[Bioperl-l] using Bio::Structure::IO for homology models

Carlo Lapid cmlapid at up.edu.ph
Sun Sep 17 23:21:05 EDT 2006


Hi,

I used the SWISS-MODEL homology modelling server to create a PDB structure
file for a protein sequence that I want to analyze. I then tried to use
Bioperl to open and manipulate that PDB file. Unfortunately, I get the
following error:

'x' outside of string in unpack at C:/Perl/site/lib/Bio/Structure/IO/pdb.pm
line 141, <GEN0> line 2.

I don't get the same problem when I try to open a PDB file that I obtained
directly from the PDB database. What does this error mean? Is it impossible
to use Bioperl to manipulate structures created from homology modelling?

The code that I used so far is pretty short and straightforward:

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

my $structureio = Bio::Structure::IO->new(-file => "structure.pdb");

my $structure = $structureio->next_structure;

Any help would be really appreciated.


Thanks,
Carlo


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