mkdssp - Assign secondary structure to proteins
mkdssp [OPTION] input [output]
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.
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.
- 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.
- 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.
- By default the new format does not write the structure information for OTHER. Use this flag to change that.
The DSSP algorithm assings secondary structure based on the energy
calculated for H-bonds.
Table 1. Secondary Structures recognized
|DSSP Code||mmCIF Code||Description|
|' ' (space)||OTHER||Loop|
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.
Written by Maarten L. Hekkelman <email@example.com>
Report bugs at https://github.com/PDB-REDO/cif-tools/issues
cif-drop, cif-grep, cif-merge, cif-validate, cif2pdb, mmCQL, pdb2cif.