[Bioperl-l] problem parsing pdb

[Mark A. Jensen]

Hi Paola--
I will look at this. Stay tuned-
Mark
----- Original Message ----- 
From: "Paola Bisignano" <paola_bisignano at yahoo.it>
To: <bioperl-l at bioperl.org>
Sent: Tuesday, September 08, 2009 4:55 AM
Subject: [Bioperl-l] problem parsing pdb


Hi,

I'm in a little troble because i need to exactly parse pdb file, to extract 
chain id and res id, but I finded that in some pdb the number of residue is 
followed by a letter because is probably a residue added by crystallographers 
and they didm't want to change the number of residue in sequence....for example 
the pdb 1PXX.pdb I parsed it with my script below, I didn't find any useful 
suggestion about this in bioperltutorial or documentation of bioperl online

#!/usr/local/bin/perl
use strict;
use warnings;
use Bio::Structure::IO;
use LWP::Simple;



my $urlpdb= 
"http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1PXX";
my $content = get($urlpdb);
my $pdb_file = qq{1pxx.pdb};
open my $f, ">$pdb_file" or die $!;
binmode $f;
print $f $content;
print qq{$pdb_file\n};
close $f;



my $structio=Bio::Structure::IO->new (-file=>$pdb_file);
my $struc=$structio->next_structure;
for my $chain ($struc->get_chains)
{
my $chainid = $chain->id ;
for my $res ($struc->get_residues($chain))
{
my $resid=$res-> id;
my $atoms= $struc->get_atoms($res);
open my $f, ">> 1pxx.parsed";
print $f "$chainid\t$resid\n";
close $f;
}
}



but it gives my file with an error in ILE 105A ILE 2105C because they have a 
letter that follow the number of resid.... can I solve that problem without 
writing intermediate files?
because i need to have the reside id as 105A not 105.A
so
A ILE-105A
without point between number and letter....




Thank you all,

Paola




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