Jmol

<h2 id="software">Software</h2>
<p>Jmol is written in the programming language <a href="/facts/Java_(programming_language)/9ScgFyAL">Java</a>, so it can run on different operating systems: <a href="/facts/Microsoft_Windows/bwhAhuSL">Windows</a>, <a href="/facts/MacOS/Y93vVpTm">macOS</a>, <a href="/facts/Linux/9FvCKSTq">Linux</a>, and <a href="/facts/Unix/0pNL2seI">Unix</a>, as long as they have Java installed. It is <a href="/facts/Free_and_open-source_software/1cHtjLCB">free and open-source software</a> released under the <a href="/facts/GNU_Lesser_General_Public_License/AXwkz9x3">GNU Lesser General Public License</a> (LGPL) version 2.0. The interface is translated into more than 20 languages.
</p><p>There are several products implemented:
</p>
<ul><li>A standalone application (the <i>Jmol application</i>), composed of a single Jmol.jar file that can be used without installation, requiring only that the computer has Java installed.</li>
<li>A <a href="/facts/Software_development_kit/2Hkk6Hbs">software development kit</a> (SDK), i.e. a component that can be integrated into other Java applications, such as <a href="/facts/Bioclipse/BevNhVk0">Bioclipse</a> and <a href="/facts/Apache_Taverna/Y2v63Cax">Taverna</a>.</li>
<li><i>JSmol</i>, a JavaScript library that allows integration of the 3D models in web pages and wikis.</li></ul>
<p>Molecules can be displayed in different styles of rendering, like <a href="/facts/Ball-and-stick_model/0FQhyys8">ball-and-stick models</a>, <a href="/facts/Space-filling_model/PcHWmvfV">space-filling models</a>, <a href="/facts/Ribbon_diagram/vMKYBAT5">ribbon diagrams</a>, <a href="/facts/Molecular_surface/DWmtEjRC">molecular surfaces</a>, etc.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a>
Jmol supports a wide range of <a href="/facts/Chemical_file_format/3G2T4rSk">chemical file formats</a>, including <a href="/facts/Protein_Data_Bank_(file_format)/NEMP1sAX">Protein Data Bank</a> (pdb), <a href="/facts/Crystallographic_Information_File/K1BmBU3h">Crystallographic Information File</a> (cif and mmcif), <a href="/facts/MDL_Molfile/WG8N7EhF">MDL Molfile</a> (mol and sdf), and <a href="/facts/Chemical_Markup_Language/40QHM0HD">Chemical Markup Language</a> (CML). 
It can also display other types of files for structures with 3D data.
</p><p>JSmol replaced the Jmol Java applet, which in turn had been previously developed as an alternative to the <a href="/facts/MDL_Chime/vx2XLyKk">Chime</a> plug-in,<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> both of which became unsupported by web browsers. Jmol was initiated<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a>
to reproduce functions present in Chime (with the exception of the <i>Sculpt</i> 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 (<i>JmolScript</i>)<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> that includes many characteristics of a programming language, such as variables, arrays, mathematical and Boolean operators, <a href="/facts/SQL/UjQLJcYm">SQL</a>-like queries, functions, loops, conditionals, try-catch, switch...
</p>
<h2 id="screenshots">Screenshots</h2>

<h2 id="see-also">See also</h2>
<ul>
<li>Free and open-source software portal</li></ul>
<ul><li><a href="/facts/Chemistry_Development_Kit/9hoeQIBp">Chemistry Development Kit</a> (CDK)</li>
<li><a href="/facts/Comparison_of_software_for_molecular_mechanics_modeling/RabeF7vR">Comparison of software for molecular mechanics modeling</a></li>
<li><a href="/facts/List_of_free_and_open-source_software_packages/l3x4PXwn">List of free and open-source software packages</a></li>
<li><a href="/facts/List_of_molecular_graphics_systems/syVkGJf4">List of molecular graphics systems</a></li>
<li><a href="/facts/Molecular_graphics/rLuIm8hP">Molecular graphics</a></li>
<li><a href="/facts/Molecule_editor/0qIez2t8">Molecule editor</a></li>
<li><a href="/facts/Proteopedia/C2LhX6kn">Proteopedia</a></li>
<li><a href="/facts/PyMOL/SbMJ9lPl">PyMOL</a></li>
<li><a href="/facts/SAMSON/YQltsErB">SAMSON</a></li>
<li><a href="/facts/SMILES/NUzV73WA">SMILES</a></li></ul>

<h2 id="external-links">External links</h2>

Wikimedia Commons has media related to Jmol.

<ul><li><a href="https://jmol.sourceforge.net/demo/">Demonstration of JSmol capabilities</a>. A simple page with interactive demonstrations of several features of JSmol embedded in the page.</li>
<li><a href="https://jmol.sourceforge.net/">Jmol website</a> (Official website, though not fully up to date)</li>
<li><a href="http://wiki.jmol.org/">Jmol Wiki</a> (active and updated) with, among other information, listings of <a href="http://wiki.jmol.org/index.php/Websites_Using_Jmol">websites</a>, <a href="http://wiki.jmol.org/index.php/Wikis_Using_Jmol">wikis</a>, and <a href="http://wiki.jmol.org/index.php/Moodles_Using_Jmol">moodles</a></li>
<li>Hanson, Robert M.; Prilusky, Jaime; Renjian, Zhou; Nakane, Takanori; Sussman, Joel L. (2013). <a href="https://doi.org/10.1002/ijch.201300024">"JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia"</a>. <i>Israel Journal of Chemistry</i>. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1002%2Fijch.201300024">10.1002/ijch.201300024</a>.</li>
<li>Jmol extension at MediaWiki.</li>
<li><a href="https://sourceforge.net/p/jmol/wiki/MW%20Extension/">Jmol extension for MediaWiki</a> at SourceForge.</li>
<li><a href="http://wiki.jmol.org/index.php/MediaWiki/Extension">Jmol extension for MediaWiki</a> at JmolWiki.</li>
<li><a href="https://proteopedia.org">Proteopedia - Life in 3D</a>, a collaborative and free 3D-encyclopedia of proteins and other biomolecules. <i>(Uses Jmol Extension as a core component)</i></li>
<li><a href="https://biomodel.uah.es/en/">Biomodel</a> Complements for learning biochemistry and molecular biology.</li>
<li><a href="https://molview.org/">Molview</a></li></ul>

<h2 id="references">References</h2>

<ol>
<li id="fn:1"><p>Chen, Jim X. (2008), Springer (ed.), Guide to Graphics Software Tools, p. 471, ISBN 978-1-84800-900-4 <a href="978-1-84800-900-4" target="_blank">978-1-84800-900-4</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li>
<li id="fn:2"><p>"How to cite Jmol". <a href="https://jmol.sourceforge.net/#How%20to%20cite%20Jmol" target="_blank">https://jmol.sourceforge.net/#How%20to%20cite%20Jmol</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li>
<li id="fn:3"><p>"JSmol". Retrieved 2025-01-11. <a href="http://wiki.jmol.org/index.php/JSmol" target="_blank">http://wiki.jmol.org/index.php/JSmol</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li>
<li id="fn:4"><p>Herráez, A (2006), "Biomolecules in the Computer: Jmol to the Rescue", Biochemistry and Molecular Biology Education, 34 (4): 255–61, doi:10.1002/bmb.2006.494034042644, PMID 21638687, S2CID 36319720 <a href="http://eric.ed.gov/ERICWebPortal/recordDetail?accno=EJ759053" target="_blank">http://eric.ed.gov/ERICWebPortal/recordDetail?accno=EJ759053</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li>
<li id="fn:5"><p>Hanson, Robert M. (2010), "Jmol – a paradigm shift in crystallographic visualization", Journal of Applied Crystallography, 43 (5): 1250–1260, doi:10.1107/S0021889810030256 <a href="https://journals.iucr.org/j/issues/2010/05/02/kk5066/" target="_blank">https://journals.iucr.org/j/issues/2010/05/02/kk5066/</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li>
<li id="fn:6"><p>Herráez, A (2007). How to Use Jmol to Study and Present Molecular Structures, Volume 1. Lulu Enterprises: Morrisville, NC, USA. p. 21. ISBN 978-1-84799-259-8. <a href="978-1-84799-259-8" target="_blank">978-1-84799-259-8</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li>
<li id="fn:7"><p>Herráez, A (2006), "Biomolecules in the Computer: Jmol to the Rescue", Biochemistry and Molecular Biology Education, 34 (4): 255–61, doi:10.1002/bmb.2006.494034042644, PMID 21638687, S2CID 36319720 <a href="http://eric.ed.gov/ERICWebPortal/recordDetail?accno=EJ759053" target="_blank">http://eric.ed.gov/ERICWebPortal/recordDetail?accno=EJ759053</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li>
<li id="fn:8"><p>Willighagen, Egon; Howard, Miguel (2007), "Fast and scriptable molecular graphics in web browsers without Java3D", Nature Precedings, doi:10.1038/npre.2007.50.1 <a href="http://precedings.nature.com/documents/50/version/1" target="_blank">http://precedings.nature.com/documents/50/version/1</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li>
<li id="fn:9"><p>"Jmol/JSmol Scripting Documentation". <a href="https://chemapps.stolaf.edu/jmol/docs/" target="_blank">https://chemapps.stolaf.edu/jmol/docs/</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li>
</ol>

Jmol open-in-new

Jmol