So I am using WinCoot to refine my protein, and I saw many tutorials that you have to refine by clicking on Real Space Refine Zone, and many times you click on the alfa carbon to fix the position of the residue, but when I do this, many times the bonding with previous or following amino acids break.
How can I avoid this? or is there a post-refinement process to fix the bonding breakage?
Thank you