[Bioperl-l] acceptable PDB/structure formats
djkojeti at unity.ncsu.edu
Wed Oct 13 13:05:17 EDT 2004
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):
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
> 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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