phenix.map_to_structure_factors: convert map into structure factors


The program reads a CCP4 (MRC) formatted map and converts it into structure factors.

Output: mtz file containing

  • Fourier transform of input map: complex array (F, PHIF) of given (d_min) resolution
  • Array of amplitudes F (F_ampl) and phases as HL coefficients


If the map has an origin that is not (0,0,0), by default that origin is preserved in the output mtz file (if you create a map from the output map coefficients, that map will superimpose on the input map).

You can adjust the origin of the output map with the keywords:

  • keep_origin=False: this will shift the origin to (0,0,0)

  • output_origin_grid_units=100,100,100: this will shift the origin to


Contact author

For questions, bug reports, feature requests: Pavel Afonine (

Command line usage examples:

% phenix.map_to_structure_factors map.ccp4 d_min=3

Current limitations:

X-plor formatted map files are not supported.

List of all available keywords