Script for creating an NCI surface as a JVXL compressed file from a (Gaussian) cube of total electron density

  1. Perform Gaussian calculation as per normal and obtain the .fchk file.
  2. Using eg Gaussview (or cubegen), Results/Surfaces and contours/Cube actions/New cube and select Total density (medium or fine grid).
  3. Cube actions/Save cube. Do not save on a network drive (H:).


The following parameters are used to create the NCI surface;
isosurface parameters [0.5 1 0 0.05 0.95 1.00] NCI density.cube colorscheme "bgyor";color isosurface range 0.04 -0.04; where

  1. 0.5 is the surface cutoff. Use this value to reproduce the surfaces reported in the orginal article, and reduce it for smaller surfaces.
  2. 1 is the intramolecular option (2 for intermolecular)
  3. 0.05 is the cutoff used to remove covalent density (recommended as 0.05; set to 0.02 to remove the covalent density surrounding a metal atom.
  4. 0.95, fraction of total ρ(r) that defines intramolecular
  5. scaling factor. Set to 0.01 if reading cube files from the original NCIPlot program.
  6. colorscheme "bgyor" to match the colour scheme used in the original publications (blue= attractive, red=repulsive)
  7. color isosurface range 0.04 -0.04 defines the range of gradients for the colour mapping. This might be set automatically in future versions of Jmol.
  8. To invoke the output of the above transform of a cube file, place this into the script of a Jmol invocation:
    'load "S_den.cub.xyz";connect (atomno=9) (atomno=97) PARTIAL;connect (atomno=1) (atomno=2) NONE;set fontscaling TRUE; font label 24;select atomno=96;label %A S;isosurface "S_den.cub.jvxl" translucent;zoom 120;'

See Bob Hanson's documentation for more details.


This invokes a file dialog with your local computer. This works fine on OS X using local files. On Windows, ensure you specify local files and not files on a network drive (the path to the latter is specified differently on Windows, and is not supported by Jmol). For a list of browsers that support Java, see here

H. S. Rzepa, December, 2012 and 2018


Click here for density thresholds of 0.04 or 0.06. For a Web browser that supports Java, see https://blog.waterfoxproject.org/