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density.read() -- read an EM (electron microscopy) density map file

read(file, em_map_size, voxel_size, resolution, em_density_format='XPLOR', filter_type='NONE', filter_values=(0.0, 0.0), density_type='SPHERE', px=0, py=0, pz=0, cc_func_type='CCF')
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.


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Next: density.grid_search() dock Up: The density class: handling Previous: density() create   Contents   Index
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