[Bioperl-l] problem parsing pdb

[Brian Osborne]

Mark,

There was an interesting exchange about StructureIO::pdb a few years  
ago:

http://portal.open-bio.org/pipermail/bioperl-l/2006-September/022990.html

I don't think anyone has actually worked on this code since then and I  
also don't know if Paolo's question relates to the content of the  
thread, but it's good overview.

Brian O.


On Sep 18, 2009, at 8:11 AM, Mark A. Jensen wrote:

> 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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