HOME
The Info List - JSmol



--- Advertisement ---


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

*

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 *