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Jmol / JSmol Applications

This section is devoted to published articles and books 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. ISBN 978-1-84753-710-2. Published by (2007).
    (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 34(4): 255-261 (2006).
    A review of Jmol project and features, in comparison to Rasmol and Chime. doi:10.1002/bmb.2006.494034042644 Abstract
  • Interview with Martin Walker. Reactive Reports (2006).
  • Joost Van Durme, Florence Horn, Sabine Costagliola, Gert Vriend and Gilbert Vassart: GRIS: Glycoprotein-hormone Receptor Information System. Molecular Endocrinology 20(9): 2247-2255 (2006).
    doi:10.1210/me.2006-0020 Abstract and article
  • 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 82(11):1736-1740 (2005).
  • 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 21: 2539-2540 (2005).
    Described the CoC database which uses Jmol for visualisation. doi:10.1093/bioinformatics/bti360 Abstract
  • Egon Willighagen and Miguel Howard: Jmol as 3D Viewer for CDK. CDK News 2(1): 17-20 (2005).
    Shows how Jmol can be embedded in other Java programs, in this case the Chemistry Development Kit specifically. Article.
  • Martin Reitz, Oliver Sacher, Aleksey Tarkhov, Dietrich Trumbach, and J. Gasteiger: Enabling the exploration of biochemical pathways. Org.Biomol.Chem. 2(2): 3226-3237 (2004).
    Introduces a pathway database that uses Jmol to visualize molecules. doi:10.1039/B410949J Abstract and article
  • 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
  • Andreas 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 built. 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