[Bioperl-l] PDB Parser

Hans Rudolf Hotz hrh at sanger.ac.uk
Thu Aug 16 04:48:16 EDT 2007




On Thu, 16 Aug 2007, neeti somaiya wrote:

> Hi,
>
> After a lot of search I could find this link from where PDB files can be
> downloaded :
> ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/
> Is there any other link where one can download all pdb data from?

try: ftp://pdb.protein.osaka-u.ac.jp/v3/pub/pdb/   or
      ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/

it is not BioPerl, but James Tisdall's book: O'Reilly: "Begiining Perl for 
Bioinformatics" has a nice introduction into parsing PDB files


Regards, Hans


>
> I tried using Bio::Structure::IO::pdb with some code like :-
> use Bio::Structure::IO;
>
>    $in  = Bio::Structure::IO->new(-file => "pdb100d.ent",
>                                   -format => 'pdb');
>
>    while ( my $struc = $in->next_structure() ) {
>       print "Structure ", $struc->id,"\n";
>    }
>
> It works well. But I am not able to find documentation of other methods
> which will give me various specific details available in a pdb file, right
> from title, keywords, references to structure details, atoms, coordinates
> etc. There must be different methods to fetch and parse each of this data
> from a pdb file, right? Where can I find the details? Any example code of
> the same would also be of great use.
>
> Thanks and Regards,
> Neeti Somaiya.
>
> -- 
> -Neeti
> Even my blood says, B positive
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>
>


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