{"id":19697,"date":"2018-05-16T14:06:05","date_gmt":"2018-05-16T13:06:05","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=19697"},"modified":"2018-08-13T14:13:58","modified_gmt":"2018-08-13T13:13:58","slug":"ten-years-on-jmol-and-wordpress","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19697","title":{"rendered":"Ten years on: Jmol and WordPress."},"content":{"rendered":"
\n

Ten years are a long time when it comes to (recent) technologies. The first post on this blog<\/a> was on the topic of how to present chemistry with three intact dimensions. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). Here I reflect on how ten years of progress in technology has required changes and the challenge of how any necessary changes might be kept “under the hood” of this blog.<\/p>\n

That first post described how the Java-based applet Jmol could be used to present 3D models and animations. Gradually over this decade, use of the Java technology<\/a> has become more challenging, largely in an effort to make Web-page security higher. Java was implemented into web browsers via something called Netscape Plugin Application Programming Interface  or NPAPI,<\/a> dating from around 1995. NPAPI has now been withdrawn from pretty much all modern browsers.\u2021<\/sup> Modern replacements are based on JavaScript, and the standard tool for presenting molecular models, Jmol has been totally refactored into JSmol<\/a>.\u2020<\/sup> Now the challenge becomes how to replace Jmol by JSmol, whilst retaining the original Jmol Java-based syntax (as described in the original post<\/a>). Modern JSmol uses its own improved syntax, but fortunately one can use a syntax converter script Jmol2.js which interprets the old syntax for you. Well, almost all syntax, but not in fact the variation I had used throughout this blog, which took the form:<\/p>\n

[caption]<img onclick=”jmolApplet([450,450],’load a-data-file<\/em>;spin 3;’);” src=”static-image-file” width=”450″ \/> Click for 3D structure[\/caption]<\/small><\/p>\n

This design was originally intended to allow browsers which did not have the Java plugin installed to default to a static image, but that clicking on the image would allow browsers that did support Java to replace (in a new window) the static image with a 3D model generated from the contents of a-data-file.<\/em> The Jmol2.js<\/code> converter script had not been coded to detect such invocations. Fortunately Angel came to my rescue and wrote a 39 line Javascript file that does just that (my Javascript coding skills do not extend that far!). Thanks Angel!!<\/p>\n

In fact I did have to make one unavoidable change, to;<\/p>\n

[caption]<img onclick=”jmolApplet([450,450],’load a-data-file<\/em>;spin 3;’,’c1′<\/span><\/strong>);” src=”image-file” width=”450″ \/> Click for 3D structure[\/caption]<\/small><\/p>\n

to correct an error present in the original. It manifests when one has more than one such model present in the same document, and this necessitates that each instance has a unique name\/identifier (e.g.<\/em> c1). So now, in the WordPress header for the theme used here (in fact the default theme), the following script requests are added to the top of each page, the third of which is the new script.<\/p>\n

<script type=”text\/javascript” src=”JSmol.min.js”><\/script>
\n<script type=”text\/javascript” src=”js\/Jmol2.js”><\/script>
\n<script type=”text\/javascript” src=”JmolAppletNew.js”><\/script><\/p>\n

The result is e.g.<\/em>
\n

\"Click

Click for 3D structure of GAVFIS<\/p><\/div><\/p>\n

\"Click

Click for 3D interaction<\/p><\/div>\n

\nThis solution unfortunately is also likely to be unstable over the longer term. As standards (and security) evolve, so invocations such as onclick=<\/code> have become considered “bad practice” (and may even become unsupported). Even more complex procedures will have to be devised to keep up with the changes in web browser behaviour and so I may have to again rescue the 3D models in this blog at some stage!\u00b6<\/sup> Once upon a time, the expected usable lifetime of e.g.<\/em> a Scientific Journal (print!) was a very long period (>300 years). Since ~1998 when most journals went online, that lifetime has considerably shortened (or at least requires periodic, very expensive, maintenance). For more ambitious types of content such as the 3D models discussed here, it might be judged to be <10 years, perhaps much less before the maintenance becomes again necessary. Sigh!<\/p>\n

\n

\u2021<\/sup> At the time of writing, WaterFox<\/a> is one of the few browsers to still support it. \u2020<\/sup>An early issue with using Javascript instead of Java was performance. For some tasks, the former was often 10-50 times slower. Improvements in both hardware and software have now largely eliminated this issue. \u00b6<\/sup>Thus using Jquery<\/a>.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

Ten years are a long time when it comes to (recent) technologies. The first post on this blog was on the topic of how to present chemistry with three intact dimensions. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). 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