VDW (van der Waals) radii are used to show atoms in the sphere representation and, when multiplied by the ball scale factor, the ball-and-stick representation. VDW radii are also used in calculating surfaces, finding close contacts, and rendering atoms with conic and neon.
VDW radii are stored as the atom attribute radius. Chimera assigns default values based on atom type, but radii can be changed.
For C, N, O, and S, the default VDW radii depend on whether explicit hydrogen atoms are present:
The packing density in proteins: standard radii and volumes. Tsai J, Taylor R, Chothia C, Gerstein M. J Mol Biol. 1999 Jul 2;290(1):253-66.
Ionic radii from The CRC Handbook of Chemistry and Physics, 82nd Edition (2001-2002) are used for ions. If the charge state of an ion differs from that listed in the table, a different radius may be more appropriate.
For P, and for F, Cl, Br, and I in the context of molecules (as opposed to singleton ions), all atom radii derived from the Amber parm99 parameters are used.
The default VDW radii of any remaining atoms are twice the covalent bond radii listed in Table III of:
Determination of molecular topology and atomic hybridization states from heavy atom coordinates. Meng EC, Lewis RA. J Comput Chem. 1991 Sep;12(7):891-8.
Ways to change VDW radii directly: