VDW Radii

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, but the radii can be changed.

Default Assignments

For C, N, O, and S, the default VDW radii depend on whether explicit hydrogen atoms are present:

• When a molecule model has no explicit hydrogens, "united atom" radii based on the ProtOr set are used:

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

• When there are explicit hydrogens, "all atom" radii derived from the Amber parm99 parameters are used for the filled-valence atoms. United atom radii are used for any atoms with unfilled valence (those apparently missing hydrogens).

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:

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

Changing VDW Radii

Ways to change VDW radii directly:

• with the command vdwdefine (~vdwdefine restores the default values)
• by selecting one or more atoms and then changing the radius value in the Selection Inspector
• reassigning radius values with Define Attribute or its command equivalent, defattr (can assign multiple values simultaneously; see example assignment file)
• reassigning radius with the command setattr (assigns one value at a time, although potentially to multiple atoms)
• according to attribute values using Render by Attribute (see the Radii section)