A brief plug for a workshop I'm running under the aegis of ICSTI in Paris in February (http://www.icsti.org/programme_winter2010.php) to discuss just this issue. The IUCr has been using Jmol for a while to provide interactive figures in the HTML versions of our journal articles. We're also interested in carrying the same figures into the PDF versions to give the reader a greater choice of formats, so we certainly encourage the ability to integrate Jmol models in PDFs.
However, we're very enthusiastic about Henry's point that the data are paramount, and the Java applet does allow far more interaction directly with the model data. Of course, we require deposition of the crystal structure data sets in CIF format and make these freely available. It's also the case that Jmol comes with a very nice Javascript library that makes it very easy to set up feature-rich interactive figures with buttons, checkboxes, sliders and the like; by contrast, the interactive PDF figures I've seen tend to be rather more restricted in their presentation of the 3-d object. But I believe there are opportunities to include Javascript in interactive PDFs, and I'm sure there is scope to develop the range and usability of interactive PDFs. Certainly, I'm hoping to learn more from this workshop and its sequel. It's not clear to me if many publishers yet have a coherent strategy regarding interactive figures. PDF will again appeal because it offers a single approach across different domains. Jmol is superb at molecular and crystal structure visualizations, but of limited applicability elsewhere (though the discussions about generalising it within the SAGE community are interesting and relevant); and general scientific publishers may be nervous about the prospect of having to support an ever-growing range of software applicationss for different disciplines. That's why I think the publishers should start thinking about the architectural features of visualisation programs that will facilitate their integration into standard production workflows. Here again I think Jmol sets the gold standard, and I'll be hoping to get that message and philosophy across to other publishers. On Sat, Dec 19, 2009 at 12:34:58PM +0000, Rzepa, Henry wrote: > >I would therefore advocate making this option as easy as possible > > to use within Jmol. In my view, interactive 3D pdf figures should > > really be the rule rather than the exception in scientific > > publishing, and Jmol could lead the way. > > Publishers are likely to love interactive PDF, since it is easy to > archive. However, I find one serious issue; such objects are > <<data impoverished>>. Whereas with Jmol, one is obliged to > provide semantically accurate data (for example CML or equivalent), > the PDF object is simply a (pre)rendering of that data. Thus > reconstituting a useful molecule from Jmol is trivial (and that > reconstitution can then be used for many other purposes), > reconstituting a molecule from a 3D PDF is likely to be non trivial, > and will almost certainly suffer information loss compared to the > original data. By all means, provide BOTH, but I strongly urge that > a 3D PDF should NOT be the ONLY object provided. Apart from all these > considerations, I can just imagine how publishers would treat the copyright > aspects. For example, a publisher CANNOT claim copyright for a > Jmol model, since it is basically data, which cannot be copyrighted. > But just as they do with 2D images, I should imagine publishers > will be falling over themselves to claim copyright for a 3D PDF, > since it is intrinsically not data, but in effect <<art>> (and this > can be copyrighted). > > So please, whilst 3D PDF may well have its uses (in 1994 for example, > I was a strong advocate of VRML), let us not loose sight of the > more fundamental object, which is the data model. > -- > > +44 (020) 7594 5774 (Voice); FOAF: http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf > Dept. Chemistry, Imperial College London, SW7 2AZ, UK. Cheers 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 the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
