[Bioperl-l] acceptable PDB/structure formats

Brian Osborne brian_osborne at cognia.com
Thu Oct 14 10:25:54 EDT 2004


You could also ask this group if they'd mind your creating a new
Structure::IO module for this CNS/XPLOR format and adding it to Bioperl.
There's only 2 ways of looking at this, either the HEADER (or headers) is
required in PDB format, thus CNS/XPLOR format is not PDB format and you
could write a new module, or the HEADER (or headers) is not required in PDB
format so the existing module should not be throwing this fatal exception.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Douglas Kojetin
Sent: Wednesday, October 13, 2004 1:05 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] acceptable PDB/structure formats

Howdy All-

I wanted to check one more time and see if anyone has any advice about
using structure/PDB files that do not contain all the PDB-formatted
headers.  See the blurb pasted below (the error is from the following
small-liner script, where the PDB/structure file was experimentally
calculated from CNS/XPLOR, rather than downloaded from the actual 'PDB'
protein data bank):

#!/usr/bin/perl -w
use Bio::Structure::IO;
use strict;
my $structio = Bio::Structure::IO->new(-format => 'pdb', -file =>
my $struc = $structio->next_structure;

BioPython (using 'from Bio.PDB import *') has no problem reading my
CNS/XPLOR structure files ... but I'd prefer to use BioPerl (since I'm
more familiar with perl vs. python, although I could look at this as an
opportunity to branching out ... but, graduation is close!)

Are structure (PDB) files from the protein data bank, with the proper
PDB formatting/headers, the only supported structure format?


> I am seeing an error I believe is associated with the 'format' of my
> PDB.  It was created using CNS (format similar to XPLOR).  When I try
> to run the below script, I get an error as follows:
> % ./read_pdb.pl > out
> ------------- EXCEPTION  -------------
> MSG: PDB stream with no HEADER. Not pdb in my book
> STACK Bio::Structure::IO::pdb::next_structure
> /sw/lib/perl5/Bio/Structure/IO/pdb.pm:138
> STACK toplevel ./read_pdb.pl:6
> --------------------------------------
> 1. Are CNS or XPLOR formats supported?
> 2. Is there an easy way of quickly converting to a 'PDB' authentic
> format?  It looks like it just wants some header information.

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