jmol enhanced figure toolkit

Introduction Why Jmol? When to use an enhanced figure How to submit an enhanced figure An introductory tutorial Tutorial 2: an inorganic crystal lattice Tutorial 3: a small metal-organic molecule Tutorial 4: a biological macromolecule molecule Toolkit options reference Some Jmol resources Acknowledgements Appendix: useful Jmol commands

Introduction

Although interactive graphics programs for web content have been available for some time, and have been used in some very sophisticated online tutorials, they have not been widely used by academic journals. There are many reasons for this, including the impermanence of some of the programs, their requirements for particular supporting software or browsers, the difficulty with integrating online content into a conventional publishing workflow, or the difficulty in creating suitable high-quality content.

The IUCr journals now offer to authors a toolkit allowing the creation of enhanced figures for publication (McMahon & Hanson, 2008). The enhanced figures will be integral to the research articles in which they appear (i.e. they are not supplementary documents). They comprise two components: a static image, in TIFF and PNG formats, that appears in the PDF version of the article, or as a representation in browsers that do not support or enable Java and JavaScript; and a web page in which is embedded a full visualization program, Jmol, displaying the author's preferred view of a molecular or crystal structure (identical to the static image), but which may be manipulated by the reader of the journal. The enhanced figure web page may also contain buttons, checkboxes and radiobutton options helping the reader to interact with the displayed structure in specific ways designed by the author.

In this manual we explain how authors may use this toolkit to design value-added interactive graphics to illustrate and enhance the scientific message of their articles.