Henry Rzepa's Blog

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” />

   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;'

Tags: animation, Chemical IT, editor, http, Interesting chemistry, jmol, php, Tutorial material, www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2008/04/14-knot.jpg

This entry was posted on Saturday, April 12th, 2008 at 5:15 pm and is filed under Chemical IT, Interesting chemistry. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.