Vdwdefine changes the van der Waals radii of atoms named atom_name in residues named res_name. If a plus (+) or minus (-) sign precedes value, the radii are increased or decreased, respectively, by value angstroms; otherwise, the radii are set to value angstroms. There should not be any space between the plus or minus sign and value. The optional atom-spec further restricts the set of atoms for which the radius is changed. Atom_name and res_name are case-insensitive, and the wild card * can be used to indicate all atoms or all residues.
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.
Examples:
vdwdefine * * 2.0 @c=- assign a radius of 2.0 to all atoms whose names begin with C
vdwdefine gly ca -0.5 :1-50- decrease the radii of the CA atoms of glycines occurring within residues 1-50 by 0.5 angstroms
Some tools perform related functions. Render by Attribute can assign atomic radii according to attribute values. Radii can be changed directly using Define Attribute (see the examples) or its command implementation, defattr. The radii of atoms that are selected can be changed with the Selection Inspector.
See also: vdw, vdwdensity