VDW Radii

The VDW radii of atoms are used not only in displaying VDW surfaces with vdw but also in representing atoms in CPK and ball-and-stick form (ball radii are smaller than but proportional to VDW radii) and similarly in rendering programs such as conic and ribbonjr.

If an atom is selected, its radius is reported in the Selection Inspector. VDW radii can be altered in the Selection Inspector or with the command vdwdefine.

The default VDW radii of some atoms depend on whether explicit hydrogen atoms are present. For ions, it does not matter; ionic radii from The CRC Handbook of Chemistry and Physics, 82nd Edition (2001-2002) are used. If the charge state of an ion differs from that listed in the table, changing the radius may be appropriate.

• When there are explicit hydrogens, the default radii are based on a set of values used in Midas. The default "all atom" radii are assigned according to standard atom and residue names. The radii of atoms other than H, C, O, N, P, S, and ions are set to twice their covalent bond radii, which are listed in Table III of

  "Determination of Molecular Topology and Atomic Hybridization States from Heavy Atom Coordinates," E.C. Meng and R.A. Lewis, J. Comp. Chem., 12, 891 (1991).

• When there are no explicit hydrogens, the radii of some atoms are enlarged slightly to compensate. The default "united atom" radii are based on the ProtOr radii in

  "The Packing Density in Proteins: Standard Radii and Volumes," J. Tsai, R. Taylor, C. Chothia, and M. Gerstein, J. Mol. Biol., 290, 253 (1999).

  The radii of atoms other than H, C, O, N, P, S, and ions are set to twice their covalent bond radii, as described above.