[BioRuby] Bio::PDB parsing problem (1B2M)

[Alex Gutteridge]

Hi Semin,

Definately a parser error - the combined HETATM/ATOM chains are  
confusing it, but they shouldn't. If you have the time and the  
inclination then patches are very welcome. If not, I can try and take  
a look next week.

AlexG

On 28 Mar 2008, at 23:27, Semin Lee wrote:
> Hi guys,
>
> I've got some problems when parsing 1B2M PDB file using Bio::PDB. It  
> doesn't seem to parse chain C to E properly. I'm currently using  
> BioRuby gem ver. 1.2.1 and Ruby 1.8.6 on Mac OS X Leopard.
>
> >> require "bio"
> => true
> >> require "open-uri"
> => true
> >> pdb = Bio::PDB.new(open("http://www.rcsb.org/pdb/files/ 
> 1b2m.pdb").read)
> => #<Bio::PDB entry_id="1B2M">
> >> p pdb.models.first.chains
> ArgumentError: ArgumentError
>       from /opt/local/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/data/ 
> aa.rb:184:in `three2one'
>       from /opt/local/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/db/ 
> pdb/chain.rb:192:in `aaseq'
>       from /opt/local/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/db/ 
> pdb/chain.rb:186:in `each'
>       from /opt/local/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/db/ 
> pdb/chain.rb:186:in `aaseq'
>       from /opt/local/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/db/ 
> pdb/chain.rb:178:in `inspect'
>       from (irb):4:in `p'
>       from (irb):4
> >>
>
> a strange error occurred, but I just overrided(?) 'aaseq' method to  
> see what happens,
>
> >> module Bio
> >>   class PDB
> >>     class Chain
> >>       def aaseq
> >>         ""
> >>         end
> >>       end
> >>     end
> >>   end
> => nil
> >> pp pdb.models.first.chains
> [#<Bio::PDB::Chain id="A" model.serial=nil residues.size=104  
> heterogens.size=0 aaseq="">,
> #<Bio::PDB::Chain id="B" model.serial=nil residues.size=104  
> heterogens.size=0 aaseq="">,
> #<Bio::PDB::Chain id="C" model.serial=nil residues.size=1  
> heterogens.size=1 aaseq="">,
> #<Bio::PDB::Chain id="D" model.serial=nil residues.size=0  
> heterogens.size=0 aaseq="">,
> #<Bio::PDB::Chain id="E" model.serial=nil residues.size=0  
> heterogens.size=0 aaseq="">,
> #<Bio::PDB::Chain id=" " model.serial=nil residues.size=0  
> heterogens.size=92 aaseq="">]
> => nil
> >>
>
> Now it doesn't complain, but Bio::PDB::Chain for chain D and E have  
> wrong number of residues and heterogens. In the 1B2M PDB file, each  
> chain D and E also has a RNA residue and a heterogen, U34, just like  
> chain C. However, Bio::PDB::Chain for chain D and E have no residues  
> and heterogens. Does anyone have any ideas? Or, am I missing  
> something?
>
> Cheers,
> Semin
>
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