[Biopython] PDBParser-chain breaks

[George Devaniranjan]

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
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>>
>
>