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.

       --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.

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

version 4.0.2                                      2021-08-31                                          mkdssp(1)