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

How to submit an enhanced figure

Before you submit your article, you may use the toolkit described in this manual to create an enhanced figure in a form that will be compatible with the journals' production workflow.

'Conventional' submissions

For most of the IUCr journals, you will submit a single file containing your article and all its tables, figures, supplementary information etc. The submission system will be revised in due course, so that you may upload individual source files for figures etc. at this stage. However, for the moment you will first prepare your enhanced figure, then provide a static version of it within your submitted article, along with a link to the online version.

The stages in this procedure are as follows.

1. Upload the Crystallographic Information File (CIF) containing structural data for the structure (or structures) you wish to illustrate. This is done through the upload page shown in Fig. 4 and discussed in more detail in the introductory tutorial.

2. Use the features of the toolkit to create the main illustration that will appear as the static figure in PDF versions of the journal. This figure will be made available to you as a static image in TIFF format.

3. If desired, make additional edits to create other custom views that the reader of the online edition will be able to access. The tutorials in this manual will explain the many options available to you.

4. When writing your article, include the TIFF of the static image to represent the main view of the figure. Provide a figure caption and discuss the information in this figure as you would for any other figure. Also supply alongside this figure the URL of the enhanced version, so that the Co-editor and referees may see the figure online. This URL will have been supplied to you when you first created the enhanced figure.

5. If any revisions to the enhanced figure are requested by the Co-editor, you may make further edits and notify the Co-editor when you have done so.

6. When your article is accepted for publication, you will proceed to the stage where individual source files (article body, figures, structure factors etc.) must be uploaded. At this point, you need simply paste into the upload page the URL of your enhanced figure, and it will be transferred to the journal production system (Figs 1, 2).

Fig. 1 Transferring an enhanced figure to the submission system once an article has been accepted.

7. When your article is published, the static version of the figure will appear in the PDF or hard-copy editions; it will also be seen in web browsers that cannot or do not show active content. For all other readers, the enhanced figure will appear in their browsers as an interactive applet, complete with the additional scripts that you have provided and that the reader may activate by clicking on buttons or checkboxes.

Fig. 2 Once transferred, the enhanced figure is treated like any other.

Submission of structure reports

Acta Crystallographica Section C publishes high-quality studies of crystal and molecular structures, and cta Crystallographica Section E publishes short reports of crystal structure determinations. In both journals, initial submission of the article is by means of a CIF that contains all the structural data for publication, along with the text of the article.

For these journals, it is possible to proceed as before, i.e. to create an enhanced figure before submission, and subsequently transfer it to the submission system. This can be done during the early stages of submission, since these journals require you to upload all the source files before the material is assigned to a Co-editor.

However, for these journals it is also possible to create the enhanced figure within the submission system itself, once the CIF has been uploaded (Fig. 3). Indeed, for these journals this may be the best way to proceed, since the enhanced figure is guaranteed to be associated with the data set that forms the essence of the article.

Fig. 3 For structural papers, the enhanced figure may be created within the submission system once the CIF has been uploaded.