Jmol

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  2. Chemistry software
  3. Molecular modelling software
  4. Bioinformatics software
  5. Free science software
  6. Free software programmed in Java
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Jmol
The Jmol logo.
260px
Jmol is a Java molecular viewer for three-dimensional chemical structures.
Developer(s) Jmol development team
Stable release 12.2.24  (8 May 2012 (2012-05-08)) [±]
Preview release 12.3.24  (8 May 2012 (2012-05-08)) [±]
Written in Java
Operating system Cross-platform
Available in Catalan, Chinese, Czech, Danish, Dutch, English, French, German, Hungarian, Indonesian, Italian, Korean, Portuguese, Spanish, Turkish, Ukrainian[1]
Type Molecular modelling
License LGPL
Website www.jmol.org and wiki.jmol.org

Jmol is an open-source Java viewer for chemical structures in 3D,[2] that does not require 3D acceleration plugins.[3] Jmol returns a 3D representation of a molecule that may be used as a teaching tool,[4] or for research e.g. in chemistry and biochemistry. It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems. There is a standalone application and a development tool kit 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" models, etc.[5] Jmol supports a wide range of molecular file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML).[6]

The Jmol applet, among other capabilities, offers an alternative to the Chime plugin,[4] which is no longer under active development. While Jmol has many features that are not available in Chime, it does not claim to reproduce all Chime functionality (most notably, Chime's 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 the MacintoshOS9. 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

  • Jmol screenshot 2hvy.jpg

    Crystal structure of an H/ACA box RNP from Pyrococcus furiosus.

  • Jmol screenshot hemoglobin.png

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

  • Jmol screenshot zincfinger.png

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

  • Jmol screenshot thermus ribosome 1jgo and 1giy.jpg

    Eubacterial 70S Ribosome from Thermus thermophilus.

See also

32x28px Free software portal

References

  1. ↑ Jmol translations
  2. ↑ Chen, Jim X. (2008), Springer, ed., Guide to Graphics Software Tools, p. 471, ISBN 978-1-84800-900-4, http://books.google.com/?id=Rv2gncprg3gC&pg=PA471&dq=jmol+is+3d#v=onepage&q=jmol%20is%203d&f=false
  3. ↑ Willighagen, E.; Howard, M. (2007), "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D", Nature Preceedings, doi:10.1038/npre.2007.50.1, http://precedings.nature.com/documents/50/version/1
  4. ↑ 4.0 4.1 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, http://eric.ed.gov/ERICWebPortal/recordDetail?accno=EJ759053
  5. ↑ 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, http://books.google.com/?id=59kQFyfbsJMC&pg=PA21&dq=jmol+applet+web#v=onepage&q=jmol%20applet%20web&f=false
  6. ↑ Willighagen, E (2001), "Processing CML conventions in Java", Internet Journal of Chemistry 4 (4): 1–9, http://www.mendeley.com/download/public/2225521/3634250982/f7c33288f4a8512172f0810947f082c55fbe72d3/dl.pdf

External links

Notes


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