Vdw displays dot van der Waals surfaces for the atoms in atom-spec.
The default radii depend on whether explicit hydrogen atoms are present. When there are no explicit hydrogens, the radii of some atoms are enlarged to compensate. VDW radii can be altered with vdwdefine and the density of dots can be changed using vdwdensity.
Details of the vdw algorithm can be found in:
Van der Waals Surfaces in Molecular Modeling: Implementation with Real-Time Computer Graphics. Bash PA, Pattabiraman N, Huang C, Ferrin TE, Langridge R. Science. 1983 Dec 23;222(4630):1325-1327.See also: surface, vdwdefine, vdwdensity