Hi Uma, when I do the same procedure (in OSX, but the problem seems to be the same), the new residue is stored in a new chain with residue number 1. So you would need to renumber the residue and change the chain ID back to the original chain ID. It's annoyingly complicated, but it works for me.
Hope that helps, Bernhard On Sep 11, 2013, at 12:56 PM, Uma Ratu <rosiso2...@gmail.com<mailto:rosiso2...@gmail.com>> wrote: Hello, I try to replace one of cysteine residue to CSX using Win-coot. Here is how I did: Extensions > Modelling > Replace Residue... and enter the three letter code. The program place the CSX residue, but with break bond. The new residue is no longer linked with other residue and not in the chain. I then try to replace with other residues, such as ALA. The results are the same: the new residues all with break bond. How could I put the replaced residue back to the main-chain? I use Win-coot-0.7. Thank you Uma
