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):


Contents

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
  • 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
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