The Jmol paper: a paradigm shift in crystallographic visualization

From the Jmol mailing list, I noticed Prof. Robert Hanson's announcement titled "Jmol and crystallography: the paper". Finally, an "official" paper has been published on Jmol, an increasing popular molecular visualization tool.

While the paper is categorized under "teaching and education" and summarized as below:

Recent advances in molecular and crystallographic visualization methods are allowing instructors unprecedented opportunities to enhance student learning using virtual models within a familiar web-browser context. In step with these advances, the latest versions of the Jmol molecular visualization applet offer capabilities that hold potential for revolutionizing the way students learn about symmetry, uncertainty and the overall enterprise of molecular structure determination.

Jmol is certainly as useful for research as other commonly used molecular visualization tools, such as PyMOL and RasMol. Specifically, Jmol applets have become dominated in web-based applications/resources (including RCSB PDB). In fact, the HTML version of the paper itself makes extensive use of Jmol applet for interactive manipulation of over 20 figures.

Over the past couple of years, I have witnessed the many new features added to Jmol, driven by an active and friendly user community. I have been particularly impressed by Prof. Hanson's quick and to-the-point responses to users' requests for new features and bug reports, including to my request for Jmol's "Support of 'alchemy' format for rectangular schematic base-pair geometry". Overall, the paper presents a nice overview of some of Jmol's new functionality, and could become highly cited.

Reading through the paper, I was just a bit surprised that PyMOL is not mentioned. Nowadays, Jmol and PyMOL are apparently the top two molecular graphics software tools, with common and complementary functionality.