Here is version 2 of my ebook mockup page (see here for a description of version 1). Actually there are two versions: one using Jmol and one for the iPad.
The Jmol version is how I would like the page to look. The static figures are replaced with interactive Jmol versions embedded right in the page, and the figure captions contain links (denoted by ">>") to larger version of the figures on a separate page, that also contain extra features such as animations (Figure 3.1) or overlays (Figure 3.2). An alternative design would have been to keep the static images, but insert links to the larger figures. I think I like the current look better. But for pages with more figures loading-time could become an issue with Jmol.
The iPad version is what is currently possible for the iPad with ChemDoodle Web Components. We are waiting for two things to happen: 1) WebGL in Mobile Safari, which will allow real 3D representations of the molecules, and 2) Implementation of contours and surface maps in ChemDoodle Web Components.
For the iPad version I generated the necessary ChemDoodle Web Component HTML code using the ChemDoodle software package, as I show in this screencast. The mol2 file I start with is generated with Avogadro.
ChemDoodle costs $60, and normally I restrict this blog to free software, but I am making an exception here because I think iChemlabs deserves to be supported since they made ChemDoodle Web Components open source. Furthermore, since I have access to the source code I could probably figure out the format for the HTML code, if I wasn't so lazy.
Interactive chemistry ebooks: highlight and annotate
Interactive chemistry ebooks: let us start now!
ChemDoodling: now in 3D, but not (yet) on the iPad
ChemDoodling on the iPad and the future of interactive chemistry text books
iPad: even 3D molecules that can be viewed from any angle
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