Bio.PDB.DSSP module

Use the DSSP program to calculate secondary structure and accessibility.

You need to have a working version of DSSP (and a license, free for academic use) in order to use this. For DSSP, see https://swift.cmbi.umcn.nl/gv/dssp/.

The following Accessible surface area (ASA) values can be used, defaulting to the Sander and Rost values:

The DSSP codes for secondary structure used here are:

Code

Structure

H

Alpha helix (4-12)

B

Isolated beta-bridge residue

E

Strand

G

3-10 helix

I

Pi helix

T

Turn

S

Bend

-

None

Usage

The DSSP class can be used to run DSSP on a PDB or mmCIF file, and provides a handle to the DSSP secondary structure and accessibility.

Note that DSSP can only handle one model, and will only run calculations on the first model in the provided PDB file.

Examples

Typical use:

from Bio.PDB import PDBParser
from Bio.PDB.DSSP import DSSP
p = PDBParser()
structure = p.get_structure("1MOT", "/local-pdb/1mot.pdb")
model = structure[0]
dssp = DSSP(model, "/local-pdb/1mot.pdb")

Note that the recent DSSP executable from the DSSP-2 package was renamed from dssp to mkdssp. If using a recent DSSP release, you may need to provide the name of your DSSP executable:

dssp = DSSP(model, '/local-pdb/1mot.pdb', dssp='mkdssp')

DSSP data is accessed by a tuple - (chain id, residue id):

a_key = list(dssp.keys())[2]
dssp[a_key]

The dssp data returned for a single residue is a tuple in the form:

Tuple Index

Value

0

DSSP index

1

Amino acid

2

Secondary structure

3

Relative ASA

4

Phi

5

Psi

6

NH–>O_1_relidx

7

NH–>O_1_energy

8

O–>NH_1_relidx

9

O–>NH_1_energy

10

NH–>O_2_relidx

11

NH–>O_2_energy

12

O–>NH_2_relidx

13

O–>NH_2_energy
Bio.PDB.DSSP.version(version_string)

Parse semantic version scheme for easy comparison.

Bio.PDB.DSSP.ss_to_index(ss)

Secondary structure symbol to index.

H=0 E=1 C=2

Bio.PDB.DSSP.dssp_dict_from_pdb_file(in_file, DSSP='dssp', dssp_version='3.9.9')

Create a DSSP dictionary from a PDB file.

Parameters:
in_filestring

pdb file

DSSPstring

DSSP executable (argument to subprocess)

dssp_versionstring

Version of DSSP executable

Returns:
(out_dict, keys)tuple

a dictionary that maps (chainid, resid) to amino acid type, secondary structure code and accessibility.

Examples

How dssp_dict_from_pdb_file could be used:

from Bio.PDB.DSSP import dssp_dict_from_pdb_file
dssp_tuple = dssp_dict_from_pdb_file("/local-pdb/1fat.pdb")
dssp_dict = dssp_tuple[0]
print(dssp_dict['A',(' ', 1, ' ')])
Bio.PDB.DSSP.make_dssp_dict(filename)

DSSP dictionary mapping identifiers to properties.

Return a DSSP dictionary that maps (chainid, resid) to aa, ss and accessibility, from a DSSP file.

Parameters:
filenamestring

the DSSP output file

class Bio.PDB.DSSP.DSSP(model, in_file, dssp='dssp', acc_array='Sander', file_type='')

Bases: AbstractResiduePropertyMap

Run DSSP and parse secondary structure and accessibility.

Run DSSP on a PDB/mmCIF file, and provide a handle to the DSSP secondary structure and accessibility.

Note that DSSP can only handle one model.

Examples

How DSSP could be used:

from Bio.PDB import PDBParser
from Bio.PDB.DSSP import DSSP
p = PDBParser()
structure = p.get_structure("1MOT", "/local-pdb/1mot.pdb")
model = structure[0]
dssp = DSSP(model, "/local-pdb/1mot.pdb")
# DSSP data is accessed by a tuple (chain_id, res_id)
a_key = list(dssp.keys())[2]
# (dssp index, amino acid, secondary structure, relative ASA, phi, psi,
# NH_O_1_relidx, NH_O_1_energy, O_NH_1_relidx, O_NH_1_energy,
# NH_O_2_relidx, NH_O_2_energy, O_NH_2_relidx, O_NH_2_energy)
dssp[a_key]
__init__(model, in_file, dssp='dssp', acc_array='Sander', file_type='')

Create a DSSP object.

Parameters:
modelModel

The first model of the structure

in_filestring

Either a PDB file or a DSSP file.

dsspstring

The dssp executable (ie. the argument to subprocess)

acc_arraystring

Accessible surface area (ASA) from either Miller et al. (1987), Sander & Rost (1994), Wilke: Tien et al. 2013, or Ahmad et al. (2003) as string Sander/Wilke/Miller/Ahmad. Defaults to Sander.

file_type: string

File type switch: either PDB, MMCIF or DSSP. Inferred from the file extension by default.