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changing the chain id

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changing the chain id



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: - change the chain ID of a specified chain from a pdb file.

but I cannot find it the Rosetta source.

Any suggestions?

Many thanks,


Post Situation: 
Tue, 2018-01-09 00:08

I'm not familiar with the 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.



Mon, 2018-01-15 14:20

Many thanks! It works just fine!

Thu, 2018-01-18 00:56