## density.read() — read an EM (electron microscopy) density map file

`read(file, resolution, em_map_size=0, voxel_size=0.0, em_density_format='XPLOR', filter_type='NONE', filter_values=(0.0, 0.0), density_type='SPHERE', px=None, py=None, pz=None, 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], CCP4, or MRC format. (Note that CCP4 and MRC files are currently read in the same way, since the formats are very similar.) file can be a filename or a readable file handle (see modfile.File()).

> The size of the cubic grid (em_map_size) and the map voxel size (voxel_size) are both taken from the density map file itself. If, however, em_map_size is specified and is non-zero, the cubic grid size must match this value. If voxel_size is specified and differs from that given in the file header, the user-specified value is used in preference.

> The density map resolution is given by resolution.

> px, py, and pz specify the origin of the map, in angstroms. If not given, it is read from the MRC or CCP4 map header (X-PLOR files do not include this information, so the origin will default to zero in this case.)

> 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.