Monday, January 19, 2009

RSC now allows Jmol in main text of publication... well, almost

Rich Kidd wrote in the ChemistryWorldBlog about Henry Rzepa to have published two papers in RSC journals where Jmol is part of the main paper, after having used Jmol in extra material in ACS journals before. The key here is that the Jmol is part of the official text... when you open the paper in a browser, you immediately get to see the Jmol live, 3D graphics! Well, so it is said in the blog.

However, when I checked the HTML of the first of the two papers (A computational investigation of the structure of polythiocyanogen, doi:10.1039/b810147g). The main HTML still links to a supplementary page. Progress, but not perfect either:

1 comment:

  1. It is a shame the RCS has locked the document away so one has to pay. :-(

    I would like to hear your thoughts about the use of CML (maybe using jmol) when viewing chemical structures on the web.

    I wanted to email you about this but the jabber email you give didn't work for me, hence this blog post.

    I am looking at using DSpace as the backbone of a digital library system. DSpace is commonly used by universities to offer journals to their students and others. I am looking into how it might be used in a commercial setting. Any changes would of course be contributed back to the open source community. At the moment this community is populated mainly by librarians.

    DSpace has support for several mimetypes, with PDF being the obvious one. I am currently opening a discussion on the DSpace mailing list about support for CML for chemical structures. You can see my blog at for what I have been doing with DSpace and CML. I provide a link back to your blog there. I hope that in in at least one of our blogs we can get the issue discussed :-) Alternatively if you are interested you might join the dspace-tech mailing list.

    My main thought is that browser addons built on jmol would allow structures to be viewed very nicely in the same way that docs are using the PDF format and associated addons. I would be grateful if you would comment on this please.

    I am also interested in adding spectra to my DSpace. I hink that just displaying a spectrum as a jpg would be good enought for that but I would be grateful for your comments in this area too.

    Andrew M.