Thursday, June 11, 2009

It takes a village to solve a Jmol puzzle


(Click-drag on the image to rotate the molecule!)

The past few days I have been trying to put Jmol animation into the blog. I knew this was possible because of the pioneering efforts of Felix over at Chemical Quantum Images.

His post on vibrations in p-cresole has been a long-time inspiration. I found the entry through google because I was interested in animating vibrations with Jmol, and it taught me a lot about that.

But more importantly, it was the first blog I came across where someone talked about the details of their computations and showed images resulting from the computations simply because they were beautiful. So Chemical Quantum Images was a major inspiration for this blog. Thanks, Felix!

And now, through the comments to that post, and some very helpful suggestions by Noel over at Noel O'Blog (thanks, Noel!), I now also know how to embed Jmol within this blog. Noel pointed me to another way of doing it, via a Microjmol Widget application written by Jeffrey Moore and that provided me with the penultimate piece of the puzzle.

Anyway, just in case anyone else is interested in doing this: the text I put into this blog window to generate the Jmol window can be found below. Note that this will not show up in Preview, only when you post (and that was the final piece of he puzzle).

<script src="http://propka.ki.ku.dk/~jhjensen/Jmol.js" type="text/javascript"></script> <script type="text/javascript"> jmolInitialize("http://propka.ki.ku.dk/~jhjensen"); jmolApplet(300, "load http://propka.ki.ku.dk/~jhjensen/cyclohexane_movie.xyz;");jmolBr();jmolButton("spin y" ,"spin y");jmolButton("spin off" ,"spin off");<br /></script>
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