SOLVENT
Solvent Region Flattening Program
SOLVENT: Solvent Region Flattening Program
This program is used to perform the calculations required for solvent flattening of poorly phased electron density maps. It can be used to calculate a mask of the solvent region and it can apply this mask to the an electron density map to produce a map where the protein region is unaffected but the solvent region is absolutely flat.
The method used to calculate the solvent mask is that of Wang (Wang, B.C., ``Resolution of Phase Ambiguity in Macromolecular Crystallography'', Methods Enzymol. (1985). 115, 90-112) as modified, to improve performance, by Leslie (Leslie, A.G.W., ``A Reciprocal-space Method for Calculating a Molecular Envelope using the Algorithm of B. C. Wang'', Acta Cryst. (1987). A43, 134-136). First the map is read and the density values less than zero are set to zero. This map is Fourier inverted and the coefficients are multiplied by a function whose own Fourier transform is a cone with a particular radius. This operation is the equivalent of a weighted local average of the map.
A new map is calculated from the modified coefficients. A level of electron density is chosen so that a certain percentage of the density points in the map are below it. These points define the solvent region of the unit cell. The percentage is the solvent fraction of the crystal and must be supplied by the user. The points in the solvent region are marked with a value of zero, which produces the envelope. This envelope can be used to ``mask'' out the solvent region of the original map or can be written to the disk for later use.
The radius of the cone used in the local averaging step depends on the size of the molecule and the quality of the data. The default value is 9.25Å, but this value may be overridden by the user. At the start you will want to examine the solvent envelope to judge its quality. It should be connected with few to no holes. You can change the envelope by varying the radius. A larger radius will produce a smoother envelope while a smaller radius will produce a more elaborate one.