[Biopython] Editing Structure and Replacing Coordinates with new set

[João Rodrigues]

Meanwhile, the way to do it is to go over all the atoms again and change
their xyz coordinates manually.

2017-05-23 4:01 GMT-07:00 Souparno Adhikary <souparnoa91 at gmail.com>:

> 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>
> 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.
>>
>> 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.
>>
>>
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>>
>>
>>
>
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