Dear haddock users
I Have a PDB file of a homodimer with overlapping numbers, each chain (A and B) from 18 to 117. I sent it to CPORT and got an error about overlapping residues. I changed the residue number of Chain B to 118-227 and also removed the waters molecule with notpad++.
My question is: "is it necessary to change chainID in my PDB? I mean B to A as if it is a monomer? and what if I only send one chain of protein to CPORT but take the result for my whole PDB ( as it is a homodimer)?
Thank you
You can easily change chain IDs using our PDB-Tools suite of python scripts. Check
Can be that CPORT will work fine without changing the ChainID
As for you second question, running the monomer, might results in predictions for the dimer interface… I would rather run the dimer.
It was really helpful. Thank you.