> 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 >
Very good! I note that on my machine the menu items overlap. You might consider adding some crystallographic-focused buttons to the interface. Take a look at http://icsdweb.fiz-karlsruhe.de/ and http://fusion.stolaf.edu/chemistry/jmol/xtalx/, for example, for some nice options that allow checking and investigation of the symmetry, displaying multiple unit cells, checking fractional coordinates, and more. > 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 > ------------------------------------------------------------------------- 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
