Author(s)

• map_correlations: Pavel Afonine, Tom Terwilliger

Purpose

Map correlations is a GUI and command-line tool for evaluating the fit of models to maps and the correlation between maps. It has the feature that the model or second map can be offset (translated) to maximize the correlation. This offset can be restricted to shifts allowed by space-group symmetry (translational_offsets=Allowed_by_symmetry) or it can be any shifts (translational_offsets=Any).

Maps can be supplied as map files or as map coefficients. Maps and map coefficients may not be both used at the same time.

If a model is supplied, the local correlation for each residue is calculated

The total number of files supplied must be exactly two.

Notes

The map_correlations tool replaces phenix.map_model_cc, phenix.model_map_cc, phenix.get_cc_mtz_mtz, phenix.get_cc_mtz_pdb, and phenix.get_cc_map_map.

How map_correlations works:

If an optimized translation is requested, map correlations finds the optimal translation using RESOLVE. The translation is calculated based on an FFT-based correlation search. If two maps (or map coefficients files) are supplied, the second map is shifted. If a model is supplied, a model-based map is calculated, and the optimal translation for that model-based map is applied to the model

If you supply a model file, by default model density is calculated using the atom types, occupancies and isotropic thermal factors (B-values) supplied in that PDB file.

If you specify b_values=Zero then all the B-values are set to zero before calculation of correlations. This is useful if you want to compare the clarities of a series of maps, all representing the same model. You calculate the map-model correlation of each map to your reference model in which all B-values in the reference model have been set to zero (Terwilliger et al., 2018):

Output files from map_correlations

xxx_offset.pdb: A PDB file offset to match the origin in the mtz file. Produced if translational_offsets are requested and a model is supplied. xxx_offset.mtz: A translated version of the second MTZ file supplied (if any), offset so that the map calculated from it optimally matches the map from the first MTZ file. xxx_offset.ccp4: A translated version of the second map file supplied, (if any) offset so that the map calculated from it optimally matches the map from the first map file.

Examples

Standard run of map_correlations:

Running map_correlations is easy. From the command-line you can type:

phenix.map_correlations map_coeffs.mtz coords.pdb

Possible Problems

Specific limitations and problems:

References

• Automated map sharpening by maximization of detail and connectivity. T.C. Terwilliger, P.V. Afonine, Sobolev, OV, and P.D. Adams. Acta Cryst. D74, 545-559 (2018).

List of all available keywords

• map_correlations
  • translational_offsets = *None Any Allowed_by_symmetry Allow origin shifts that are compatible with the map or map coefficients. For cryo-EM data, use None for no offsets or Any if you want to allow translations. For Xray data, use None for no offsets or Allowed_by_symmetry to allow origin offsets compatible with the space group.
  • minimum_cc_for_auto_resolution = 0.1 Minimum CC for automatic resolution estimation
  • b_values = *Keep Zero Keep B values as supplied, or set all to zero. Only applies if model is supplied.
• input_files
  • model = None Model
  • map_in_1 = None Map 1
  • map_in_2 = None Map 2
  • map_coeffs_1 = None Map coefficients 1
  • map_coeffs_1_virtual = None Used internally
  • map_coeffs_2_virtual = None Used internally
  • map_coeffs_2 = None Map coefficients 2
  • map_coeffs_labels_1 = None
  • map_coeffs_labels_2 = None
• control
  • clean_up = True Clean up temp directories
  • verbose = False Verbose output
• directories
  • temp_dir = None Optional temporary directory
  • gui_output_dir = None GUI use only - does not apply to command line version
• map_model_cc
  • resolution = None Data (map) resolution
  • scattering_table = wk1995 it1992 n_gaussian neutron *electron Scattering table (X-ray, neutron or electron)
  • atom_radius = None Atom radius for masking. If undefined then calculated automatically
  • keep_map_calc = False Keep model-calculated map
  • wrapping = None You can specify whether your maps wrap around outside boundaries
  • ignore_symmetry_conflicts = False You can ignore the symmetry information (CRYST1) from coordinate files. This may be necessary if your model has been placed in a box with box_map for example.
  • compute
    • cc_per_chain = True Compute local model-map CC for each chain
    • cc_per_residue = True Compute local model-map CC for each residue
    • cc_per_residue_group = False Compute local model-map CC for each residue group
    • fsc = True Compute FSC
    • cc_mask = True
    • cc_volume = True
    • cc_peaks = True
    • cc_box = True
    • cc_image = False
• output
  • file_name_prefix = None Optional prefix (including path) for output files. Default is name of the program and run number
• guiGUI-specific parameters, not used on command line
  • result_file = None
  • job_title = None Job title in PHENIX GUI, not used on command line