changing the chain id

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    • January 9, 2018 at 8:08 am #2827
      Anonymous

        Hi!

         

        I need to change the chain ids for 10000 pdb structures generated by the relax protocol. I have 2 chains A and B in each protein (antibody) and I want to change them yo H and L (as antibody_H3 seems to request that the heavy chain of the antibody should be name d’H’).  I saw in older posts that there should be an utility:

        changeChain.pl – change the chain ID of a specified chain from a pdb file.

        but I cannot find it the Rosetta source.

        Any suggestions?

        Many thanks,

        Andrei

      • January 15, 2018 at 10:20 pm #13987
        Anonymous

          I’m not familiar with the changeChain.pl utility, so I can’t say where it’s gone to. Frankly speaking, for something this straight-forward, I’d probably just use `sed`: 


          
sed -i 's/^(ATOM.{17})A/1H/' *.pdb
          
sed -i 's/^(ATOM.{17})B/1L/' *.pdb

          What that will do is an in-place (-i) substitution of ATOM lines with chain A (the chain letter is the 18th character after the ATOM designation) to chain H, and those with chain B to chain L. This should work, so long as you’re only dealing with protein residues, and don’t have any non-protein HETATM lines.  (I encourage you to look up some sed tutorials/manuals and understand what those lines are doing.)

          If you’re interested in doing more sophisticated manipulation, you may want to look at BioPython, BioPerl, etc.

           

           

        • January 18, 2018 at 8:56 am #14001
          Anonymous

            Many thanks! It works just fine!

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