[Biopython] Editing Structure and Replacing Coordinates with new set

João Rodrigues j.p.g.l.m.rodrigues at gmail.com
Wed May 24 08:04:59 UTC 2017


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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