[Bioperl-l] PDB Parser

neeti somaiya neetisomaiya at gmail.com
Thu Aug 16 01:56:21 EDT 2007


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?

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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