[Bioperl-l] extract and write a pdb chain

Joan Segura Mora umjsm at leeds.ac.uk
Fri Dec 11 11:44:42 EST 2009


I am trying to do a very easy think but I don't get it. I want to write
in a file a chain of a pdb. I have try a lot of thinks but what I think
that it should work is the next script:

use Bio::Structure::IO;
use strict;

my $structio = Bio::Structure::IO->new(-file => "101m.pdb",'-format' =>
my $struc = $structio->next_structure;

my $new_entry = Bio::Structure::Entry->new( -id  => 'structure_id');

for my $chain ($struc->get_chains) {
	if($chain->id eq "A"){

my $out = Bio::Structure::IO->new(-file => ">out.pdb",'-format' =>

it doesn't. I get the next error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: add_chain: first argument needs to be a Model object ()

STACK: Error::throw
Bio::Root::Root::throw /usr/local/share/perl/5.8.8/Bio/Root/Root.pm:368
Bio::Structure::Entry::add_chain /usr/local/share/perl/5.8.8/Bio/Structure/Entry.pm:335
Bio::Structure::Entry::get_chains /usr/local/share/perl/5.8.8/Bio/Structure/Entry.pm:391
Bio::Structure::Entry::chain /usr/local/share/perl/5.8.8/Bio/Structure/Entry.pm:304
STACK: read_pdb.pl:10

As far I understand the documentation, the method chain of the object
Bio::Structure::Entry requires an as input an object of type Chain.

Any solution will be very welcome.

best regards,

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