Dear Jmol users The International Union of Crystallography has been developing a system to allow authors to publish interactive figures using Jmol in IUCr journals. This system is almost ready to go live as a beta release to our authors.
You are invited to preview and comment on the Jmol authoring toolkit that will form part of this service. This preview version is available at http://sandbox.iucr.org/jtktalpha Feel free to upload structures in CIF format to test this toolkit. You will find that saving your edits will take a very long time; the demonstration machine is a very low-powered one and struggles to render the saved view (the server that our authors will use is much faster). Nevertheless, you may find it interesting to explore the way that the interface is intended to work. The application will be integrated seamlessly into our submission and review system. Authors may create enhanced figures and make them accessible to referees as part of normal peer review. After acceptance, the enhanced figure is automatically managed within the electronic journal workflow. The initial rendering is saved as a TIFF image for incorporation in the PDF of the article (this is why I have a need to obtain, say, 300 dpi resolution output from jmol). The online figure contains the same static rendering, but also the Jmol applet and the set of Jmol scripts that the author has assembled. The page degrades well for readers with limited browsers; if they do not have Java or JavaScript, they will see only the static view. Much of the development effort has gone into the integration of this toolkit with the submission system. This is important in a journal production environment to provide capacity to accommodate large numbers of figures. Recently we have been publishing over 1000 crystal structures per month. We wish to be able to publish that many Jmol-enhanced figures if the community sees a need to do so. The next stage will be to collect user feedback and refine the palette of features offered within the toolkit interface. We are aiming to provide a service that will be quite usable by Jmol novices, but that can also be used to good effect by experts. I must pay tribute to the enormous developments in Jmol over the past few years that have made this project possible: the very clean export of the graphics state; the very powerful and useful Jmol.js library; the great improvement in handling crystallographic information (symmetry operations, coordination polyhedra etc.). I also acknowledge the inspiration of the many excellent tutorial and educational sites that are using Jmol, and the efforts of journals such as ACS Chemical Biology and the Biochemical Journals to incorporate enhanced figures into their publications. The Jmol community itself is a wonderful one, and thanks to all of you for your continuing contributions of tools, ideas and know-how! Enjoy Brian _________________________________________________________________________ Brian McMahon tel: +44 1244 342878 Research and Development Officer fax: +44 1244 314888 International Union of Crystallography e-mail: [EMAIL PROTECTED] 5 Abbey Square, Chester CH1 2HU, England ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
