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

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

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

2008

• C. Forlines, R. Lilien: Adapting a single-user, single-display molecular visualization application for use in a multi-user, multi-display environment. In: Proceedings of the Working Conference on Advanced Visual Interfaces, 2008, pp. 367-371. doi:10.1145/1385569.1385635 Article

• 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

2007

• Angel Herráez: How to use Jmol to study and present molecular structures, Vol.1. ISBN 978-1-84799-259-8. Published by Lulu.com (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 Lulu.com (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

2006

• 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).

  Article

• 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

2005

• 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).

  Abstract

• 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

2004

• 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

2003

• 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

• F.T. Marchese, J. Mercado, Y. Pan: Adapting single-user visualization software for collaborative use. In: Proceedings of the Seventh International Conference on Information Visualization - An International Conference on Computer Visualization and Graphics Applications, 2003, pp. 252-257. ISBN 0-7695-1988-1. Article

2001

• 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