I am looking fora command that will modify 3 chains available in the original pdb into a single chain and then renumber all of the residues. I have tried using alter command but when I export the pdb I get only one chain (of the initial trimer) and not the merged chain
Annemarie Honegger
You can first renumber the chains using the alter command (https://pymolwiki.org/index.php?title=Alter&redirect=no) in such a way that each residue has a unique residue number,
e.g.
alter (chain B),resi=str(int(resi)+100)
alter (chainC),resi=str(int(resi)+200)
to give chains B and C an offset of 100 and 200, respectively.
then again use the alter command to change the chain label
e.g.
alter (all), chain='A'
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