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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):

  • B. McMahon and Robert M. Hanson: A toolkit for publishing enhanced figures. Journal of Applied Crystallography, 41(4): 811-814 (2008)
    doi:10.1107/S0021889808015616 Abstract and article
  • Angel Herráez: How to use Jmol to study and present molecular structures, Vol.1. ISBN 978-1-84799-259-8. Published by (2007).
    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: Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1. ISBN 978-1-84753-710-2. Published by (2007).
    (In Spanish) Info, preview and on-line shop
  • Egon Willighagen & Miguel Howard: Fast and scriptable molecular graphics in web browsers without Java3D. Nature Precedings 14 June (2007). doi:10.1038/npre.2007.50.1
  • D.A. Evans, M.J. Bodkin, S.R. Baker & G.J. Sharman: Janocchio - a Java applet for viewing 3D structures and calculating NMR couplings and NOEs. Magnetic Resonance in Chemistry 45(7): 595-600 (2007).
    Janocchio is a Java applet based on Jmol; it calculates both H-H and H-C 3-bond coupling constants and NOEs from a three-dimensional structure. doi:10.1002/mrc.2016
  • 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 Now freely available in full-text.
  • Interview with Martin Walker. Reactive Reports 54 (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, and C.K. Williams: 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. Organic and Biomolecular Chemistry 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. Journal of Chemical Information and Computer Sciences 44(2): 462-469 (2004).
    Describes a CDK plugin that acts as a RSS agregator and show its application as pluged in Jmol. doi:0.1021/ci034244p Abstract
  • Andreas Bohne-Lang, and Elke Lang: 3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets. BIOspektrum 2004(2): 167-169 (2004).
    Compares Jmol with other chemistry visualisation applets. Article
  • 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. Journal of Chemical Information and Computer Sciences 43(2): 493-500 (2003).
    Describes CDK, the library on which Jmol v6 to v9 is built. doi:10.1021/ci025584y 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