The second step in generating a preliminary model is a self-symmetry search. This, and all of the remaining steps in generating a preliminary model are performed automatically by startcsym or starticos.
In this stage, each particle is assigned a quality factor based on its symmetry. Then the best particles with each required symmetry are pulled out and stored in a separate files. For icosahedral symmetry, 5-fold, 3-fold and 2-fold rotational symmetries are searched for. For particles with a single n-fold rotational symmetry, 2 views are searched for. The top view will contain the Cn symmetry. The side view will contain particles with a mirror symmetry (when n is even) or a near-mirror symmetry (when n is odd). In this case particles are also ranked based on how poorly the particle matches the Cn symmetry.
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