The command EXTRA will bring you to the so-called EXTRA menu. This menu holds
a multitude of options that were hard to place in any other menu because
they logically did not really belong anywhere.
Several commands in this menu start with FOLD, these commands all have to do
with protein folding analysis and prediction.
These commands are experimental, and are still being worked on.
The command HELANG will cause WHAT IF to prompt you for two residue
ranges. You are supposed to give helical ranges, but you can try
to fudge WHAT IF... The best helical axis is calculated for each of
the ranges, and the angle between these two axes is calculated.
THe command HELANS will cause WHAT IF to calculate the angles between
all helix pairs in the soup. As output the residues that make the
helices and the angle in degrees is given for every pair.
A + sign is added to every pair of helices that makes at least one
inter helical atomic contact.
The command HLANDB will cause WHAT IF to loop over its entire databes
and calculate the interhelix angel
for every pair of helices that shares at least one
atomic contact. The results are tabulated in a histogram where
every bin represents one degree spread in angle. Two numbers
are given per bin, the actual counts, and a smoothed number (moving
average over a window of 11 degrees).
The command RANDOM will prompt you for a molecul number. All atoms
in this molecule get a random translation in the range -0.25 till
0.25 Angstrom added (independently) to each of their three coordinates.
The average movements of atoms will thus not have a gaussian
distribution.
Nevertheless, this option is nice to check refinement or energy
minimization techniques, and to check the dependence of certain
algorithms on atomic errors.