FFT-ing map coefficients

If you already have map coefficients in an MTZ file and just want to run an FFT to produce X-plor or CCP4 map files, use phenix.fft or phenix.mtz2map (these are synonyms for the same program). In most cases this can be run automatically by passing the name of the MTZ file. MTZ files generated by phenix.maps, phenix.refine, SOLVE/RESOLVE, and REFMAC are supported, and additional combinations of map coefficients are possible if defined by the user. By default, output files will take the base name of the MTZ file, with the appropriate map type appended if it can be guessed from the column labels, otherwise a unique integer, followed by the file type extension (.ccp4 or .xplor).

Other map types

  • For isomorphous difference maps (Fobs-Fobs), use phenix.fobs_minus_fobs_map (documentation to be added).
  • For omit maps, including composite omit maps and iterative build omit maps, use the AutoBuild wizard.
  • You can also generate a simple simulated-annealing omit map by deleting the relevant part of the molecule and running phenix.refine with simulated_annealing=True. (This is essentially the same was what is done by AutoBuild, however.)

List of all available keywords

  • mtz_file = None MTZ file containing map coefficients
  • pdb_file = None Model file around which to draw the map. If not supplied, the map will fill the unit cell.
  • labels = None Map column labels. Common examples are 2FOFCWT,PH2FOFCWT and FP,SIGFP PHIM FOMM . If left blank, all maps present in the input file will be used.
  • buffer = 5.0 Extra padding (in Angstroms) around the selected region (or unit cell)
  • selection = None Atom selection around which to draw map (plus buffer). If left blank, the entire model file will be used.
  • d_min = None High-resolution cutoff
  • d_max = None Low-resolution cutoff
  • grid_resolution_factor = 0.25 Grid spacing (multiplied by the high-resolution limit)
  • scale = *sigma volume Scaling method for map values
  • include_fmodel = False
  • show_maps = False
  • output
    • directory = None Output directory (defaults to current)
    • prefix = None Output file prefix (defaults to the MTZ file name base)
    • job_title = None Job title in PHENIX GUI, not used on command line
    • format = xplor *ccp4 dsn6
    • extension = *Auto ccp4 xplor map dsn6
  • r_free_flags
    • remove = False
    • file_name = None
    • label = None
    • test_flag_value = None