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The problem of atomic overlap has already been mentioned in connection with 2D searches in which the minimum number of fragments to be located in a given entry can be greater than one.
Resetting NUMBER-OF-FRAGS in a 2D search is a relatively rare occurrence, and the decision whether to permit overlapped fragments is a simple user decision.
In 3D searching the decision of whether to allow overlap among the atoms of successive crystal fragments located in an entry must be made on each and every occasion. Allowance for overlap of crystal fragments ensures that no crystal fragments are missed from the analysis. However, the user may require the located crystal fragments to be separate and not overlapping.
Some examples of exhaustive fragment (4-membered carbon ring) location, with and without atomic overlap, for a variety of crystallographic situations are shown below, with reference to the diagrams below:
BHPNPH C2/c Z = 16 Z' = 2
BILSUK P21/c Z = 4 two half-molecules per asymmetric unit
BIRGEO P21/c Z = 4 Z' = 1
BORVOT Pbca Z = 16 Z' = 2
Exhaustive fragment location Exhaustive fragment location and atomic overlap without atomic overlap BHPNPH C51 C61 C71 C11 BHPNPH C51 C61 C71 C11 C52 C62 C72 C12 C52 C62 C72 C12 BILSUK C7 C5 C6 C1 BILSUK C7 C5 C6 C1 C7' C5' C6' C1' C7' C5' C6' C1' BIRGEO C1 C6 C10 C5 BIRGEO C1 C6 C10 C5 C1 C6 C7 C2 C2 C7 C8 C3 C2 C7 C8 C3 C5 C10 C9 C4 C3 C4 C9 C8 BORVOT C1 C10 C11 C12 BORVOT C1 C10 C11 C12 C15 C24 C25 C26 C15 C24 C25 C26 C2 C5 C4 C3 C2 C5 C4 C3 C16 C19 C18 C17 C16 C19 C18 C17 C9 C6 C7 C8 C9 C6 C7 C8 C23 C20 C21 C22 C23 C20 C21 C22
Volume 1 Chapter 7 Handling Structure Inversion.