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mkdssp(1) User Commands mkdssp(1)

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 PP helices.

OPTIONS

The input file can be either mmCIF or PDB format and the file may be gzip or bzip2 compressed.

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/cif-tools/issues

SEE ALSO

cif-drop, cif-grep, cif-merge, cif-validate, cif2pdb, mmCQL, pdb2cif.
2020-11-23 version 1.0.0