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Concept
Jmol
Summary
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 s, including (pdb), (cif), (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.
NOTOC
File:Jmol screenshot 2hvy.jpg|Crystal structure of an H/ACA box RNP from ''Pyrococcus furiosus''.
File:Jmol screenshot hemoglobin.png|Highlighting two salt bridges in hemoglobin tetramer (hemo group as sticks at bottom-right).
File:Jmol screenshot zincfinger.png|A fragment of transcription factor TFIIIA forming three consecutive zinc finger motifs, bound to a stretch of DNA.
File:Jmol screenshot thermus ribosome 1jgo and 1giy.
Official source
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