Author(s)

• remove_free_from_map: Tom Terwilliger

Purpose

remove_free_from_map is a tool to remove test set reflections from a map coefficients file so that the map can be used in real-space refinement without including the test set reflections.

NOTE: Normally remove_free_from_map is called from build_one_model or phase_and_build, but you can run it interactively if you want.

Usage

How remove_free_from_map works:

remove_free_from_map uses resolve to set all test set reflections to zero.

Output files from remove_free_from_map

map_coeffs_without_freer_set.mtz: An MTZ file with test set reflections set to F=0

Examples

Standard run of remove_free_from_map:

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

phenix.remove_free_from_map   map_coeffs.mtz free_r.mtz

where free_r.mtz has your FreeR_flag indicating which reflections are in the test set.

• remove_free_from_map
  • input_files
    • free_in = None MTZ file with FreeR_flags
    • map_coeffs = None MTZ file with coefficients for a map
    • labin_map_coeffs = "" Labin line for MTZ file with map coefficients. This is optional if remove_free_from_map can guess the correct coefficients for FP PHI and FOM. Otherwise specify: LABIN FP=myFP PHIB=myPHI FOM=myFOM where myFP is your column label for FP
    • labin_free = "" Labin line for MTZ file with FreeR_flags. This is optional if remove_free_from_map can guess the correct coefficients for FreeR_flags.Otherwise specify: FreeR_flags==myFreeR_flags
    • test_flag_value = None This parameter sets the value of the test set that is to be free. Normally phenix sets up test sets with values of 0 and 1 with 1 as the free set. The CCP4 convention is values of 0 through 19 with 0 as the free set. Either of these is recognized by default in Phenix. If you have any other convention (for example values of 0 to 19 and test set is 1) then you can specify this with test_flag_value.
  • output_files
    • mtz_out = map_coeffs_without_freer_set.mtz Output MTZ file with coefficients for a map without freeR set. Labels will be FP PHIM FOMM always
    • params_out = remove_free_from_map_params.eff Parameters file to rerun remove_free_from_map
  • directories
    • temp_dir = "temp_dir" Optional temporary work directory
  • control
    • verbose = True Verbose output
    • raise_sorry = False Raise sorry if problems
    • debug = False Debugging output
    • dry_run = False Just read in and check parameter names