# CalcSecondary

NAME

    CalcSecondary - calculate secondary structure

SYNOPSIS

    CalcSecondary

DESCRIPTION

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

SEE ALSO

`SelectMol`, `SelectRes`, `CalcAtom`, `DefPropRes`, `WriteSecondary`, `AddRibbon`

DATE

960815