Section 25.2.2.4.1. Density-modification modes

(1) Solvent flattening: This is the most common density-modification technique and is powerful for improving phases at fixed resolution, but weaker at extending phases to higher resolution. Its phasing power is highly dependent on the solvent content. Solvent flattening can be applied at comparatively low resolutions, down to around 5.0 Å.

(2) Histogram matching: This method is applied only to the density in the protein region. This method is weaker than solvent flattening for improving phases, but is much more powerful at extending phases to higher resolutions. This is due to a unique feature of histogram matching which uses a resolution-dependent target for phase improvement. The phasing power of histogram matching is inversely related to the solvent content. Therefore, histogram matching plays a more important role in phase improvement when the solvent content is low. Histogram matching works to as low as 4.0 Å, but does no harm below that. Histogram matching should probably be applied as a matter of course in any case where the structure is not dominated by a large proportion of heavy-metal atoms. Even in this case, histogram matching may be applied by defining a solvent mask with solvent, protein and excluded regions.

(3) Multi-resolution modification: This method controls the level of detail in the map as a function of resolution by applying histogram matching and solvent flattening at multiple resolutions. This strengthens phase improvement at fixed resolution, although it generally improves phase-extension calculations too.

(4) Noncrystallographic symmetry averaging: Averaging is one of the most powerful techniques available for improving phases and is applicable even at very low resolutions. In extreme cases, averaging may be used to achieve an ab initio structure solution (Chapman et al., 1992; Tsao et al., 1992). It should therefore be applied whenever it is present and the operators can be determined.

(5) Skeletonization: Iterative skeletonization is the process of tracing a `skeleton' of connected densities through the map and then building a new map by filling density around this skeleton. The implementation in DM is adapted for use on poor maps, where it is sometimes but not always of use. To bring out side chains and missing loops, the ARP program (Lamzin & Wilson, 1997) is more suitable.

(6) Sayre's equation: This method is more widely used in small-molecule calculations, and is very powerful at better than 2.0 Å resolution and when there are no heavy atoms in the structure. However, its phasing power is lost quickly as resolution decreases beyond 2.0 Å. The calculation takes significantly longer than other density-modification modes.