This command reads a density map from file, which should be provided as a cubic grid of intensities, in the X-PLOR ([Brünger, 1992]) or MRC format. The size of the cubic grid is given by em_map_size. The density map resolution and the map voxel size are given by resolution and voxel_size, respectively.
When fitting the probe into the EM grid, the probe structure is converted first into probe density, by using the function indicated in the density_type variable. Each atom can be represented by one of several atomic density functions, including, the uniform sphere model ('SPHERE'), the Gaussian function ('GAUSS'), a normalized Gaussian function ('NORM'), a hybrid Gaussian/sphere model ('HYBRID'), and an interpolation to the closest point on the grid ('TRACE'). The recommended function is 'SPHERE'.
filter_type is used to filter the values of the EM density during this calculation. Filters that can be used are: 'THRESHOLD' for a lower threshold (any density value below the first value set in filter_values will be set to 0); 'SQUARE' for a square filter; and 'LAPLACIAN' for a Laplacian filter. 'NONE' is the default option, and means that no filter is used.
When calculating the cross-correlation coefficient between a probe model and the density map, ccf_func_type specifies if you want the normalized cross-correlation coefficient ('CCF'), or the local cross-correlation coefficient ('LCCF').
Example: See density.grid_search() command.