Jmol

From Encoresoup - The Ultimate Guide to Free/Open Source Software

Jmol is a molecule viewer for use in chemistry and biochemistry. It is free and open source. It can be used as a teaching tool or in research. It is Java based and 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. The most notable 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", etc. 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).

The Jmol applet, among other capabilities, offers an alternative to the Chime plugin, 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 Mozilla Firefox 2 on Microsoft Windows, or OS 9/Netscape Communicator 4.8 on the Macintosh. Jmol requires Java installation and operates on a wide variety of platforms. Jmol is fully functional in Mozilla Firefox on Microsoft Windows and Linux, and in Safari on Mac OS X.

Version 11.4 of Jmol was released in January 2008.

[edit] Screenshots

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.

[edit] See also

• CDK
• Molecular graphics

[edit] External links

• Jmol web site
• Jmol Wiki
• FirstGlance in Jmol, an easy web-based user-interface for seeing the major structural features of any macromolecule in Jmol.
• Websites using Jmol
• Wikis using Jmol
• Moodles using Jmol
• MolviZ.Org: Jmol-based tutorials on DNA Structure, Hemoglobin, Lipid Bilayers and Channels, and more.
• Dublin City University CHIME and Jmol Pages
• A lecture course on pericyclic reactions using Jmol
• Molecular symmetry illustrated using Jmol
• Berry and other modes of pseudorotation illustrated using Jmol
• Molecular modelling case studies illustrated using Jmol

[edit] Notes