|file = <str:1>||'default'||input electron density map file|
|em_density_format = <str:1>||'XPLOR'||input density map file format for EM_GRID_SEARCH; 'MRC' | 'XPLOR'|
|density_type = <str:1>||'SPHERE'||Function used to calculate density map cross-correlation in EM_GRID_SEARCH; 'SPHERE' | 'GAUSS' | 'HYBRID' | 'GAUSS_NORM' | 'TRACE'|
|voxel_size = <float:1>||0||EM density map voxel size for EM_GRID_SEARCH|
|resolution = <float:1>||0||EM density map resolution for EM_GRID_SEARCH|
|em_map_size = <int:1>||0||size of the density map, for EM_GRID_SEARCH|
|ccf_func_type = <str:1>||type of correlation 'CCF' | 'LCCF'|
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'.
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.