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You can specify the residues that you want to refine without using a
linear or sphere selection usine refine-residues. For example:
(refine-residues 0 '(("L" 501 "") ("L" 503 "")))
will refine residues A501 and A503 (and residue A502 (if it exists) will be an anchoring residue - used in optimizing the link geometry of the atoms in A501 and A503).