[Bioperl-l] acceptable PDB/structure formats

Douglas Kojetin djkojeti at unity.ncsu.edu
Thu Oct 14 13:49:17 EDT 2004

Thanks Gary-

This header and the one I created still give errors (although different 
than when I do not have a header at all).

# no header:

------------- EXCEPTION  -------------
MSG: PDB stream with no HEADER. Not pdb in my book
STACK Bio::Structure::IO::pdb::next_structure 
STACK toplevel ./read_pdb.pl:21

# either one of the headers:

Use of uninitialized value in pattern match (m//) at 
/sw/lib/perl5/Bio/Structure/IO/pdb.pm line 453, <GEN0> line 4196.

I beginning to wonder if it's a problem with the atom nomenclature.  
There are documented differences between XPLOR/CNS and PDB nomenclature 
(and a few other formats as well).  See this link for details:


I realize it could be a semi-quick conversion, but it's getting more 
complex than I need at the moment ... I'll probably just learn some 
basic python and use BioPython for the moment since it appears to work 
with the different formats (or at least has not reported any errors 

Thanks again for the input, and I'll try to make some contributions 
once finish my project(s) and graduate!


On Oct 14, 2004, at 1:00 PM, Gary wrote:

> Hey Guys,
> I had this problem as well.  I used the same workaround as you 
> (prepending
> the file with a HEADER line).  My recollection is that the header line
> needs to be pretty strictly formatted.  This header string works for 
> me:
>     my $header = "HEADER    DEFAULT CLASSIFICATION                  
> 24-JAN-70   XXXX\n";

More information about the Bioperl-l mailing list