[BioRuby] How to renumber a PDB file using BioRuby ?

[Alex Gutteridge]

On 10 Apr 2008, at 07:32, K. Shameer wrote:
> Dear All,
>
> I have  a pdb file ( in perfect pdb format, no hetatm, no solvent,  
> single
> chain file). I need to renumber the whole pdb file, for example if my
> input file is 1CRN.pdb and it starts with residue number 1, I need to
> renumber them so that first resiude number will be 12, next 13,  
> 14... like
> that. I want to know if I can specifically access the residue number  
> and
> increment it from first residue using my new number (here it will be
> residue_number  +  12)and regenerate the file.
>
> Anybody had tried this before,
>
> Thanks in advance for any help,
> K. Shameer
>
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>


hi,

You have to alter the number by atom rather than by residue. Altering  
the residue object directly used to work, but has been broken  
recently. Anyway, this seems to work for your purpose:

require 'bio'

pdb = Bio::PDB.new(File.read(ARGV[0]))

pdb.each_atom do |atom|
  atom.resSeq += 12
end

puts pdb

It would be good (IMHO) to have:

require 'bio'

pdb = Bio::PDB.new(File.read(ARGV[0]))

pdb.each_residue do |residue|
  residue.resSeq += 10
end

puts pdb

Do the same thing, but currently changes to residue objects don't  
propagate back down to the atoms they contain so the above code  
doesn't do anything useful.

Alex Gutteridge

Department of Biochemistry
University of Cambridge