The torsion angle part of WHAT IF not very tightly grouped in one menu.
This is because torsion angles, or chi-angles
as the phi, psi, omega and chi-1 through chi-5 together are normally
called in WHAT IF, are a rather intricate part of many other options.
You will therefore find some chi-angle related options outside the chi-angle
menu. If you type CHIANG, you will enter the chi-angle manipulation and
evaluation menu.
The command SHOCHI will cause WHAT IF to prompt you for a residue range. All
torsion angles in this range will be listed at the screen. this option only
works for amino acids.
The command EVACHI will cause WHAT IF to prompt you for a residue range. All
torsion angles in this range will be compared with the distribution of the
same torsion angle in the 30 best refined proteins from the PDB. You will
get a score for `normallity`, not for `correctness` or energetics. In
this score 0.0 means that this torsion angle value is unique, whereas 5.0
means that this torsion angle has the most common value. You will also
get a total normality-value, and the average normality value (with standard
deviation) for this torsion angle as found in those same 30 proteins.
WARNING. A low normality value does not mean that something is wrong. Also
a high normality value is no reason to believe that your protein is perfect.
In case of unlikely conformations, or energetically unfavourable conformations
a warning will be given.
At the bottom of the table the averages per torsion angle type are given. These
numbers are only usefull for crystallographers and NMR spectroscopists that
want to compare subsequent steps in structure refinement procedures.
The command SETCHI will cause WHAT IF to prompt you for a residue. Here you
may only enter amino acids. Thereafter you will be prompted for the name
of the torsion angle. This can be F, P, O (O, not zero), 1, 2, 3, 4, or 5
for phi, psi,
omega, and chi-1 till chi-5 respectively. The old values for all torsion
angles in the chosen residue will be shown, and you will be prompted for the
new value. This value will then immediately be applied to all atoms
needed. This means that if you change a phi, psi, or omega angle then all
residues C-terminal of this angle will also be rotated. This has often
created unexpected results! If you do not want this, you should use the
CUT command in the SOUP menu to put a chain break immediately C-terminal
of the residue for which you want to change a backbone torsion angle.
The command RNGCHI will cause WHAT IF to prompt you for a residue range. Here you
may only enter amino acids. Thereafter you will be prompted for the name
of the torsion angle. This can be F, P, or O (O, not zero) for phi, psi and
omega respectively. You will be prompted for the
new value of this angle. This value will then immediately be applied to all atoms
needed. This means that all
residues C-terminal of every angle will also be rotated. This has often
created unexpected results! If you do not want this, you should use the
CUT command in the SOUP menu to put a chain break immediately C-terminal
of the last residue to which you want to apply the changes.
Under normal conditions WHAT IF will only work with phi, psi, omega and
chi-1 of cysteines. The administration involved in the manipulation of
the other torsion angles of cysteines that are part of a cys-cys bridge
is too much for WHAT IF (and for me). However, if you are interested in these
angles, you can use the CYSCHI option. If will for all cys-cys bridges
show the five side chain torsion angles.