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Thursday, March 30, 2023

Net web page decay and Journals: How an interactive “ESI” from 2006 was rescued.

In 2006[1] we printed an article illustrating numerous sorts of pseudorotations in small molecules. It’s been cited 20 instances since then, so affordable curiosity! We described rotations generally known as Lever and Turnstile in addition to the higher recognized Berry mode. As a result of the variations between these rotations are fairly delicate, we included an interactive digital supporting info as an example them. That ESI was written in HTML and used Jmol to animate the rotations. Now, 16 years is a very long time within the Net ecosystem (some early wag urged, like canine, that one yr in regular time approximates to about 7 years in Net time) and inevitably, like e.g. each Rasmol[2] and Chime earlier than it, Jmol not works when invoked from a Net browser; Java applets are very a lot lifeless and we at the moment are on the fourth era of molecule viewer, JSmol. Two days in the past I used to be contacted by somebody (thanks Peter!) who had observed that the journal touchdown web page didn’t appear to level to any ESI. Right here I inform the story of what occurred subsequent.

Thus the touchdown web page[1] doesn’t point out any technique for accessing any ESI. However because the web page is paywalled, it’s important to login to see extra. While you do that, you get a reference to “enhanced objects”, so I ought to clarify what these had been.

The norm these days appears to be that ESI is expressed as a PDF file, however that enables interactivity solely with excessive problem. In 2006, in case you wished this function, you used HTML. The writer (ACS) coined the expression of WEO, or Net-enhanced object. We produced maybe 50 or so of those for numerous publishers and in these days they had been hosted on publishers’ personal websites. At some stage since 2006, these pages have been moved and the improved object for this text has been (quickly?) “misplaced”. It’s maybe straightforward to know why, since modifications to the publishers publication workflows would wish to consider such pages and doubtless there weren’t sufficient of them to advantage inclusion within the workflow.

So on to 2022, after I was contacted by Peter about this concern. Each time we submitted such interactive ESI, we all the time stored a neighborhood copy, and certainly this was shortly situated at DOI: 10.14469/hpc/10849, now in fact allotted its personal DOI. By now the ESI had misplaced its interactivity, however extra worryingly, was missing any error messages. Why? This was the  HTML code then used:

<applet width="300" title="ClF5-gsA"
 top="250" archive="JmolApplet.jar" code="JmolApplet"
 <param title="progressbar" worth="true" />
 <param title="progresscolor" worth="blue" />
 <param title="boxmessage"
 worth="Downloading JmolApplet.jar" />
 <param title="boxbgcolor" worth="black" />
 <param title="boxfgcolor" worth="white" />
 <param title="load" worth="ClF5-gsAC2vpTZ.mol" />
 <param title="script"
 worth="choose all; labels off; spacefill 0.25; 
 wireframe 0.1; heart atomno=2" />

In fashionable net browsers that is merely ignored. So the answer is to rewrite this code into fashionable syntax, and for this I turned to a very long time hero and skilled, Angel, who is without doubt one of the lively maintainers of JSmol, the successor to  Jmol.  A number of hours later a conversion script got here again. It’s simply 55 strains lengthy!  It’s invoked within the header of the HTML doc as: 

<script kind="textual content/javascript" src="https://www.ch.imperial.ac.uk/rzepa/weblog/JSmol.min.js"></script>
<script kind="textual content/javascript" src="convertJmolApplets.js"></script>

and hey presto, all works as initially. I transclude a small snippet right here to offer a flavour, though the unique is formatted for broad pages, so go see all of the ESI there.

So what’s the take house message? Effectively, it seems that the Java/Jmol syntax developed for the Net greater than 20 years in the past has really proved fairly resilient. And so pages the place know-how has overtaken them can typically be fairly simply rescued and restored again to life. Numerous these WEOs from the early naughties have certainly been rescued by expedients equivalent to described above. And maybe in 10 years time when Javascript and JSmol have themselves moved on, additional rescues will probably be wanted. However had I been requested again in 2006 or earlier whether or not I anticipated these interactive ESI pages to nonetheless be working 16+ years later, I could effectively have replied that it appeared unlikely. So it’s a very nice shock to search out that they (now) are. All we’d like is for the journal itself to level to a working model; for that, preserve your eyes peeled.

On a extra basic level, a historical past of “ESI” as utilized in chemistry can be an attention-grabbing subject. Though usually regarded as having its roots round 1996, it could effectively return additional. Any historians round?

Accessible at https://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Legacy and 10.14469/hpc/10852

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