Jmol

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Jmol
J(S)mol logo 2013.svg
Jmol screenshot streptavidin.png
Jmol, a Java molecular viewer for three-dimensional chemical structures
Developer(s) Jmol development team
Initial release 2001; 16 years ago (2001)
Stable release 14.6.4 (October 15, 2016; 3 months ago (2016-10-15)) [±]
Preview release 14.5.0 (7 November 2015; 14 months ago (2015-11-07)) [±]
Repository sourceforge.net/projects/jmol
Development status Active
Written in Java
Operating system Cross-platform
Platform Web browsers with Java
Available in 16 languages
Type Molecular modelling
License LGPL 2.0
Website www.jmol.org

Jmol is computer software for molecular modelling chemical structures in 3-dimensions.[2] Jmol returns a 3D representation of a molecule that may be used as a teaching tool,[3] 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.[4] 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).[5] There is also a JavaScript-only (HTML5) version, JSmol, that can be used on computers with no Java.[6]

The Jmol applet, among other abilities, offers an alternative to the Chime plug-in,[3] 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[edit]

  • 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[edit]

References[edit]

  1. ^ Jmol translations
  2. ^ Chen, Jim X. (2008), Springer, ed., Guide to Graphics Software Tools, p. 471, ISBN 978-1-84800-900-4 
  3. ^ 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 
  4. ^ 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 
  5. ^ Willighagen, E (2001), "Processing CML conventions in Java" (PDF), Internet Journal of Chemistry, 4 (4): 1–9 
  6. ^ "JSmol". Retrieved 2015-11-02. 

External links[edit]

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