“within” finds atoms in the first selection within a cutoff distance of atoms in the second selection.

selection within distance of selection

chain A within 5.0 of chain B

By default, this operation is performed over all states. However, when a state number is provided to the select operator, the operation can be restricted to a single state.

If the two selections overlap, “within” will return atoms in both selections which meet the geometric criteria. Note that this behavior is different than that of near_to, which will only return atoms in the first selection that are not present in the second.

beyond | around | expand | extend | near_to

Selections