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

of known formats.

How to run the command line version:

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

Alternately, you may specify input files (and additional parameters) directly on the command line:

% phenix.maps model.pdb data.mtz

and it will automatically generate the default maps as described above.

Important Facts:

• 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, llg. 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.
• For LLG map calculation, if you specify the wavelength any existing heavy atoms (P or heavier) will be modeled as anomalous scatterers using the theoretical values of f' and f''.

All phenix.maps parameters:

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
    include_r_free_flags = False
  }
  scattering_table = wk1995 it1992 *n_gaussian neutron
  wavelength = None
  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
  }
}