{"id":25369,"date":"2022-08-12T08:33:49","date_gmt":"2022-08-12T07:33:49","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=25369"},"modified":"2022-09-11T06:16:08","modified_gmt":"2022-09-11T05:16:08","slug":"web-page-decay-and-journals-how-an-interactive-esi-from-2006-was-rescued","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25369","title":{"rendered":"Web page decay and Journals: How an interactive “ESI” from 2006 was rescued."},"content":{"rendered":"
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In 2006[1]<\/a><\/span> we published an article illustrating various types of pseudorotations in small molecules. It’s been cited 20 times since then, so reasonable interest! We described rotations known as Lever and Turnstile as well as the better known Berry mode. Because the differences between these rotations are quite subtle, we included an interactive electronic supporting information to illustrate them. That ESI was written in HTML and used Jmol to animate the rotations. Now, 16 years is a long time in the Web ecosystem (some early wag suggested, like dogs, that one year in normal time approximates to about 7 years in Web time) and inevitably, like e.g. both Rasmol[2]<\/a><\/span> and Chime before it, Jmol no longer works when invoked from a Web browser; Java applets are very much dead and we are now on the fourth generation of molecule viewer, JSmol. Two days ago I was contacted by someone (thanks Peter!) who had noticed that the journal landing page did not seem to point to any ESI. Here I tell the story of what happened next.<\/p>\n

Thus the landing page[1]<\/a><\/span> does not mention any method for accessing any ESI. But since the page is paywalled, you have to login to see more. When you do this, you get a reference to “enhanced objects”, so\u00a0I should explain what these were.
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The norm nowadays seems to be that ESI is expressed as a PDF file, but that allows interactivity only with extreme difficulty. In 2006, if you wanted this feature, you used HTML. The publisher (ACS) coined the expression of WEO, or Web-enhanced object. We produced perhaps 50 or so of these for various publishers and in those days they were hosted on publishers’ own sites. At some stage since 2006, these pages have been moved and the enhanced object for this article has been (temporarily?) “lost”. It is perhaps easy to understand why, since changes to the\u00a0publishers publication workflows would need to factor in such pages and probably there were not enough of them to merit inclusion in the workflow.<\/p>\n

So on to 2022, when I was contacted by Peter about this issue.\u00a0Whenever we submitted such interactive\u00a0ESI, we always kept a local copy, and indeed this was quickly located at DOI:\u00a010.14469\/hpc\/10849<\/a>, now of course allocated its own DOI. By now the ESI had lost its interactivity, but more worryingly, was\u00a0lacking any error messages. Why? This was the \u00a0HTML code then used:<\/p>\n

<applet width=\"300\" name=\"ClF5-gsA\"\r\n height=\"250\" archive=\"JmolApplet.jar\" code=\"JmolApplet\"\r\n mayscript=\"true\">\r\n <param name=\"progressbar\" value=\"true\" \/>\r\n <param name=\"progresscolor\" value=\"blue\" \/>\r\n <param name=\"boxmessage\"\r\n value=\"Downloading JmolApplet.jar\" \/>\r\n <param name=\"boxbgcolor\" value=\"black\" \/>\r\n <param name=\"boxfgcolor\" value=\"white\" \/>\r\n <param name=\"load\" value=\"ClF5-gsAC2vpTZ.mol\" \/>\r\n <param name=\"script\"\r\n value=\"select all; labels off; spacefill 0.25; \r\n wireframe 0.1; center atomno=2\" \/>\r\n <\/applet><\/code><\/small><\/pre>\n
In modern web browsers this is simply ignored. So the solution is to rewrite this code into modern syntax, and for this I turned to a long time hero and expert, Angel, who is one of the active maintainers of JSmol, the successor to \u00a0Jmol. \u00a0A few hours later a conversion script came back.\u2021<\/sup> It is just 55 lines long! \u00a0It is invoked in the header of the HTML document as:\u00a0<\/p>\n
<script type=\"text\/javascript\" src=\"JSmol.min.js\"><\/script>\r\n<script type=\"text\/javascript\" src=\"convertJmolApplets.js\"><\/script><\/code><\/small><\/pre>\n
and hey presto, all works as originally. I transclude a small snippet here to give a flavour, although the original is formatted for wide pages, so go see all the ESI there.<\/p>\n