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 = 1./3 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