Imperial College London

Henry Rzepa

![](https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2021/07/a80.jpg){loading="lazy"
decoding="async" width="292" height="354"
onclick="jmolApplet([500,500],'load wp-content/uploads/2021/07/a73.xyz;isosurface wp-content/uploads/2021/07/a73.jvxl;isosurface append wp-content/uploads/2021/07/a80.jvxl translucent;','c1');"}

Click on the static image to get an active model. The code used to
obtain the above was:

1.  <script src="../Jmol/Jmol.js" type="text/javascript" />

2.  This line is best added to the theme header by editing the file
    /wp-content/themes/default/header.php to add the following line in
    the header:

    `<script src="../Jmol/Jmol.js" type="text/javascript"></script>`

3.  [\<img
    onclick="jmolInitialize('../Jmol/','JmolAppletSigned.jar');jmolSetAppletColor('yellow');  
    jmolApplet(\[450,450\],'load
    wp-content/uploads/2009/08/HV2-62.jvxl;isosurface translucent;zoom
    5;moveto 4 0 2 0 90 70;');"  alt="A lemniscular molecular orbital"
    src="http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2008/04/14-knot.jpg"
    /\>]{.small}

    where of course the uploads directory needs to be modified to
    correspond to your own content, and the file and script following it
    also correspond to the effect you wish to achieve.

The path **wp-content/uploads/2009/08/** is that created by the built-in
editor using the **Add media file upload** mechanism. The Jmol directory
is located at the level above that of the blog itself. The JVXL file is
created from either the corresponding (Gaussian) output file, or a CUB
file created using a program such as Gaussview. Any suitable surface can
be displayed using JVXL. In addition to MOs, we have also displayed ELF
(Electron localization function) isosurfaces and molecular vibrations.
For the latter, use a script of the form

`'load wp-content/uploads/2008/04/vibration.log; frame 9; vectors on;vectors 4;vectors scale 5.0; color vectors green; vibration 10;animation mode loop;'`

where the vibration you want is contained in e.g. frame 9.

There does appear to be a display bug with the above; the Jmol model
replaces the window rather than being inlined in it. Once the model is
displayed, just refresh the page to return to the blog entry.

A recent addition is the display of non-covalent-interaction (NCI)
surfaces, which are colour coded by using the values in one cube of
points to colorize a second cube.

`'load wp-content/uploads/2011/05/isobornyl1.xyz;isosurface wp-content/uploads/2011/05/isobornyl1.jvxl colorscheme translucent bgyor;'`

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


Click on the static image to get an active model.

Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog

[does what it says on the
tin](feed://www.ch.ic.ac.uk/rzepa/blog/?feed=rss2).

<table data-bgcolor="#FFFFFF">
<colgroup>
<col style="width: 100%" />
</colgroup>
<tbody>
<tr class="odd">
<td><a href="http://scholar.google.com/"><img
src="http://scholar.google.com/scholar/scholar_sm.gif" loading="lazy"
decoding="async" data-border="0" data-align="absmiddle" width="105"
height="40" alt="Google Scholar" /></a><br />
<br />
<br />
</td>
</tr>
</tbody>
</table>

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


Messaggi di Rogue Scholar

Jmol and WordPress: Loading 3D molecular models, molecular isosurfaces and molecular vibrations into a blog

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