CalcSecondary

CalcSecondary - calculate secondary structure

CalcSecondary

Calculate the secondary structure of a protein using the algorithm published by Kabsch/Sander. The command operates on all selected residues of all selected molecules. It will set various properties on these residues, depending on the secondary structure. These properties are listed in a text window. They are used by the AddRibbon command to produce schematic drawings.

Note that editing the text has no effect on the definitons used. For changing the definitons it is most convenient to use the WriteSecondary command.

Since the calculation is based on hydrogen bonding patterns, the coordinates of HN atoms are required. So before using the command for a structure without coordinates for hydrogen atoms (X-ray), use the CalcAtom command for adding them.

EXAMPLE

CalcSecondary

SelectMol, SelectRes, CalcAtom, DefPropRes, WriteSecondary, AddRibbon

DATE

960815