WHAT IF uses a consistent set of Van der Waals radii. You can use this menu
to change these radii if you want to alter the behaviour of accessibility
calculations or graphical options like the Van der waals surface, or the
RIBBONS radii.
The command SETVDW brings you in the Van der Waals menu manipulation menu.
This menu allows you to change Van der Waals radii. This might be needed to
check if other programs give the same results as WHAT IF, or to fudge the
program. It might also help in enhancing the graphics quality of some options.
The command VDWATT will show you a small mini-menu. You can choose between
S, which will show the present default radii; R, which will allow you to
change these defaults; A, which applies the default radii to a range of
residues etc. for which you will be prompted; and 0 (zero) which will leave
this mini-menu.
The command VDWBB will cause WHAT IF to prompt you for a residue range and
for a radius. All backbone atoms (N, C-alpha and C) within the given range
will get the requested Van der Waals radius. The default radii will not
be changed. See also VDWBBO.
The command VDWBBO will cause WHAT IF to prompt you for a residue range and
for a radius. All backbone oxygens within the given range
will get the requested Van der Waals radius. The default radii will not
be changed. See also VDWBB.
The command VDWSS will cause WHAT IF to prompt you for a residue range and
for a radius. All side chain atoms within the given range
will get the requested Van der Waals radius. The default radii will not
be changed.
The command VDWCA will cause WHAT IF to prompt you for a residue range and
for a radius. All alpha carbons within the given range
will get the requested Van der Waals radius. The default radii will not
be changed.
The command VDWRNG will cause WHAT IF to prompt you for a residue range and
for a radius. All atoms within the given range
will get the requested Van der Waals radius. The default radii will not
be changed.