phenix.map_to_structure_factors: convert map into structure factors

Description

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

Notes

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

  (100,100,100)

Contact author

For questions, bug reports, feature requests: Pavel Afonine (PAfonine@lbl.gov)

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

• output_file_name = map_to_structure_factors.mtz
• d_min = None Resolution of output structure factors. Default is based on the gridding of the map and can lead to map coefficients that are at much higher resolution than the map.
• resolution_factor = 0.333 Scale factor to guess resolution of output structure factors. A scale factor of 0.5 gives the highest-resolution data allowed by the map. Usual is 0.33 or 0.25.
• scale_max = 99999 Maximum value of output map coefficients amplitudes. If None use volume scaling
• k_blur = 1 Scale applied to HL coefficients. The HL coefficients are arbitrary as no error information is available. The HL coefficients will have values of k_blur at low resolution, falling off with an effective B-value of b_blur at higher resolution.
• b_blur = 100 Blurring applied to HL coefficients. The HL coefficients are arbitrary as no error information is available. The HL coefficients will have values of k_blur at low resolution, falling off with an effective B-value of b_blur at higher resolution.
• box = False You can choose to generate a full box of map coefficients based on the gridding of the map. Default is to generate map coefficients to a specific resolution
• keep_origin = True Default (keep_origin=True) is to set the origin for the output map coefficients to be the same as the input map. A map calculated from the output map coefficients will superimpose on the input map. If keep_origin=False then the new origin will be at (0,0,0). Note: keep_origin=True is only available if the map covers an entire unit cell. It will be automatically set to False if less than a full unit cell is available.
• output_origin_grid_units = None You can set the origin of the output map (in grid units)
• map_file = None Input map file
• job_title = None Job title in PHENIX GUI, not used on command line
• guiGUI-specific parameter required for output directory
  • output_dir = None