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The Info List - JSmol



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JMOL is computer software for molecular modelling chemical structures in 3-dimensions . Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry . It is written in the programming language Java , so it can run on the operating systems Windows , macOS , Linux , and Unix , if Java is installed. It is free and open-source software released under a GNU Lesser General Public License (LGPL) version 2.0. A standalone application and a software development kit (SDK) exist that can be integrated into other Java applications, such as Bioclipse and Taverna .

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 diagrams , etc. Jmol supports a wide range of chemical file formats , including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML). There is also a JavaScript -only ( HTML5 ) 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 6.0 or Firefox 2.0 on Microsoft Windows , or Netscape Communicator 4.8 on Mac OS 9 . Jmol requires Java installation and operates on a wide variety of platforms. For example, Jmol is fully functional in Mozilla Firefox , Internet Explorer , Opera , Google Chrome , and Safari .

SCREENSHOTS

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Crystal structure of an H/ACA box RNP from _Pyrococcus furiosus_. *

Highlighting two salt bridges in hemoglobin tetramer (hemo group as sticks at bottom-right). *

A fragment of transcription factor TFIIIA forming three consecutive zinc finger motifs, bound to a stretch of DNA. *

Eubacterial 70S Ribosome from _Thermus thermophilus_.

SEE ALSO

* Free software portal

* Chemistry Development Kit (CDK) * Comparison of software for molecular mechanics modeling * Jmol extension for MediaWiki * List of molecular graphics systems * Molecular graphics * Molecule editor * Proteopedia * PyMOL * SAMSON

REFERENCES

* ^ Jmol translations * ^ Chen, Jim X. (2008), Springer, ed., _Guide to Graphics Software Tools_, p. 471, ISBN 978-1-84800-900-4 * ^ _A_ _B_ Herráez, A (2006), "Biomolecules in the Computer: Jmol to the Rescue", _ Biochemistry and Molecular Biology Education_, 34 (4): 7, doi :10.1002/bmb.2006.494034042644 * ^ Herráez, A (2007), Lulu, ed., _How to Use Jmol to Study and Present Molecular Structures, Volume 1_, p. 21, ISBN 978-1-84799-259-8 * ^ Willighagen, E (2001), "Processing CML conventions in Java" (PDF), _Internet Journal of Chemistry_, 4 (4): 1–9 * ^ "JSmol". Retrieved 2015-11-02.

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