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Jmol / JSmol Applications

Jmol Literature

This section is devoted to published articles that describe Jmol features or uses.

Please add additional literature (sorted on descending publication year):

  • Angel Herráez, Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1, 2007, ISBN 978-1-84753-710-2. Published by
    (In Spanish; English translation in preparation) A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels. info, preview and on-line shop
  • Angel Herráez, Biomolecules in the computer: Jmol to the rescue, Biochemistry and Molecular Biology Education, 2006, 34(4): 255-261.
    A review of Jmol project and features, in comparison to Rasmol and Chime. abstract
  • Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend and Gilbert Vassart, GRIS: Glycoprotein-hormone Receptor Information System., Molecular Endocrinology, 2006, doi:10.1210/me.2006-0020 (Rapid Electronic Publication). The article can be downloaded here.
  • M.E. Cass, H.S. Rzepa, D.R. Rzepa, et al., The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry, Journal of Chemical Education, 2005, 82(11):1736-1740
  • Jason E. Donald, Isaac A. Hubner, Veronica M. Rotemberg, Eugene I. Shakhnovich and Leonid A. Mirny, CoC: a database of universally conserved residues in protein folds, Bioinformatics, 2005, vol 21, 2539-2540
    Described the CoC database which uses Jmol for visualisation. abstract
  • Egon Willighagen and Miguel Howard, Jmol as 3D Viewer for CDK, CDK News, 2005, vol 2, issue 1, 17-20
    Shows how Jmol can be embedded in other Java programs, in this case the Chemistry Development Kit specifically. The article can be downloaded here.
  • Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, and J. Gasteiger, Enabling the exploration of biochemical pathways, Org.Biomol.Chem., 2004, 3226-3237
    Introduces a pathway database that uses Jmol to visualize molecules.
  • Peter Murray-Rust, Henry S. Rzepa, Mark J. Williamson, and Egon L. Willighagen, Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators, J.Chem.Inf.Comp.Sci., 2004
    Describes a CDK plugin that acts as a RSS agregator and show its application as pluged in Jmol abstract.
  • Anreas Bohne-Lang, and Elke Lang, 3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets, BIOspektrum, 2004
    Compares Jmol with other chemistry visualisation applets.
  • Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, and Egon Willighagen, The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics, J.Chem.Inf.Comp.Sci., 2003
    Describes CDK the library on which Jmol v6 to v9 is build abstract.
  • E.L. Willighagen, Processing CML Conventions in Java, Internet Journal of Chemistry, 4, 2001
    Describes how Jmol upto and including v9 read CML abstract.