The modify surrounding residues panel
A mutation to a residue may cause knock-on effects to the positions of atoms in the surrounding region of the protein. The minimize button preserves the selected residue, while minimizing the positions of surrounding side chain atoms on the same protein chain. As with the modify panel, all visible molecules are taken into account during minimization, such that toggling a ligand on and off may change the results.
Note: Minimization is a stochastic process, meaning that pressing the minimize button twice may give slightly different results.