.org/10.1002/ijch.201300024 |title= JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia |first1= Robert M. |last1= Hanson |first2= Jaime |last2= Prilusky |first3= Zhou |last3= Renjian |first4= Takanori |last4= Nakane |first5= Joel L. |last5= Sussman |journal= Israel Journal of Chemistry |date= 2013 |doi= 10.1002/ijch.201300024 |url-access= subscription }}
• Jmol extension at MediaWiki.
• [https://sourceforge.net/p/jmol/wiki/MW%20Extension/ Jmol extension for MediaWiki] at SourceForge.
• [http://wiki.jmol.org/index.php/MediaWiki/Extension Jmol extension for MediaWiki] at JmolWiki.
• [https://proteopedia.org Proteopedia - Life in 3D], a collaborative and free 3D-encyclopedia of proteins and other biomolecules. (Uses Jmol Extension as a core component)
• [https://biomodel.uah.es/en/ Biomodel] Complements for learning biochemistry and molecular biology.
• [https://molview.org/ Molview]

Category:Chemistry software for Linux

Category:Free chemistry software

Category:Free software programmed in Java (programming language)

Category:Molecular modelling software

{{Chemistry software}}