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
Category:
Post Situation:
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`:
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.
Many thanks! It works just fine!