[Biopython] ligand PDB files
paul at tonair.de
paul at tonair.de
Fri Oct 14 12:00:04 UTC 2011
Dear all,
I'm having trouble to read in the attached PDB file - this
is my code:
"
from Bio.PDB import
*
parser=PDBParser()
structure=parser.get_structure("PHA-L","./2w26_lig.pdb")
for model in structure:
for chain in model:
for residue in chain:
for atom in residue:
print atom
"
which gives this error:
"
File
"/SW/python/lib/python2.6/site-packages/biopython/Bio/PDB/PDBParser.py",
line 66, in get_structure
self._parse(file.readlines())
File
"/SW/python/lib/python2.6/site-packages/biopython/Bio/PDB/PDBParser.py",
line 89, in _parse
self.trailer=self._parse_coordinates(coords_trailer)
File
"/SW/python/lib/python2.6/site-packages/biopython/Bio/PDB/PDBParser.py",
line 205, in _parse_coordinates
fullname, serial_number, element)
File
"/SW/python/lib/python2.6/site-packages/biopython/Bio/PDB/StructureBuilder.py",
line 197, in init_atom
fullname, serial_number, element)
File
"/SW/python/lib/python2.6/site-packages/biopython/Bio/PDB/Atom.py", line
68, in __init__
assert not element or element == element.upper(),
element
AssertionError: Cl
"
Does this mean that the PDB parser only
recognizes "amino acid-atoms", i.e. a chlorine does not work?
Cheers &
Thanks,
Paul
-------------- next part --------------
COMPND 2w26_LIG.pdb_0
AUTHOR GENERATED BY OPEN BABEL 2.3.0
ATOM 1 C1 RIV A 1 9.643 1.777 18.433 1.00 0.00 C
ATOM 2 N1 RIV A 1 8.303 2.377 18.109 1.00 0.00 N
ATOM 3 C2 RIV A 1 10.053 0.667 17.441 1.00 0.00 C
ATOM 4 C3 RIV A 1 7.671 2.122 16.881 1.00 0.00 C
ATOM 5 O1 RIV A 1 9.768 1.124 16.111 1.00 0.00 O
ATOM 6 C4 RIV A 1 8.355 1.223 15.853 1.00 0.00 C
ATOM 7 C5 RIV A 1 6.487 4.959 20.981 1.00 0.00 C
ATOM 8 C6 RIV A 1 7.333 5.468 19.984 1.00 0.00 C
ATOM 9 C7 RIV A 1 6.237 3.551 21.013 1.00 0.00 C
ATOM 10 C8 RIV A 1 7.918 4.619 19.048 1.00 0.00 C
ATOM 11 C9 RIV A 1 6.837 2.690 20.070 1.00 0.00 C
ATOM 12 C10 RIV A 1 7.682 3.222 19.078 1.00 0.00 C
ATOM 13 O2 RIV A 1 6.583 2.613 16.630 1.00 0.00 O
ATOM 14 N2 RIV A 1 5.906 5.863 21.947 1.00 0.00 N
ATOM 15 C11 RIV A 1 5.040 5.543 22.995 1.00 0.00 C
ATOM 16 C12 RIV A 1 6.146 7.326 22.000 1.00 0.00 C
ATOM 17 O3 RIV A 1 4.690 6.614 23.757 1.00 0.00 O
ATOM 18 C13 RIV A 1 5.213 7.787 23.134 1.00 0.00 C
ATOM 19 O4 RIV A 1 4.634 4.419 23.228 1.00 0.00 O
ATOM 20 C14 RIV A 1 5.924 8.721 24.155 1.00 0.00 C
ATOM 21 N3 RIV A 1 7.078 8.136 24.932 1.00 0.00 N
ATOM 22 C15 RIV A 1 8.402 8.558 24.672 1.00 0.00 C
ATOM 23 S1 RIV A 1 11.131 8.264 25.063 1.00 0.00 S
ATOM 24 C16 RIV A 1 11.805 7.503 26.288 1.00 0.00 C
ATOM 25 C17 RIV A 1 9.567 8.044 25.466 1.00 0.00 C
ATOM 26 C18 RIV A 1 10.794 7.011 27.130 1.00 0.00 C
ATOM 27 C19 RIV A 1 9.509 7.324 26.659 1.00 0.00 C
ATOM 28 O5 RIV A 1 8.611 9.379 23.797 1.00 0.00 O
ATOM 29 Cl1 RIV A 1 13.544 7.302 26.531 1.00 0.00 Cl
ATOM 30 H RIV A 1 9.643 1.777 18.433 1.00 0.00 H
ATOM 31 H RIV A 1 9.643 1.777 18.433 1.00 0.00 H
ATOM 32 H RIV A 1 10.053 0.667 17.441 1.00 0.00 H
ATOM 33 H RIV A 1 10.053 0.667 17.441 1.00 0.00 H
ATOM 34 H RIV A 1 8.355 1.223 15.853 1.00 0.00 H
ATOM 35 H RIV A 1 8.355 1.223 15.853 1.00 0.00 H
ATOM 36 H RIV A 1 7.333 5.468 19.984 1.00 0.00 H
ATOM 37 H RIV A 1 6.237 3.551 21.013 1.00 0.00 H
ATOM 38 H RIV A 1 7.918 4.619 19.048 1.00 0.00 H
ATOM 39 H RIV A 1 6.837 2.690 20.070 1.00 0.00 H
ATOM 40 H RIV A 1 6.146 7.326 22.000 1.00 0.00 H
ATOM 41 H RIV A 1 6.146 7.326 22.000 1.00 0.00 H
ATOM 42 H RIV A 1 5.213 7.787 23.134 1.00 0.00 H
ATOM 43 H RIV A 1 5.924 8.721 24.155 1.00 0.00 H
ATOM 44 H RIV A 1 5.924 8.721 24.155 1.00 0.00 H
ATOM 45 H RIV A 1 7.078 8.136 24.932 1.00 0.00 H
ATOM 46 H RIV A 1 10.794 7.011 27.130 1.00 0.00 H
ATOM 47 H RIV A 1 9.509 7.324 26.659 1.00 0.00 H
CONECT 1 3 2 30 31
CONECT 1
CONECT 2 4 1 12
CONECT 3 5 1 32 33
CONECT 3
CONECT 4 6 13 2
CONECT 5 6 3
CONECT 6 5 4 34 35
CONECT 6
CONECT 7 8 9 14
CONECT 8 10 7 36
CONECT 9 11 7 37
CONECT 10 12 8 38
CONECT 11 12 9 39
CONECT 12 2 10 11
CONECT 13 4
CONECT 14 7 16 15
CONECT 15 14 19 17
CONECT 16 14 18 40 41
CONECT 16
CONECT 17 15 18
CONECT 18 16 17 20 42
CONECT 18
CONECT 19 15
CONECT 20 18 21 43 44
CONECT 20
CONECT 21 20 22 45
CONECT 22 28 21 25
CONECT 23 25 24
CONECT 24 23 29 26
CONECT 25 22 23 27
CONECT 26 24 27 46
CONECT 27 25 26 47
CONECT 28 22
CONECT 29 24
CONECT 30 1
CONECT 31 1
CONECT 32 3
CONECT 33 3
CONECT 34 6
CONECT 35 6
CONECT 36 8
CONECT 37 9
CONECT 38 10
CONECT 39 11
CONECT 40 16
CONECT 41 16
CONECT 42 18
CONECT 43 20
CONECT 44 20
CONECT 45 21
CONECT 46 26
CONECT 47 27
MASTER 0 0 0 0 0 0 0 0 47 0 47 0
END
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