ksdssp (1) - generate HELIX and SHEET records from protein coordinates

KSDSSP(1)

NAME

ksdssp - generate HELIX and SHEET records from protein coordinates

SYNOPSIS

ksdssp [ -c cutoff ] [ -h length ] [ -s length ] [ -S file ]

[ PDB_file [ output_file ] ]

DESCRIPTION

Ksdssp is an implementation of the Kabsch and Sander algorithm for defining secondary structure of proteins. Ksdssp reads a Protein Data Bank format file containing coordinates of the backbone atoms (N, CA, C, O, and optionally H) of a protein and generates HELIX and SHEET records. If an amide hydrogen is missing, it is placed 1.01 angstroms from N along the bisector of (1) the vector opposite the bisector of C-N-CA, and (2) the vector opposite the C-O vector from the previous amino acid.

COMMAND ARGUMENTS

-c energy_cutoff: The default energy cutoff for defining hydrogen bonds as recommended by Kabsch and Sander is -0.5 kcal/mol (``A good H-bond has about -3 kcal/mol binding energy''). This option allows the user to change the cutoff.

-h minimum_helix_length: Normally, HELIX records for helices of length three residues or greater are generated. This option allows the user to change the minimum helix length.

-s minimum_strand_length: Normally, SHEET records for strands of length three residues or greater are generated. This option allows the user to change the minimum strand length. Reducing the minimum strand length to 1 is not recommended, as there are bridges in many structures that confuse the algorithm for defining sheets.

-S summary_file: Normally, ksdssp silently discards all the hydrogen- bonding information after generating the HELIX and SHEET records. This option makes ksdssp print the information to a file. The notation is similar to that used by Kabsch and Sander, but is in a vertical instead of horizontal format.

PDB_file: The input Protein Data Bank (PDB) file may contain any legal PDB records. Only ATOM records will be used. All others are silently discarded. If no PDB_file argument is given, the data is read from standard input.

output_file: The output of ksdssp is a set of PDB HELIX and SHEET records. If no output_file argument is given, the records are written to standard output.

AUTHORS

Conrad Huang