[Biopython] PDBParser-chain breaks

[João Rodrigues]

Of course. Since they throw a warning just make sure to count the warnings,
parse the chain break ones, and if they are more than 0, you have chain
breaks.

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2012/5/8 George Devaniranjan <devaniranjan at gmail.com>

> Hi João,
>
> Is there a way though to find PDB's with chain breaks? using biopython?
>
> Thank you,
> George
>
> On Tue, May 8, 2012 at 3:34 PM, João Rodrigues <anaryin at gmail.com> wrote:
>
>> Hi George,
>>
>> Chain breaks are pretty "harmless" and usually do not represent a faulty
>> PDB file. The PERMISSIVE flag is for "features" like missing b-factors.
>>
>> Cheers,
>>
>> João [...] Rodrigues
>> http://nmr.chem.uu.nl/~joao
>>
>>
>>
>> 2012/5/8 George Devaniranjan <devaniranjan at gmail.com>
>>
>>>  Hi,
>>>
>>> I thought using PERMISSIVE=0 would raise an exception if I pass a PDB
>>> with
>>> chain breaks.
>>> However, nothing like that seems to happen.....
>>>
>>> For instance
>>>
>>> P=PDBParser(PERMISSIVE=0)
>>> structure=P.get_structure('test', '7ODC.pdb')
>>>
>>>
>>> 7ODC has 3 chain breaks but it does not raise an exception.
>>>
>>> Thank you
>>> George
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>
>>
>>
>