Provided by: dssp_4.4.10-1_amd64 
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
version 4.3.2 2023-06-13 mkdssp(1)