Literature

Jmol / JSmol Applications

• Websites Using J(S)mol
• J(S)mol in the Classroom
• Journals Using J(S)mol
• J(S)mol Literature
• Articles Using J(S)mol
• Books Using J(S)mol
• Wikis Using J(S)mol
• Blogs Using J(S)mol
• CMS Using J(S)mol (Moodle and others)
  Course Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms
• Applications Embedding Jmol
• Distributions Including Jmol
• Blue Obelisk

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 Lulu.com

  (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

• 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