[Biopython] Editing Structure and Replacing Coordinates with new set

[João Rodrigues]

Go over all atoms, average them xyz and store it somewhere where you can
know their order. The just go over the atoms of the representative again
and replace them.

A qua, 24/05/2017, 10:00, Souparno Adhikary <souparnoa91 at gmail.com>
escreveu:

> Joao,
>
> I'm quite sure you are not suggesting to change the co-ordinates
> "manually" i.e. one by one like in a text file. I'm writing some code to do
> that. Also, I am yet to check out Patrick Kunzmann's code. I think
> Patrick's code would do a great job.
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
>
> On Tue, May 23, 2017 at 6:54 PM, João Rodrigues <
> j.p.g.l.m.rodrigues at gmail.com> wrote:
>
>> 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.
>>>>
>>>>
>>>> _______________________________________________
>>>> Biopython mailing list  -  Biopython at mailman.open-bio.orghttp://mailman.open-bio.org/mailman/listinfo/biopython
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at mailman.open-bio.org
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>>>
>>
>>
>
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