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.
To correct an error present in the original. In fact I did have to make one unavoidable change, to 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!). The Jmol2.js converter script had not been coded to detect such invocations. 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. Well, almost all syntax, but not in fact the variation I had used throughout this blog, which took the form: 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.
#Jmol applet download how to
† Now the challenge becomes how to replace Jmol by JSmol, whilst retaining the original Jmol Java-based syntax (as described in the original post).
‡ Modern replacements are based on JavaScript, and the standard tool for presenting molecular models, Jmol has been totally refactored into JSmol. NPAPI has now been withdrawn from pretty much all modern browsers. Java was implemented into web browsers via something called Netscape Plugin Application Programming Interface or NPAPI, dating from around 1995. Gradually over this decade, use of the Java technology has become more challenging, largely in an effort to make Web-page security higher.
That first post described how the Java-based applet Jmol could be used to present 3D models and animations. 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. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). The first post on this blog was on the topic of how to present chemistry with three intact dimensions. Ten years are a long time when it comes to (recent) technologies.
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