phenix.maps: a command line tool to compute various maps and save them in most

of known formats.

1. Run phenix.maps without any arguments: just type phenix.maps in the command line and hit Enter. This will creare a parameter file called maps.params, which can be renamed if desired.
2. Edit maps.params file to specify input/output file names, data labels and the desired maps. It is possible to request as many maps as desired. By default, the file maps.params specifies 5 maps to be created: 2mFo-DFc, 2mFo-DFc with missing Fobs filled with DFcalc, mFo-DFc and anomalous difference maps will be output in MTZ format, and one 2mFo-DFc map will be output in CCP4 format. NOTE: the anomalous difference map will only be created if the input reflection data file contains Bijvoet maps (F+/F- or I+/I-).
3. Run this command to compute requested maps: phenix.maps maps.params

% phenix.maps model.pdb data.mtz

• phenix.maps is available in PHENIX GUI.
• The scope of parameters 'map_coefficients' defines the map that will be output as Fourier map coefficients. The scope of parameters 'map' defines the maps that will be output as CCP4 or X-plor format.
• To create several maps: duplicate either 'map_coefficients' or 'map' or both scopes of parameters as many times as many maps is desired. Then edit each of them to define the maps.
• A map is defined by specifying a map type using 'map_type' keyword available within each scope of parameters: 'map_coefficients' or 'map'. The general supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[_kick][_filled]. For example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, anom. The 'map_type' parser will automatically recognize which map is requested.
• The program creates as many files with CCP4 or X-plor formatted maps as is requested, and it creates only one MTZ formatted file with all Fourier map coefficients in it.
• The CCP4 or X-plor formatted maps can be computed in the entire unit cell or around selected atoms only.
• Kick maps and missing Fobs filling is done (if requested) as described in Adams et al. (2010). Acta Cryst. D66, 213-221.
• Twinning (if detected) will be accounted for automatically. This can be disabled by using "skip_twin_detection=True" keyword.
• All arrays used in map calculation, for example: Fobs, Fmodel, Fcalc, Fmask, m, D, etc., can be output into a CNS or MTZ formatted reflection file.
• For those who likes to experiment: bulk solvent correction and anisotropic scaling can be turned off, the data can be filtered by sigma and resolution.
• For some map types certain 'map_coefficients' or 'map' scope parameters may not be applicable. For example, for "map_type=anomalous" the keywords "kicked", "fill_missing_f_obs" and some other are not applicable.

maps {
  input {
    pdb_file_name = None
    reflection_data {
      file_name = None
      labels = None
      high_resolution = None
      low_resolution = None
      outliers_rejection = True
      french_wilson_scale = True
      french_wilson {
        max_bins = 60
        min_bin_size = 40
      }
      sigma_fobs_rejection_criterion = None
      sigma_iobs_rejection_criterion = None
      r_free_flags {
        file_name = None
        label = None
        test_flag_value = None
        ignore_r_free_flags = False
      }
    }
  }
  output {
    directory = None
    prefix = None
    title = None
    fmodel_data_file_format = mtz cns
  }
  scattering_table = wk1995 it1992 *n_gaussian neutron
  bulk_solvent_correction = True
  anisotropic_scaling = True
  skip_twin_detection = False
  omit {
    method = *simple
    selection = None
  }
  map_coefficients {
    map_type = 2mFo-DFc
    format = *mtz phs
    mtz_label_amplitudes = 2FOFCWT
    mtz_label_phases = PH2FOFCWT
    kicked = False
    fill_missing_f_obs = False
    sharpening = False
    sharpening_b_factor = None
    exclude_free_r_reflections = False
    isotropize = True
  }
  map_coefficients {
    map_type = 2mFo-DFc
    format = *mtz phs
    mtz_label_amplitudes = 2FOFCWT_fill
    mtz_label_phases = PH2FOFCWT_fill
    kicked = False
    fill_missing_f_obs = True
    sharpening = False
    sharpening_b_factor = None
    exclude_free_r_reflections = False
    isotropize = True
  }
  map_coefficients {
    map_type = mFo-DFc
    format = *mtz phs
    mtz_label_amplitudes = FOFCWT
    mtz_label_phases = PHFOFCWT
    kicked = False
    fill_missing_f_obs = False
    sharpening = False
    sharpening_b_factor = None
    exclude_free_r_reflections = False
    isotropize = True
  }
  map_coefficients {
    map_type = anomalous
    format = *mtz phs
    mtz_label_amplitudes = ANOM
    mtz_label_phases = PHANOM
    kicked = False
    fill_missing_f_obs = False
    sharpening = False
    sharpening_b_factor = None
    exclude_free_r_reflections = False
    isotropize = True
  }
  map {
    map_type = 2mFo-DFc
    format = xplor *ccp4
    file_name = None
    kicked = False
    fill_missing_f_obs = False
    grid_resolution_factor = 1/4.
    region = *selection cell
    atom_selection = None
    atom_selection_buffer = 3
    sharpening = False
    sharpening_b_factor = None
    exclude_free_r_reflections = False
    isotropize = True
  }
}