During calculations of the packing similarities for a set of structure pairs I got the following results:

pair_of_structures cell_formula_units_Zprime match_15
ABUDAD_ABUDAD01 1_1 [2, 2]
ASATET_ASATET01 1_3 [15, 11, 11, 15, 11, 11, 15, 11, 11]
DHXANT12_DHXANT13 1_8 [14, 10, 10, 10, 12, 14, 9, 12, 12]
DOPPAB_DOPPAB02 1_4 [5, 3, 6, 3, 4]
DOPPAB01_DOPPAB02 2_4 [11, 9, 11, 9, 11]

where in the last column are listed the .nmatched_molecules values of the packing similarity Comparison() instance. Options for the PackingSimilarity() instance are in the attached file. My questions is what determines the number of the nmatched_molecules values returned, given that I got the same number of these values (9 values) for structures under comparison with Z' equal to 1 and 3 (pair ASATET ASATET01), and 1 and 8 (pair DHXANT12 DHXANT13). CSD API version 2.0.0

The algorithm used is described in J. A. Chisholm and S. Motherwell, J. Appl. Cryst. (2005) 38:228–231. http://scripts.iucr.org/cgi-bin/paper?S0021889804027074

The method finds arrangements of molecules that match between the query structure and the comparison structure to within your specified tolerances.  The nmatched_molecules is then the number of molecules within those arrangements.

Thank you for the fast reply, but the question is why do we obtain two numbers for pair ABUDAD_ABUDAD01, each with Z'=1. As far as I understand, the program takes non-equivalent molecule from each structure, then builds a shell made of specified number of molecules (14 in my case), and then tries to match these two clusters (cluster_1 and cluster_2) made of 15 molecules each. Why do we get two numbers then? Is the comparison of cluster_1 to cluster_2 non-equivalent to comparison of cluster_2 to cluster_1? Further, if we compare structures with Z'=1 (ASATET) and Z'=3 (ASATET01), then we need to match 3 pairs of clusters from combinations of one cluster taken from ASATET and three clusters taken from ASATET01, though we obtain 9 numbers with nmatched_molecules values.

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