With the recent disclosure of a major security hole in Java, I have been wondering if perhaps my continued use of the Jmol utility for displaying 3-D molecular structures makes sense. Perhaps it is time to consider alternatives. (Right now if you click on a molecule image in one of my blog posts and you are using Firefox, a big warning sign comes up first requiring the user to actively decide to invoke the Jmol viewer. Might this warning be enough to discourage some users?)

In addition, the increasing use of mobile devices, which most often are not Java-enabled, suggests that moving to a new display option is warranted.

So, I am asking the community to participate in a conversation about how we might best address this issue in the (near) future. Is a Javascript widget the way to go? If so, which current program are people happy with? Or should we move to an HTML5 approach? And if this is the way to go, what tools are people suggesting?

If you want to see some fine examples of all three approaches (Java-based: Jmol, Javascipt-based: Chemdoodle, and HTML5-based: GLMol) I strongly encourage you to read Henry Rzepa’s recent brilliant article in Journal of Cheminformatics (DOI: 10.1186/1758-2946-5-6). This is a fantastic article to compare the old-school publication technology (as presented in modern day PDF form) and new-school enabled technology (what Henry calls a datument). First download the pdf version and read it, and then access the HTML version; I guarantee you will be impressed by the difference in the experience.

So, please chime in on what molecular viewers I might adopt for this blog, and perhaps we as a community might be able to encourage the use of and further the development of these enhanced publication technologies.