Section 25.2.1.4. Fourier-map calculations

Selected regions of an electron-density map that are useful for NC symmetry applications can be extracted from the full-cell maps produced by FSFOUR with the programs EXTRMAP (batch) or MAPVIEW (interactive). The `submap' regions can cover any arbitrary volume and cross multiple cell edges if desired.

Programs MAPORTH and SKEW (both run in batch mode) are provided to modify submaps, as modification is sometimes useful or required with NC symmetry applications. MAPORTH simply converts the map to correspond to an orthogonal grid, which simplifies refinement of NC symmetry operators. SKEW also converts the map to an orthogonal grid, but changes the axis directions such that the new b axis can be arbitrarily oriented. This is useful in NC symmetry applications where one may want to examine maps looking directly down the NC symmetry rotation axis. Both programs compute density values at the new grid points by using a 64-point cubic spline interpolation and can also orthogonalize or skew masks to maintain correspondence with the modified submaps.

Program GMAP (interactive) is used to extract any region from a FSFOUR map, possibly crossing multiple cell edges, and convert it to a form directly readable by the external interactive graphics programs TOM [SGI version of FRODO (Jones, 1978)], O (Jones et al., 1991) or CHAIN (Sack, 1988). In addition to the output map file, one may also output a corresponding skeleton (Greer, 1974) file (for TOM) or skeleton data block (for O) to facilitate chain tracing.

Program PSRCH (batch) lists the largest peaks in a Fourier map and is useful in identifying additional heavy-atom or anomalous-scatterer sites from a map phased by a tentative model. Either positive or negative peaks can be listed, with the latter sometimes useful in MAD phasing applications, depending on the assignment of `native' and `derivative' data sets. Only unique peaks are listed, and the peak positions are interpolated from the map.