VNL uses the
JMol color map to assign a unique color to each element. There is a reference in the manual too, but I find the attached pictures to be quite useful.
In addition to the color, they also indicate the van der Waals and covalent radii in a nice way.
I have also attached the input file I created to generate the figures. It's a simple XYZ file of the periodic table; just import it in VNL and drop it on the Nanoscope!
