Jmol is a free molecular visualization program that allows you to explore protein structures in a fully interactive 3-dimensional display and 'design' protein models for 3D printing.

• Jmol /JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a 'headless' server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan.
• Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. Cross-platform, running on Windows, OS X, and Linux/Unix systems. The JmolApplet is a Web browser applet that can be integrated into Web pages. The Jmol application is a standalone Java application that runs on the desktop.

Jmol is computer software for molecular modellingchemical 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). There is also a JavaScript-only (HTML5) version, JSmol, that can be used on computers with no Java.^[5]

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]

• Chemistry Development Kit (CDK)

References[edit]

1. ^Jmol translations
2. ^Chen, Jim X. (2008), Springer (ed.), Guide to Graphics Software Tools, p. 471, ISBN978-1-84800-900-4
3. ^ ^abHerráez, A (2006), 'Biomolecules in the Computer: Jmol to the Rescue', Biochemistry and Molecular Biology Education, 34 (4): 255–61, doi:10.1002/bmb.2006.494034042644, PMID21638687, S2CID36319720
4. ^Herráez, A (2007), Lulu (ed.), How to Use Jmol to Study and Present Molecular Structures, Volume 1, p. 21, ISBN978-1-84799-259-8
5. ^'JSmol'. Archived from the original on 2018-01-01. Retrieved 2015-11-02.

External links[edit]

• Official website
  • Wiki with listings of websites, wikis, and moodles
• Willighagen, Egon; Howard, Miguel (June 2007). 'Fast and Scriptable Molecular Graphics in Web Browsers without Java3D'. Nature Precedings. doi:10.1038/npre.2007.50.1.

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