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

When to use an enhanced figure

In general, the same principle should be followed as when creating normal figures: the author wishes to demonstrate to the reader something of scientific importance that is best shown in a visual way. Where all the important information can be seen in a static figure, that may still be the best way to present it.

However, an advantage that Jmol offers over a static view is that the reader may interact with the molecular structure, rotating it, viewing it from any angle, highlighting regions of particular interest, hiding those that clutter the view, measuring arbitrary distances and angles between atoms, etc.

If you are reporting a simple molecular or crystal structure, with no deviation from canonical bond lengths or geometries, you may feel that there is no real benefit to the reader in having access to an enhanced figure. (Remember that the online editions of the IUCr journals already provide a three-dimensional visualization using Jmol of every structure. The visualizations are accessible from the contents pages to non-subscribers, or from within the HTML edition of the articles by following the `supplementary files' link.)

However, if your structure is complex in shape, or packs in ways that are difficult to represent clearly in a two-dimensional projection, then you may find it convenient and easy to prepare a simple enhanced figure that demonstrates these features, with little investment of time on your part.

As you become more experienced with the use of the enhanced figure toolkit, you will find it increasingly easy to add scripts to the enhanced figure, which will provide the reader with different views of the structure, or with animations that demonstrate particular features of the structure and its properties.

The toolkit is designed to make it easy to create enhanced figures, and to include them as part of a submitted article. It integrates fully with the submission and review system operated by the IUCr journals, so that Co-editors and referees can see the enhanced figure and assess its worth to the article. Of course, this means that you must be willing to respond to reviewers' comments regarding the enhanced figure, and be prepared to make appropriate revisions if requested to do so.