Section 15.1.4.2. Reflection omit

The modified map may be made more independent of the original map, as was assumed when multiplying the phase probability distributions in equation (15.1.4.1), through a reciprocal-space analogue of the omit map, the reflection-omit method.

The reflections are divided into (typically 10 or 20) sets and density-modification calculations are performed, excluding each set in turn from the calculation of the starting map, in a manner similar to a free-R-value calculation (Brünger, 1992). Density modification is applied to each map in turn, and the modified reflections from each of the free sets are combined to give a new, complete data set. This data set should be less dependent on the original amplitudes; therefore, the amplitudes may be expected to give a better indication of the quality of the modified phases.

The resulting maps obtained using solvent flattening and/or histogram matching are dramatically improved using the reflection-omit method (Cowtan & Main, 1996). In the case of averaging calculations, however, the reflection-omit approach makes little difference, since omitted reflections tend to be restored through noncrystallographic symmetry relationships to other regions of reciprocal space. It is possible that further improvements may be achieved by selecting reflection sets that approximately obey the NCS relationships.