NAME

       mkdssp - Assign secondary structure to proteins

SYNOPSIS

       mkdssp [OPTION] input [output]

DESCRIPTION

       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

       ┌────────────┬──────────────┬─────────────┐
       │ DSSP Code  │  mmCIF Code  │ Description │
       ├────────────┼──────────────┼─────────────┤
       │H           │ HELX_RH_AL_P │ Alphahelix  │
       ├────────────┼──────────────┼─────────────┤
       │B           │ STRN         │ Betabridge  │
       ├────────────┼──────────────┼─────────────┤
       │E           │ STRN         │ Strand      │
       ├────────────┼──────────────┼─────────────┤
       │G           │ HELX_RH_3T_P │ Helix_3     │
       ├────────────┼──────────────┼─────────────┤
       │I           │ HELX_RH_PI_P │ Helix_5     │
       ├────────────┼──────────────┼─────────────┤
       │P           │ HELX_LH_PP_P │ Helix_PPII  │
       ├────────────┼──────────────┼─────────────┤
       │T           │ TURN_TY1_P   │ Turn        │
       ├────────────┼──────────────┼─────────────┤
       │S           │ BEND         │ Bend        │
       ├────────────┼──────────────┼─────────────┤
       │' ' (space) │ OTHER        │ Loop        │
       └────────────┴──────────────┴─────────────┘

BUGS

       The mmCIF format currently lacks a lot of information that was available in the old format
       like information about the bridge pairs or the span of the various helices recognized.
       Also the accessibility information is left out.

       If you think this information should be part of the output, please contact the author.

AUTHOR

       Written by Maarten L. Hekkelman <maarten@hekkelman.com>

REPORTING BUGS

       Report bugs at https://github.com/PDB-REDO/dssp/issues