I would like find matches on at least 2 of n sites, where n ≥ 3, but Phase only allows matches on at least 3 of n sites. Why does Phase require matching on at least 3 sites?

Phase requires a minimum of 3 sites in order to get a proper alignment.

A possible workaround is to add one (or more) dummy sites to the hypothesis. These could be actual sites in the reference ligand or fictitious sites created using the freestyle edit mode. Here you want to use the feature matching rules to allow each dummy site to match anything (A,D,H,N,P,R), and you want to assign it a really large positional tolerance (e.g. 10 angstroms). The idea is that you will always be able to match the dummy site(s), so the real matching will be governed by the 2 sites of interest.

Keywords: Phase, pharmacophore, hypothesis, partial matching

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