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:


All phenix.maps parameters:

maps {
  input {
    pdb_file_name = None
    reflection_data {
      file_name = None
      labels = None
      high_resolution = None
      low_resolution = None
      twin_law = 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
        required = True
        test_flag_value = None
        ignore_r_free_flags = False
      }
    }
  }
  output {
    directory = None
    prefix = None
    job_title = None
    fmodel_data_file_format = mtz
    include_r_free_flags = False
  }
  scattering_table = wk1995 it1992 *n_gaussian neutron electron
  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
    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
    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
    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
    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
    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
  }
}