dssp - Secondary structure assignment

Introduction

DSSP is a program developed by Wolfgang Kabsch and Chris Sander to assign secondary structure states to protein structures. The assignment is based on hydrogen bonding patterns and geometric features.

The program can be downloaded from http://swift.cmbi.ru.nl/gv/dssp/.

Warning

Support of the DSSP program has been deprecated. OpenStructure provides functionality to assign equivalent secondary structures (ost.mol.alg.AssignSecStruct()) and solvent accessibility (ost.mol.alg.Accessibility()). You’re advised to use these algorithms.

AssignDSSP() still exists and provides the “old” interface but internally uses the OpenStructure impmlementations and does not call an external program anymore.

Examples

The following example assigns secondary structure states to an entity by using the DSSP program.

from ost.bindings import dssp
ent=io.LoadPDB('1ake.pdb')
dssp.AssignDSSP(ent)

Now we fetch structure information plus solvent accessibility for an entity using the mmCIF interface.

from ost.bindings import dssp
ent=io.LoadMMCIF('1ake.cif')
dssp.AssignDSSP(ent, extract_burial_status=True)
for chain in ent.chains:
  if chain.is_polypeptide:
    for res in chain.residues:
      print(res.GetFloatProp('relative_solvent_accessibility'))

DSSP bindings Usage

AssignDSSP(ent, pdb_path='', extract_burial_status=False, tmp_dir=None, dssp_bin=None)

Assign secondary structure states to peptide residues in the structure. This function replaces the “old” AssignDSSP which relies on the DSSP command line program and uses OpenStructure internal functionality only. The sole purpose is to retain the “old” interface and you’re adviced to directly use ost.mol.alg.AssignSecStruct() and ost.mol.alg.Accessibility().

If you already have a DSSP output file and would like to assign the secondary structure states to an entity, use LoadDSSP().

Parameters:

  • ent (EntityHandle or EntityView) – The entity for which the secondary structure should be calculated

  • extract_burial_status – If true, also extract burial status and store as float-property relative_solvent_accessibility at residue level

  • tmp_dir – If set, overrides the default tmp directory of the operating system - deprecated, has no effect

  • dssp_bin – The path to the DSSP executable - deprecated, has no effect

LoadDSSP(file_name, model, extract_burial_status=False, entity_saved=False, calculate_relative_sa=True)

Loads DSSP output and assigns secondary structure states to the peptidic residues.

If you would like to run dssp and assign the secondary structure, use AssignDSSP() instead.

Parameters:

  • file_name – The filename of the DSSP output file

  • model – The entity to which the secondary structure states should be assigned

  • extract_burial_status – If true also calculates burial status of residues and assigns it to the burial_status string property.

  • calculate_relative_sa – If true also relative solvent accessibility and and assigns it to the relative_solvent_accessibility float property of the residue.

  • entity_save – Whether the entity was saved.