Imperial College London

Henry Rzepa

A word of explanation about this test page for experimenting with JSmol.
Many moons ago [I
posted](http://www.ch.imperial.ac.uk/rzepa/blog/?p=8 "Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog"){target="_blank"}
about how to include a generated 3D molecular model in a blog post, and
have used that method on many posts here ever since. It relied on Java
as the underlying software (first introduced in 1996), or almost 20
years ago. Like most software technologies, much has changed, and Java
itself (as a compiled language) has had to move to improve its
underlying security. In the last year, the Java code itself (in this
case Jmol) has needed to be digitally signed in a standard manner, and
this meant that many an old site that used unsigned older versions has
started to throw up increasingly alarming messages.

To continue to experience the intended effect of eg Jmol, the user in
turn has had to increasingly accept or tinker with their local Java
settings; this has indeed become increasingly intrusive. And less
experienced users often do not wish to engage with any of this activity.
About two years ago, the Jmol community started having
concerted discussions about what to do regarding Java, and they also
started to converge with other developers and communities about a
solution based on Javascript (which despite the name operates in an
entirely different way from Java). Some of this early activity I tried
to capture in a datument written during the summer of
2012\[cite\]10.1186/1758-2946-5-6\[/cite\]. The magnitude of the problem
was considerable, how to refactor tens of thousands of Java-Code into
JavaScript. The story of how this miracle was accomplished must be
written by people like [Bob
Hanson](http://wiki.jmol.org/index.php/Jmol_JavaScript_Object){target="_blank"}
and [Takanori
Nakane](%C2%A0http://webglmol.sourceforge.jp/index-en.html){target="_blank"} and
perhaps some day they will. However, inserting all this wonderful
technology into eg a WordPress blog still needed doing, and this task
was undertaken by [Jim
Hu](https://github.com/jimhu-tamu/wordpress/tree/master/){target="_blank"} (and
there are many others that are part of this effort, they all need to be
thanked).

I volunteered to test, but so that Jim could see the effects of this
testing, this (public) test page was created. Behind the scenes, the
bugs have been winkled out, although much still remains to be done. This
page will no doubt continue to evolve as this is done, and when it all
works, I will no doubt add a postscript. So keep watching this space. It
has two examples, each of which should produce a box with a molecule, as
per [this blog
post](http://www.rzepa.net/blog/?p=14272){target="_blank"}.

1.  \[jsmol pdb='1PRC' caption='Load 1PRC' commands=" id='a1′
    debug='true'\]
2.  \[jsmol caption='Load local file'
    fileurl='http://rzepa.net/blog/wp-content/uploads/2014/06/test2.pdb'
    id='a2′ commands='=spacefill 23%;wireframe 0.15;color cpk;'
    debug='true'\]

::: {.wp_orcid_field}
[https://orcid.org/0000-0002-8635-8390](https://orcid.org/0000-0002-8635-8390){target="_blank"
rel="author"}
:::


A word of explanation about this test page for experimenting with JSmol. Many moons ago I posted about how to include a generated 3D molecular model in a blog post, and have used that method on many posts here ever since. It relied on Java as the underlying software (first introduced in 1996), or almost 20 years ago.

Publicaciones de Rogue Scholar

Test of JSmol in WordPress: the background story.