Torsion angle evaluation and manipulation (CHIANG)

Introduction.

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.

Showing chi-angles (SHOCHI)

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.

Evaluation of chi-angles (EVACHI)

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.

Manually setting individual chi-angles (SETCHI)

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.

Manually setting groups of chi-angles (RNGCHI)

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.

Cysteine bridge torsion angles (CYSCHI)

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.