Module: Compute Secondary Structure ()

Description:

Using the Kabsch-Sander algorithm to detect secondary structures, this module creates a new molecule filled with generated hydrogen bonds and possibly found secondary structures, such as helices, strands, sheets, and turns. Chains are not detected.

Press the Apply button to start the computation.

Connections:

Molecule [required]
A molecule for which the secondary structure should be generated.

Ports:

Minimum Angle

This angle determines the minimum angle a hydrogen bond must have. The angle of each bond is defined as the angle between the three atoms involved in the bond (alpha carbon - oxygen - nitrogen). The ideal value is about 180 degrees, representing a perfectly aligned hydrogen bond. Realistically this value may range from 120 to 240 degrees.

Considered Atoms

This port allows you to select which atoms will be considered during the computation. Better results may be obtained when only backbone-enriched atoms are used for the computation.

Write HBonds

This port lets you specify which hydrogen bonds to write out.

Maximum HBonds per Atom

Specifies the maximum allowable number of hydrogen bonds per atom.