[Biojava-l] Disulfide information in PDB files

[Andreas Prlic]

Hi Brendan,

I just committed the patches to CVS so
BioJava can now parse the SSBond records.

Andreas


On 14 Nov 2007, at 16:28, Brendan Duggan wrote:

> Hi Andreas
>
> Thanks for the quick response.  I submitted a bug
> request (#2400) as suggested by Richard.  Parsing the
> SSBOND records is indeed what I was talking about.  I
> want to identify the disulfides then calculate their
> torsions, dihedrals and bond lengths, all of which I
> believe can be implemented with the existing code.  If
> you could implement this parsing in a few days that
> would be great!
>
> Thanks
>
> Brendan
>
>
> --- Andreas Prlic <ap3 at sanger.ac.uk> wrote:
>
>> Hi Brendan,
>>
>> SSBOND lines are currently not parsed. If this is
>> what you need,
>> I can add this over the next couple of days.
>>
>> If you want to compute the bonds yourself, the
>> framework can
>> e.g. calculate distances between the sulphur atoms
>> for you. -
>>
>> Andreas
>>
>>
>>
>>
>>
>> On 14 Nov 2007, at 00:48, Brendan Duggan wrote:
>>
>>> Greetings
>>>
>>> I'm trying to mine some information on disulfides
>> in
>>> the PDB and was hoping there might be a way of
>>> obtaining this information with the BioJava PDB
>>> parser.  However, I haven't been able to see
>> anything
>>> like this mentioned in the API docs.  If it is
>>> currently not possible to extract disulfide
>>> information from PDB files are there any plans to
>>> implement this?
>>>
>>> Thanks!
>>>
>>> Brendan
>>>
>>>
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>>
> ---------------------------------------------------------------------- 
> -
>>
>> Andreas Prlic      Wellcome Trust Sanger Institute
>>                                Hinxton, Cambridge
>> CB10 1SA, UK
>> 			 +44 (0) 1223 49 6891
>>
>>
> ---------------------------------------------------------------------- 
> -
>>
>>
>>
>> -- 
>>  The Wellcome Trust Sanger Institute is operated by
>> Genome Research
>>  Limited, a charity registered in England with
>> number 1021457 and a
>>  company registered in England with number 2742969,
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>
>
> Brendan M. Duggan, PhD
>
> bmduggan at yahoo.com
> (858) 692-2298
>
>
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>

-----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891

-----------------------------------------------------------------------



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.