Script for creating a JVXL compressed surface file from a (Gaussian) cube

This script will invoke a file dialog to open a .cub file and will save tworesulting files to your local directory (in the downloads area by default). Important:. The .cub files must be located in a directory for a local hard drive rather than in a network directory. Thus drive C:\temp is fine, but drive H: is not (it is a network drive).

The .jvxl file will be around 100 to 150 times smaller than the original .cub (which is pretty much the purpose of doing all of this). You could if you wanted reduce it further in size by compressing it using gzip (Jmol will automatically detect and decompress this). You will end up with something that looks like name.jvxl.gz and you can safely rename this file to the original name.jvxl

To load the .xyz and .jvxl files into a Wiki or a blog, upload these two files and then invoke them with the following jmol script (changing the string isosurface to whatever your file is named. The path to the file name also has to be inserted, and how to do this is described on the Wiki link).

<jmol>
   <jmolApplet>
       <title>Orbital</title><color>white</color><size>300</size>
       <script>isosurface color orange purple "images/4/42/AHB_mo22.jvxl" translucent;</script>
       <uploadedFileContents>AHB_mo22.xyz</uploadedFileContents>
    </jmolApplet>
</jmol>

You can add a second surface as:

<jmol>
   <jmolApplet>
       <title>Orbital</title><color>white</color><size>300</size>
       <script>isosurface color orange purple "images/4/42/AHB_mo22.jvxl" translucent;isosurface append color red blue "images/4/42/isosurface2.jvxl" translucent;</script>
       <uploadedFileContents>AHB_mo22.xyz</uploadedFileContents>
    </jmolApplet>
</jmol>

the colours orange purple can be transposed to say purple orange if that matches the desired phases of the first and second orbitals.