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:
- Ahmad
Ahmad et al. 2003 https://doi.org/10.1002/prot.10328
- Miller
Miller et al. 1987 https://doi.org/10.1016/0022-2836(87)90038-6
- Sander
Sander and Rost 1994 https://doi.org/10.1002/prot.340200303
- Wilke
Tien et al. 2013 https://doi.org/10.1371/journal.pone.0080635
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.