dssp1

Usage

Overview

The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). mkdssp is the program that calculates DSSP entries from PDB entries. mkdssp does not predict secondary structure.

The original DSSP program wrote output in a fixed format, this version by default writes annotated mmCIF files, storing the secondary structure information in the _struct_conf category.

Since version 4.0 the mkdssp program also assigns PPII helices.

Options

The input file can be either mmCIF or PDB format and the file may be gzip compressed. Note that input files must be formatted correctly. E.g. PDB files must have a CRYST1 record. More info: https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1

The output is optional, if omitted the output is written to stdout. If the name of the output file ends with either .gz or .bz2 the output is compressed accordingly.

--output-format=[dssp|mmcif]

If an output file is specified, the extension of the filename is used to choose to output format, but if it is unclear, mmcif is the default. Use this option to force output in either the old fixed column DSSP format or the new annotated mmCIF format.

--no-dssp-categories

When writing mmCIF files, suppress the output of all dssp_ categories.

--min-pp-stretch

This option can be used to define the minimal number of residues with PHI/PSI angles within the range required to assing a PP helix.

--write-other

By default the new format does not write the structure information for OTHER. Use this flag to change that.

--components

The knowledge of compounds is loaded from the CCD file components.cif that should have been installed by libcifpp. You can override that file by using this option.

--extra-compounds

As an addition to the standard components.cif file, you can add more files using this option. Files should be either in CCD format or should be CCP4 restraints files.

--mmcif-dictionary

The default mmCIF dictionary file is installed by the libcifpp library but you can override it using this option.

Details

The DSSP algorithm assings secondary structure based on the energy calculated for H-bonds.
Table 1. Secondary Structures recognized