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Wednesday, June 7, 2023

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

In 2006[1] we revealed an article illustrating numerous kinds of pseudorotations in small molecules. It’s been cited 20 instances since then, so cheap curiosity! We described rotations often known as Lever and Turnstile in addition to the higher identified Berry mode. As a result of the variations between these rotations are fairly refined, we included an interactive digital supporting data as an instance them. That ESI was written in HTML and used Jmol to animate the rotations. Now, 16 years is a very long time within the Internet ecosystem (some early wag prompt, like canine, that one yr in regular time approximates to about 7 years in Internet time) and inevitably, like e.g. each Rasmol[2] and Chime earlier than it, Jmol now not works when invoked from a Internet browser; Java applets are very a lot useless and we are actually 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 methodology for accessing any ESI. However for the reason that web page is paywalled, it’s a must to login to see extra. Whenever 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 permits interactivity solely with excessive issue. In 2006, in the event you needed this function, you used HTML. The writer (ACS) coined the expression of WEO, or Internet-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 (briefly?) “misplaced”. It’s maybe simple to know why, since modifications to the publishers publication workflows would wish to consider such pages and possibly there weren’t sufficient of them to advantage inclusion within the workflow.

So on to 2022, once I was contacted by Peter about this challenge. At any time when we submitted such interactive ESI, we all the time saved a neighborhood copy, and certainly this was shortly positioned 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" identify="ClF5-gsA"
 peak="250" archive="JmolApplet.jar" code="JmolApplet"
 <param identify="progressbar" worth="true" />
 <param identify="progresscolor" worth="blue" />
 <param identify="boxmessage"
 worth="Downloading JmolApplet.jar" />
 <param identify="boxbgcolor" worth="black" />
 <param identify="boxfgcolor" worth="white" />
 <param identify="load" worth="ClF5-gsAC2vpTZ.mol" />
 <param identify="script"
 worth="choose all; labels off; spacefill 0.25; 
 wireframe 0.1; heart atomno=2" />

In trendy internet browsers that is merely ignored. So the answer is to rewrite this code into trendy syntax, and for this I turned to a very long time hero and professional, Angel, who is likely one of the lively maintainers of JSmol, the successor to  Jmol.  Just a few hours later a conversion script got here again. It’s simply 55 traces lengthy!  It’s invoked within the header of the HTML doc as: 

<script kind="textual content/javascript" src="
<script kind="textual content/javascript" src="convertJmolApplets.js"></script>

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

So what’s the take house message? Properly, it seems that the Java/Jmol syntax developed for the Internet greater than 20 years in the past has truly proved fairly resilient. And so pages the place expertise 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 corresponding to described above. And maybe in 10 years time when Javascript and JSmol have themselves moved on, additional rescues will likely 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’ll nicely have replied that it appeared unlikely. So it’s a very nice shock to seek out that they (now) are. All we want is for the journal itself to level to a working model; for that, maintain your eyes peeled.

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

Accessible at and 10.14469/hpc/10852

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