Volume 1 Chapter 7 Topological Symmetry and Fragment Location

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7.12 Atomic Overlap in Multiple Fragment Situations

We must also consider the question of atomic overlap between fragments, i.e. the sharing of atoms in two or more different fragments located by the exhaustive search process.

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

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Volume 1 Chapter 7 Handling Structure Inversion.