Docking sidechains means adding sidechains to a model or fragment that has currently only poly-Ala, where the sequence assignment is unknown. The algorithm is basically the same as in Cowtan's Buccaneer, but with some corners cut to make things (more or less) interactive. The algorithm uses the shape of the density around the C-beta position to estimate the probability of each sidechain type at that position.
The function is accessed via the Extensions -> Dock Sequence menu item. First, a sequence should be assigned from a PIR file to a particular chain-id and model number. Secondly Extensions -> Dock Sequence -> Dock Sequence on this fragment.... Choose the model to build on and then Dock Sequence! If all goes well, the model will be updated with mutated residues and undergo rotamer seach for each of the new residues. If the sequence alignment is not sufficiently clear, then you will get a dialog suggesting that you extend or improve the fragment.