Plotting wave functions using Jmol

In order to plot the Wavefunction files that NRLMOL genertates, you must do the following steps:

1. Take each one of the generated files (WFHOMO with some numbers next to it) and run the perl script that you can download from this article (you need to remove the .txt extension, the website puts in for security reasons), let's use the filename WFHOMO01 as an example. execute the command:
   ./adjust_cude_file.pl < WFHOMO01 > WFHOMO01.cube
   What this does is take the coordinates for the atoms that are in atomic units (which NRLMOL handles) in the WFHOMO01 file, and converts them to angstroms and rewrites the file into the WFHOMO01.cube file. (NOTE: This step is no longer needed in newer versions of NRLMOL, as the program creates the WFHOMO files with the units already in angstroms and with the .cube extension).
   The .cube file extension is necessary so thart Molekel or Jmol can process it, you must do this conversion for all the WFHOMO file that NRLMOL created.
2. Open Jmol and open one of the .cube file you just generated.
   The structure will show up, but nothing else.
3. Open the command console from: File -> Console
4. You can now plot the wave function density with:isosurface homo cutoff 0.00001 "WFHOMO01.cube"
5. You may need to run this command several times with different values to get it just right (it does have to be a really small number).
6. It is necessary to set the color for the HOMO and the LUMO levels.
   If plotting HOMO, it needs to be blue, so issue this command in the console:color isosurface blue
   If plotting LUMO, it needs to be red, so issue this command in the console:color isosurface red