Hi @user123
Thanks for the reply. Local refinement does improve the protein features so it looks like a worthwhile strategy. I am just concerned about the artifacts that appear at the boundary and have tried to adjust the static refinement mask but haven’t been able to get rid of them. The two domains are unfortunately very close so I can’t manage to exclude the linker from the subtraction mask without losing protein density of the refined domain.
I will give your first 2 suggestions a try, thanks!