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Jmol
Jmol
is computer software for molecular modelling chemical structures in 3-dimensions.[2] Jmol
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
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
Jmol
supports a wide range of chemical file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile
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
Jmol
applet, among other abilities, offers an alternative to the Chime plug-in,[3] which is no longer under active development. While Jmol
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
Internet Explorer
6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator
Netscape Communicator
4.8 on Mac OS 9. Jmol requires Java installation and operates on a wide variety of platforms. For example, Jmol
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]

Free software portal

Chemistry
Chemistry
Development Kit (CDK) Comparison of software for molecular mechanics modeling Jmol
Jmol
extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule
Molecule
editor Proteopedia PyMOL SAMSON

References[edit]

^ Jmol
Jmol
translations ^ Chen, Jim X. (2008), Springer, ed., Guide to Graphics Software Tools, p. 471, ISBN 978-1-84800-900-4  ^ a b Herráez, A (2006), "Biomolecules in the Computer: Jmol
Jmol
to the Rescue", Biochemistry
Biochemistry
and Molecular Biology Education, 34 (4): 7, doi:10.1002/bmb.2006.494034042644  ^ Herráez, A (2007), Lulu, ed., How to Use Jmol
Jmol
to Study and Present Molecular Structures, Volume 1, p. 21, ISBN 978-1-84799-259-8  ^ "JSmol". Retrieved 2015-11-02. 

External links[edit]

Wikimedia Commons has media related to Jmol.

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". doi:10.1038/npre.2007.50.1. 

v t e

Chemistry
Chemistry
software

Molecule
Molecule
modelling

Open-source
Open-source
(Ascalaph Designer Avogadro BALL Gabedit Ghemical Jmol Molekel PyMOL QuteMol) Proprietary (ACD/ChemSketch ChemDraw MarvinSketch MarvinView Molecular Operating Environment Spartan)

Skeletal structure
Skeletal structure
drawing

Open-source
Open-source
(BKChem Chemtool JChemPaint Molsketch SketchEl XDrawChem) Proprietary (ACD/ChemSketch ChemDoodle ChemDraw MarvinSketch)

Cheminformatics

Open-source
Open-source
(Avalon Cheminformatics Toolkit Avogadro Bioclipse Blue Obelisk Chemistry
Chemistry
Development Kit JOELib OELib Open Babel)

Computational chemistry

Open-source
Open-source
(APBS MPQC NWChem PSI PQS) Proprietary (Abalone DelPhi Firefly GAMESS (UK) GAMESS (US) Gaussian Q-Chem)

Others

CHROMuLAN CP2K GenX GSim

.