Literature

See also Articles Using Jmol In Figures and Books Using Jmol In Figures.

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, 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
• 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, 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.

Contributors

AngelHerraez, Rzepa, Gutow, NicolasVervelle, BrianMcMahon, Pimpim