[BioRuby] How to renumber a PDB file using BioRuby ?
Yen-Ju Chen
yjchen at reciprocallattice.com
Thu Apr 10 08:14:57 UTC 2008
This is how I do it for atom number. You probably can find a way for residues.
require 'bio'
file = File.new('a.pdb').gets(nil)
structure = Bio::PDB.new(file)
structure.each do |model|
model.each do |chain|
chain.each do |residue|
residue.each do |atom|
atom.resSeq += 400
end
end
end
end
File.open('x.pdb', 'w') do |file|
file << structure.to_s
end
Yen-Ju
On Thu, Apr 10, 2008 at 2:32 PM, K. Shameer <shameer at ncbs.res.in> 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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