[BioRuby] bug in pdb.rb bio-1.0.0

Mikael Borg mikael.borg at utoronto.ca
Fri Apr 13 22:23:54 UTC 2007

Hello bioruby,

I think I discovered a bug in the pdb parser. Below, a description of
the bug and a one-liner fix that I hope corrects the problem.

When parsing a pdb file with many models, but only one chain per model,
all atoms are added to residues in the first Bio::PDB::Model of the
Bio::PDB structure.

The reason is that the pdb parser doesn't reset the variable for the
current chain (cChain) when the 'MODEL' keyword is encountered, so atoms
keep getting assigned to the chains in the first model.

Suggested patch:
# diff pdb.rb pdb.rb.orig
<         cChain = nil

Thank you for your efforts, I am looking forward to the next release!


Mikael Borg

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