[Biopython] PDBParser

[George Devaniranjan]

Thank you everyone,

I just need the coordinates of certain fragments from PDB files and this
works for me.
I was trying to use the PDBParser only, but thank you for pointing out
PDBIO to me.

Thank you,
George

On Tue, May 8, 2012 at 4:16 AM, João Rodrigues <anaryin at gmail.com> wrote:

> Hello George,
>
> You want to write only a part of the PDB file? What do you mean by 'all
> the info'? If it is header information as well, then this is not possible,
> but coordinates it is. You can do it in two ways:
>
> 1. Delete all residues/chains/models that are not part of your region of
> interest and then write the structure with PDBIO.
>
> 2. Use the 'Select' class from PDBIO.py and trim the region of interest.
> For example, for residues 1-10 you could do something like this:
>
> from Bio.PDB import PDBIO
> from Bio.PDB import Select
>
> class ResidueFilter(Select):
>     def accept_residue(self, residue):
>         if residue.id[1] in range(1,11):
>             return 1
>
> P = PDBParser()
> s = P.get_structure('dummy', 'foo.pdb')
>
> io = PDBIO()
>
> io.set_structure(s)
> io.save('foo_1-10.pdb', ResidueFilter())
>
>
> Check the FAQ for a more detailed explanation:
>
> http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf
>
> Cheers,
>
> João [...] Rodrigues
> http://nmr.chem.uu.nl/~joao
>
>
>
> 2012/5/8 George Devaniranjan <devaniranjan at gmail.com>
>
>> Hi,
>>
>> I have a question about using  PDBParser
>>
>>
>> from Bio.PDB.PDBParser import PDBParser
>>
>> parser=PDBParser()
>>
>> structure=parser.get_structure("test", "1fat.pdb")
>> model=structure[0]
>> chain=model["A"]
>> residue=chain[1]
>>
>> I want to use it to extract and WRITE to a file the coordinates of
>> residues
>> 10 to 20 only.
>> (or whatever residue range I specify)
>>
>> Using the PDB Parser file I can extract residue id  in the range but how
>> to
>> I back trace and write the file in the exact format that is found in the
>> PDB so that I can view it in a program like VMD/Pymol?
>> (that is I want to write the coordinates and all information as found in
>> the PDB but only for selected residues that I pass into it )
>> I know I can do it using VMD but I want to do it for thousands of PDB and
>> would like to write a database of such extracted fragments.
>>
>> The other alternative is of course to go line by line in each file and
>> write the lines that match the residue range specified but I was wondering
>> if there is a way of doing the same thing using the PDBParser?
>>
>> Thank you,
>> George
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>>
>
>