A previous post was triggered by Peter alerting me that interactive electronic supporting information (IESI) we had submitted to a journal in 2005[1] appeared to be strangely missing from the article landing page. This set me off recollecting our journey, which had started around 1998, and to explore what the current state of these ancient IESIs were in 2022. I have now reached 2014 in this journey, which is being recorded as it happens in the comments page of the post. I discovered there were four distinct stages in that evolution of IESI which I thought it would be of interest to record here.
<EMBED border=0 src="geom+vib/12e-dft.gau" name="12e-dft" align=center width=150 height=150 spiny=36 startspin=true display3D=sticks PLUGINSPAGE="http://www.ch.ic.ac.uk/cgi-bin/plugin.cgi" script="zoom 175;"></EMBED>
I have to say that access to the data underpinning this IESI is still good; but the interactive component itself has long gone, along with Chime itself.
<applet height="300" archive="JmolApplet.jar" width="300" code="JmolApplet" name="TS2" mayscript="true" id="TS2"> <param name="progressbar" value="true" /> <param name="progresscolor" value="blue" /> <param name="boxmessage" value="starting JmolApplet ..." /> <param name="emulate" value="chime" /> <param name="boxbgcolor" value="black" /> <param name="load" value="RRSS_fm-5-ts2-49.xyz" /> </applet>
It is this invocation where the interactivity was rescued by Angel as described in the earlier post comments page in the form of an adaptor library that converts the syntax above to modern form.
<script type="text/javascript" src="JSmol.min.js"></script> <script type="text/javascript" src="js/Jmol2.js"></script> <!-- The second command is modern, to convert to using JSmol -->
and then to invoke a molecule:
<script type="text/javascript"> jmolApplet(300,"load GaL3.mol; select all; spacefill 0.25; wireframe 0.1; center atomno=1")</script>
Here again an adapter library to update this syntax is available as Jmol2.js.
<script type="text/javascript" src="JSmol.min.js"></script>
is needed to set things up, whilst the molecule call is illustrated by eg
<a href="javascript:Jmol.script(jmolApplet0, 'load 24880.log',%20';frame 13;spin 3;')">log</a>
Now, ten years on from the genesis of JSmol, the functionality and capability of this program have continued to increase by leaps and bounds, but the general form has remained stable.
One other change in our usage did also occur in 2014. Previously the content being viewed came from a local file installed on the web server, as per eg 24480.log above. However we were now starting to source such files directly from a data repository, being a specialist resource to host such content. All that would be needed was the DOI of the repository collection where the data was being hosted, along with the Media type of the desired file. But that comes with its own issues and this is another story that will be told elsewhere.
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