Journals Using Jmol

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

Please, feel free to add here a link to any journal that uses Jmol for publishing molecular structures (e.g. as supplementary materials for articles). The history of interactive 3D molecular visualization in scientific journals is summarized in articles in Proteopedia.Org, namely Kinemages, Mage and KiNG and Jmol.

Interactive Usage

• ACS Chemical Biology, from the American Chemical Society (USA), is providing interactive Jmol renderings of structures matching figures in articles (look for enhanced objects link). Examples are linked to MoleculesInMotion.Com.
• ACS Inorganic Chemistry, as far back as 2005, supported Electronic Supplements that used interactive Jmol renderings of structures that expanded the contents of articles. Here is an example; although the link to the supplemental material has now disappeared from the publisher's page, a backup copy has been hosted by the authors and converted from old Jmol syntax (applet tags) to current JSmol syntax, allowing one to examine the material as it was originally designed. The journal has been contacted to update their page.
• Biochemical Journal is including interactive Jmol renderings of structures matching figures in articles (look for 3D interactive structure link). First article with this feature (27 June 2007) is "Structures and metal-ion-binding properties of the Ca²⁺-binding helix-loop-helix EF-hand motifs"; abstract and citation; 3D model (access is restricted to subscribers).
• Crystallography Journals Online, the web site for journals of the International Union of Crystallography (IUCr), is using Jmol to visualize published crystal structures: click on any 3d view button on a journal table of contents page, e.g. Acta Crystallographica Section C (2007) Part 1.
• Elsevier uses Jmol to display structures along the articles in several journals.
• Molecular BioSystems, from the Royal Society of Chemistry (UK), provides 3D visualisation of macromolecules in articles, by using FirstGlance in Jmol to show the associated PDB file. Links to the 3D images can be found on the Electronic Supplementary Information (ESI) page of the online article.
• Nature offers 3D View links for every new molecular structure. These use FirstGlance in Jmol. The debut was November 30, 2007. Consistent with FirstGlance in Jmol being free and open source, structure viewing at this journal is free (the 3D View links are accessible to non-subscribers). Nature is a strong supporter of open-source software, as evidenced by their Connotea project.
• Nature Chemical Biology and Nature Chemistry use Jmol to display chemical compounds related to articles, in the compound data index page for a paper. Examples: NCB and NC.
• Nature Structural & Molecular Biology displays new protein structures in FirstGlance in Jmol. The debut was February, 2006. See We're Living in a 3D World. Structure viewing at this journal is free, via 3D View links visible to non-subscribers. Nature is a strong supporter of open-source, as evidenced by their Connotea project.
• Protein Science announced the adoption of FirstGlance in Jmol, and interactive figures in Jmol, in late 2009. See Interactive graphics return to Protein Science. Protein Science was the first journal to offer interactive computer graphics of protein structure figures, in the form of Kinemages on floppy disks in the 1990's.

• Example of Jmol interactive figures: fig. 1, fig. 2 of Li and Palmer's article, DOI 10.1002/pro.98

Cover Images

• RNA Issue Feb 2010 - cover image of PDB entry 3CW1 generated with the Jmol-based Jena3D viewer.

Contributors

AngelHerraez, EricMartz, Rzepa, Rhuehne