[Bioperl-l] fetch protein-na-complexes from pdb

Ulf Lenski lenski at mdc-berlin.de
Tue Feb 12 08:43:51 EST 2008


hi bernd,
thanks a lot - that helps me for my first question.
but how can I distinguish the nuc chains?
How I can find out the type of a single chain?
ss-rna
ss-dna
ds-rna
ds-dna

regards, ulf.


Bernd Web schrieb:
> Hi Ulf,
>
> At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and
> even download the entries there. See
> http://www.rcsb.org/pdb/statistics/holdings.do
> Also see "webdownload" on the RCSB site.
>
> Alternatively, you could fetch the files one by one (e.g. with wget).
> The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt"
> contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc
> and diffraction/NMR).
>
> Regards,
> Bernd
>
>
> 2008/2/12 Ulf Lenski <lenski at mdc-berlin.de>:
>   
>> is there a bioperl modul for fetching protein-na-complexes from the pdb?
>> and can i distinguish ss-dna from dna chains without parsing the pdb
>> files and go through the coordinates (calculate distances etc...)?
>>
>> tx - ulf.
>>
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