Direct methods at high resolution have depended on the resolution of atomic like features in the map. At data resolutions more typical for protein structures (2–3 Å) individual atoms may not be resolved, so larger features must be identified. At one extreme the whole molecule may be located using the diffraction magnitudes alone by the molecular-replacement method. At the other extreme it is possible to locate individual residues in a well phased map. In this paper an intermediate problem is addressed: the location of multi-residue fragments on the basis of weak phase information. An agreement function based on the mean-squared difference between model and map over a masked region is shown to be more effective than a simple overlap integral, and may be efficiently calculated by Fourier methods. The techniques are compared using poorly phased electron-density maps at ∼3 Å for the proteins RNAse and O6-methylguanine-DNA-methyltransferase.