[Biopython] Editing Structure and Replacing Coordinates with new set

[Patrick Kunzmann]

Using my subpackage, this might work for you:

import Biopython.Bio.Structure as struc
from Bio.PDB import PDBParser
from Bio.PDB import PDBIO
from Bio.PDB.Structure import Structure

parser = PDBParser(PERMISSIVE=True)
structure = parser.get_structure("", "1l2y.pdb")
stack = struc.stack([struc.to_array(model) for model in structure])
average_atom_array = struc.average(stack)
structure_new = Structure("result")
structure_new.add(struc.to_model(average_atom_array))
io = PDBIO()
io.set_structure(structure_new)
io.save("result.pdb")


Am 23.05.2017 um 13:03 schrieb Souparno Adhikary:
> Oh, got it. It's only a dot problem.
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
>
> On Tue, May 23, 2017 at 4:31 PM, Souparno Adhikary 
> <souparnoa91 at gmail.com <mailto:souparnoa91 at gmail.com>> wrote:
>
>     The page shows a 404 error. Can you please check the link again?
>
>     Regards,
>
>     Souparno Adhikary,
>     CHPC Lab,
>     Department of Microbiology,
>     University of Calcutta.
>
>     On Tue, May 23, 2017 at 4:01 PM, Patrick Kunzmann
>     <padix.kleber at gmail.com <mailto:padix.kleber at gmail.com>> wrote:
>
>         I am currently working on a subpackage for Biopython (called
>         Bio.Structure), that converts a Bio.PDB.Model.Model into a
>         numpy array containing coordinates and annotations for doing
>         easily efficient calculations (for example calculating average
>         structure). This array can be converted back into a
>         Bio.PDB.Model.Model and than saved as PDB file using PDBIO().
>         Currently docstrings and code comments are missing, so I will
>         contribute this code only in a few days, but you can check out
>         the source code at
>         https://github.com/padix-key/biopython/tree/numpy-structure
>         <https://github.com/padix-key/biopython/tree/numpy-structure>.
>
>         Best regards,
>
>         Patrick Kunzmann
>
>
>         Am 23.05.2017 um 12:04 schrieb Souparno Adhikary:
>>         I want to calculate the average structure from multiple
>>         frames in a pdb file and save it to another pdb file.
>>
>>         I wrote the code to calculate the average co-ordinates
>>         successfully like below:
>>
>>         #!/usr/bin/python
>>
>>         from Bio.PDB.PDBParser import PDBParser
>>
>>         import numpy as np
>>
>>         parser=PDBParser(PERMISSIVE=1)
>>
>>         structure_id="mode_7"
>>         filename="mode_7.pdb"
>>         structure=parser.get_structure(structure_id, filename)
>>         model1=structure[0]
>>         s=(124,3)
>>         newc=np.zeros(s,dtype=np.float32)
>>         counter=1
>>         fincoord=[]
>>         for i in range(0,29):
>>             coord=[]
>>             model=structure[i]
>>             for chain in model.get_list():
>>                 for residue in chain.get_list():
>>                     ca=residue["CA"]
>>         coord.append(ca.get_coord())
>>
>>             newc=np.add(newc,coord)
>>             counter+=1
>>
>>         fincoord=np.divide(newc,counter)
>>
>>         print fincoord
>>
>>         print "END"
>>
>>         Now I want to write the coordinates in fincoord to a new pdb
>>         file i.e. everything will be the same like the structure[0]
>>         except the coordinates. Can you tell me how can I edit the
>>         coordinates of a specific model or replace it with my array
>>         and save it to another file?
>>
>>         Thanks
>>
>>         Souparno Adhikary,
>>         CHPC Lab,
>>         University of Calcutta.
>>
>>
>>         _______________________________________________
>>         Biopython mailing list  -Biopython at mailman.open-bio.org
>>         <mailto:Biopython at mailman.open-bio.org>
>>         http://mailman.open-bio.org/mailman/listinfo/biopython
>>         <http://mailman.open-bio.org/mailman/listinfo/biopython>
>
>
>

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