I am adding solvent molecules into unmodelled blobs of density in Coot. When I am finished, I merge molecules, then save my coordinates. For some reason Coot is saving two copies of each molecule that I have modelled and assigns them different chain ID's. I notice this when I open it in PyMol and when I open the coot pdb file using a text editor. Is there a reason why Coot does this?, or a way that I can save my work in the same state that I prepared it in?
