Literature

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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):


2021

  • Jeffrey A. Cohlberg: Exploring Proteins and Nucleic Acids with Jmol. A 121-page e-book (pdf). Free download.
A manual containing self-guided exercises that enable the user to learn how to download structures from the Protein Data Bank, display and manipulate them using the Jmol application. The user gradually acquires the skills to use Jmol while proceeding to learn the basics of protein structure in a manner that parallels the way they will be learning the material in an introductory biochemistry course.

2017

  • Johannes Pernaa, Maija Aksela and Shenelle Pearl Ghulam: Introduction to Molecular Modeling in Chemistry Education. e-Oppi Ltd. & Edumendo Publishing, 2017; 120 pp. ISBN 978-952-6649-94-8 (ePub), ISBN 978-952-6649-93-1 (paperback). Details at: bit.ly/immice
A small introductional book for molecular modeling in chemistry education, using JSmol. It includes theoretical background suitable for chemistry teachers, chemistry educational researchers and chemistry teachers students, and about 20 exercises that can be used in e.g. teacher training. It is being used as a part of a course material in an undergraduate molecular modeling and visualizaton course for chemistry teachers students.
  • Robert M. Hanson and Xiang-Jun Lu: DSSR-enhanced visualization of nucleic acid structures in Jmol. Nucleic Acids Research 2017, gkx365 (2017) doi:10.1093/nar/gkx365 Open access article.

2016

  • Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie, and Jason E. Bara: Programmatic conversion of crystal structures into 3D printable files using Jmol. Journal of Cheminformatics 8, 66 (2016) doi:10.1186/s13321-016-0181-z Open access article.
  • Robert M. Hanson: Jmol SMILES and Jmol SMARTS: specifications and applications. Journal of Cheminformatics 8, 50 (2016) doi:10.1186/s13321-016-0160-4 Open access article.

2013

  • Robert M. Hanson, Jaime Prilusky, Zhou Renjian, Takanori Nakane and Joel L. Sussman: JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia. Israel Journal of Chemistry 53, 207-216 (2013). doi:10.1002/ijch.201300024
    Abstract and article
    Also featured in the cover picture, Israel Journal of Chemistry 53 (3-4) 2013. doi:10.1002/ijch.201390002
  • H. S. Rzepa, "Chemical datuments as scientific enablers", J. Chemoinformatics, 2013, 4 10.1186/1758-2946-5-6
  • H. S. Rzepa, "Changing ways of sharing research in Chemistry", in "The future of scholarly communication: all change", M. Jubb and D. Shorley (Eds), 2013, ISBN 1-85604-817-0
  • Shane P. Tully, Thomas M. Stitt, Robert D. Caldwell, Brian J. Hardock, Robert M. Hanson, and Przemyslaw Maslak: Interactive web-based pointillist visualization of hydrogenic orbitals using Jmol. Journal of Chemical Education 90, 129-131 (2013). doi:10.1021/ed300393s Article with complimentary full-text access.

2011

  • Tim Wallace: Using Java applets to enhance online teaching and assessment in Blackboard. In Symposium on the Benefits of eLearning Technologies. University of Manchester, 2011.
    Article
  • H. S. Rzepa, "The past, present and future of scientific discourse", J. Cheminformatics, 2011, 3, 46. doi:10.1186/1758-2946-3-46

2010

  • G. Rule, D. Bajzek & A. Kessler: Molecular visualization in STEM education: Leveraging Jmol in an integrated assessment platform. In Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2010, pp. 304-309 (J. Sanchez & K. Zhang, eds.). Chesapeake, VA: AACE, 2010.
    Abstract and article
  • Robert M. Hanson: Jmol – a paradigm shift in crystallographic visualization. Journal of Applied Crystallography, 43(5): 1250-1260 (2010)
    doi:10.1107/S0021889810030256 - Abstract and article
  • J. H. Gutow, Easy Jmol Web Pages using the Jmol Export to Web Function. Journal of Chemical Education WebWare. Publication Date (Web): April 8, 2010.
    Link
  • O. Casher and H. S Rzepa, "Using Semantically-enabled Components for Social-Web based Scientific Collaborations", in "Enhancing Learning with Online Resources, Social Networking, and Digital Libraries", Editor(s): Robert E. Belford, John W. Moore, Harry E. Pence, 2010, DOI: 10.1021/bk-2010-1060.ch003.

2009

  • Jeroen Logtenberg: Multi-user interaction with molecular visualizations on a multi-touch table. MSc Thesis, University of Twente, Enschede, The Netherlands (2009).
    Full document

2008

  • Clifton Forlines, Ryan 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, pp. 367-371 (2008).
    doi:10.1145/1385569.1385635 - [1]
  • Brian McMahon, 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
  • M. E. Cass and H. S. Rzepa, "Visualizing metal tris chelates - Visualizations to examine the structure and symmetry of metal tris chelates: Symmetry operations, chirality, and mechanisms (Bailar Twist and Ray-Dutt) that racemize the Δ and Λ isomers", J. Chem. Ed., 2008, 85, 750-751.

2007

  • Angel Herráez: How to use Jmol to study and present molecular structures, Vol.1. Lulu Enterprises: Morrisville, NC, USA (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 - ISBN 978-1-84799-259-8
    An update and an extra chapter: Supplement 2011
  • Angel Herráez: Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1. Lulu Enterprises: Morrisville, NC, USA (2007).
    (In Spanish) - Info, preview and on-line shop - ISBN 978-1-84753-710-2
  • 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
  • David A. Evans, Michael J. Bodkin, S. Richard Baker, Gary 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
  • H. S. Rzepa, "Achieving a Holistic Web in the chemistry curriculum", Ann. Rep. Comp. Chem., 2007, 3, 99-133.

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, 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

  • Marion E. Cass, Henry S. Rzepa, David R. Rzepa, Charlotte 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, Leonid A. Mirny: CoC: a database of universally conserved residues in protein folds. Bioinformatics 21: 2539-2540 (2005).
    Describes the CoC database which uses Jmol for visualisation. - doi:10.1093/bioinformatics/bti360 - Abstract
  • Egon Willighagen, 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, Johann 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, 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, 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, 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
  • Francis T. Marchese, Jude Mercado, Yi 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, pp. 252-257 (2003).
    ISBN 0-7695-1988-1 - Article

2001

  • Egon 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

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