helix_kinks – Algorithms to Calculate Helix Kinks¶

Functions to calculate helix kinks: bend, face shift and wobble angles

Author: Niklaus Johner

AnalyzeHelixKink(t, sele, proline=False)¶

This function calculates the bend, wobble and face-shift angles in an alpha- helix over a trajectory. The determination is more stable if there are at least 4 residues on each side (8 is even better) of the proline around which the helix is kinked. The selection should contain all residues in the correct order and with no gaps and no missing C-alphas.

Parameters:

• t (CoordGroup) – The trajectory to be analyzed

• sele (EntityView) – A selection containing the alpha helix to be analyzed

• proline (ost.mol.EntityView) – A selection containing only the proline (or another residue) around which the helix is kinked. If False, the proline will be searched for automatically

Returns:

A tuple (bend_angle, face_shift, wobble_angle).

Return type:

(FloatList, FLoatList, FloatList)

CalculateHelixKink(sele, proline=False)¶

This function calculates the bend, wobble and face-shift angles in an alpha- helix of an EntityView. The determination is more stable if there are at least 4 residues on each side (8 is even better) of the proline around which the helix is kinked. The selection should contain all residues in the correct order and with no gaps and no missing C-alphas.

Parameters:

• sele (EntityView) – A selection containing the alpha helix to be analyzed

• proline (ost.mol.EntityView) – A selection containing only the proline (or another residue) around which the helix is kinked. If False, the proline will be searched for automatically

Returns:

A tuple (bend_angle, face_shift, wobble_angle).

Return type:

(float, float, float)