How to unfold only protein atoms using Bio.PDB.Selection?
3
from Bio.PDB import PDBParser
from Bio.PDB import Selection
structure = PDBParser().get_structure('4GBX', '4GBX.pdb') # load your molecule
atom_list = Selection.unfold_entities(structure[0]['E'], 'A') # 'A' is for Atoms in the chain 'E'
When I unfold chain E in the PDB 4GBX using the code above, the last 2 Oxygen atoms in atom_list belong to water heteroatoms in the same chain. How can I get a list of only protein residue atoms and avoid other ligands or water molecules in the selection?
python bioinformatics biopython pdb protein-database
asked Nov 15 '18 at 20:08
mahaswapmahaswap
518
add a comment |
3
from Bio.PDB import PDBParser
from Bio.PDB import Selection
structure = PDBParser().get_structure('4GBX', '4GBX.pdb') # load your molecule
atom_list = Selection.unfold_entities(structure[0]['E'], 'A') # 'A' is for Atoms in the chain 'E'
When I unfold chain E in the PDB 4GBX using the code above, the last 2 Oxygen atoms in atom_list belong to water heteroatoms in the same chain. How can I get a list of only protein residue atoms and avoid other ligands or water molecules in the selection?
python bioinformatics biopython pdb protein-database
asked Nov 15 '18 at 20:08
mahaswapmahaswap
518
I seem to be a bit blind - 4gbx (rcsb.org/structure/4GBX) ... chain E? Are you speaking of atom number 6089 and 6091? However they belong to THR no?
– quant
Nov 15 '18 at 20:44
4gbx: chain E: water residue numbers 101 and 102: atom numbers 6190 and 6191. Thanks.
– mahaswap
Nov 15 '18 at 21:21
atom_list[-1].get_full_id() Out[21]: ('4GBX', 0, 'E', ('W', 102, ' '), ('O', ' '))The 'W' here is for water heteroatom.
– mahaswap
Nov 15 '18 at 21:33
1
Yes, saw that too. However are you sure that the 'W' only occurs for heteroatoms? If yes, you can use something likeprint([atom for atom in atom_list if atom.get_full_id()[3][0] == " "])to filter your list ...
– quant
Nov 15 '18 at 21:35
1
Thanks @quant . I think that should do the trick. I guess I need a coffee or two. I remember now that I had done the exact same thing some months ago.
– mahaswap
Nov 15 '18 at 21:58
add a comment |
3
3
3
from Bio.PDB import PDBParser
from Bio.PDB import Selection
structure = PDBParser().get_structure('4GBX', '4GBX.pdb') # load your molecule
atom_list = Selection.unfold_entities(structure[0]['E'], 'A') # 'A' is for Atoms in the chain 'E'
When I unfold chain E in the PDB 4GBX using the code above, the last 2 Oxygen atoms in atom_list belong to water heteroatoms in the same chain. How can I get a list of only protein residue atoms and avoid other ligands or water molecules in the selection?
python bioinformatics biopython pdb protein-database
asked Nov 15 '18 at 20:08
mahaswapmahaswap
518
from Bio.PDB import PDBParser
from Bio.PDB import Selection
structure = PDBParser().get_structure('4GBX', '4GBX.pdb') # load your molecule
atom_list = Selection.unfold_entities(structure[0]['E'], 'A') # 'A' is for Atoms in the chain 'E'
When I unfold chain E in the PDB 4GBX using the code above, the last 2 Oxygen atoms in atom_list belong to water heteroatoms in the same chain. How can I get a list of only protein residue atoms and avoid other ligands or water molecules in the selection?
python bioinformatics biopython pdb protein-database
python bioinformatics biopython pdb protein-database
asked Nov 15 '18 at 20:08
mahaswapmahaswap
518
asked Nov 15 '18 at 20:08
mahaswapmahaswap
518
edited Nov 15 '18 at 21:16
mahaswap
asked Nov 15 '18 at 20:08
mahaswapmahaswap
518
asked Nov 15 '18 at 20:08
mahaswapmahaswap
518
asked Nov 15 '18 at 20:08
mahaswapmahaswap
518
518
I seem to be a bit blind - 4gbx (rcsb.org/structure/4GBX) ... chain E? Are you speaking of atom number 6089 and 6091? However they belong to THR no?
– quant
Nov 15 '18 at 20:44
4gbx: chain E: water residue numbers 101 and 102: atom numbers 6190 and 6191. Thanks.
– mahaswap
Nov 15 '18 at 21:21
atom_list[-1].get_full_id() Out[21]: ('4GBX', 0, 'E', ('W', 102, ' '), ('O', ' '))The 'W' here is for water heteroatom.
– mahaswap
Nov 15 '18 at 21:33
1
Yes, saw that too. However are you sure that the 'W' only occurs for heteroatoms? If yes, you can use something likeprint([atom for atom in atom_list if atom.get_full_id()[3][0] == " "])to filter your list ...
– quant
Nov 15 '18 at 21:35
1
Thanks @quant . I think that should do the trick. I guess I need a coffee or two. I remember now that I had done the exact same thing some months ago.
– mahaswap
Nov 15 '18 at 21:58
add a comment |
I seem to be a bit blind - 4gbx (rcsb.org/structure/4GBX) ... chain E? Are you speaking of atom number 6089 and 6091? However they belong to THR no?
– quant
Nov 15 '18 at 20:44
4gbx: chain E: water residue numbers 101 and 102: atom numbers 6190 and 6191. Thanks.
– mahaswap
Nov 15 '18 at 21:21
atom_list[-1].get_full_id() Out[21]: ('4GBX', 0, 'E', ('W', 102, ' '), ('O', ' '))The 'W' here is for water heteroatom.
– mahaswap
Nov 15 '18 at 21:33
1
Yes, saw that too. However are you sure that the 'W' only occurs for heteroatoms? If yes, you can use something likeprint([atom for atom in atom_list if atom.get_full_id()[3][0] == " "])to filter your list ...
– quant
Nov 15 '18 at 21:35
1
Thanks @quant . I think that should do the trick. I guess I need a coffee or two. I remember now that I had done the exact same thing some months ago.
– mahaswap
Nov 15 '18 at 21:58
I seem to be a bit blind - 4gbx (rcsb.org/structure/4GBX) ... chain E? Are you speaking of atom number 6089 and 6091? However they belong to THR no?
– quant
Nov 15 '18 at 20:44
I seem to be a bit blind - 4gbx (rcsb.org/structure/4GBX) ... chain E? Are you speaking of atom number 6089 and 6091? However they belong to THR no?
– quant
Nov 15 '18 at 20:44
4gbx: chain E: water residue numbers 101 and 102: atom numbers 6190 and 6191. Thanks.
– mahaswap
Nov 15 '18 at 21:21
4gbx: chain E: water residue numbers 101 and 102: atom numbers 6190 and 6191. Thanks.
– mahaswap
Nov 15 '18 at 21:21
atom_list[-1].get_full_id() Out[21]: ('4GBX', 0, 'E', ('W', 102, ' '), ('O', ' ')) The 'W' here is for water heteroatom.– mahaswap
Nov 15 '18 at 21:33
atom_list[-1].get_full_id() Out[21]: ('4GBX', 0, 'E', ('W', 102, ' '), ('O', ' ')) The 'W' here is for water heteroatom.– mahaswap
Nov 15 '18 at 21:33
1
1
Yes, saw that too. However are you sure that the 'W' only occurs for heteroatoms? If yes, you can use something like
print([atom for atom in atom_list if atom.get_full_id()[3][0] == " "]) to filter your list ...– quant
Nov 15 '18 at 21:35
Yes, saw that too. However are you sure that the 'W' only occurs for heteroatoms? If yes, you can use something like
print([atom for atom in atom_list if atom.get_full_id()[3][0] == " "]) to filter your list ...– quant
Nov 15 '18 at 21:35
1
1
Thanks @quant . I think that should do the trick. I guess I need a coffee or two. I remember now that I had done the exact same thing some months ago.
– mahaswap
Nov 15 '18 at 21:58
Thanks @quant . I think that should do the trick. I guess I need a coffee or two. I remember now that I had done the exact same thing some months ago.
– mahaswap
Nov 15 '18 at 21:58
add a comment |
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I seem to be a bit blind - 4gbx (rcsb.org/structure/4GBX) ... chain E? Are you speaking of atom number 6089 and 6091? However they belong to THR no?
– quant
Nov 15 '18 at 20:44
4gbx: chain E: water residue numbers 101 and 102: atom numbers 6190 and 6191. Thanks.
– mahaswap
Nov 15 '18 at 21:21
atom_list[-1].get_full_id() Out[21]: ('4GBX', 0, 'E', ('W', 102, ' '), ('O', ' '))The 'W' here is for water heteroatom.– mahaswap
Nov 15 '18 at 21:33
1
Yes, saw that too. However are you sure that the 'W' only occurs for heteroatoms? If yes, you can use something like
print([atom for atom in atom_list if atom.get_full_id()[3][0] == " "])to filter your list ...– quant
Nov 15 '18 at 21:35
1
Thanks @quant . I think that should do the trick. I guess I need a coffee or two. I remember now that I had done the exact same thing some months ago.
– mahaswap
Nov 15 '18 at 21:58