Remove test set reflections from a map file with remove_free_from


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Remove test set reflections from a map file with remove_free_from_map

Author(s)
Purpose
Usage: How remove_free_from_map works:; Output files from remove_free_from_map
Examples: Standard run of remove_free_from_map:
Possible Problems: Specific limitations and problems:
Literature
Additional information: List of all remove_free_from_map keywords

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.

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all remove_free_from_map keywords

------------------------------------------------------------------------------- 
Legend: black bold - scope names
        black - parameter names
        red - parameter values
        blue - parameter help
        blue bold - scope help
        Parameter values:
          * means selected parameter (where multiple choices are available)
          False is No
          True is Yes
          None means not provided, not predefined, or left up to the program
          "%3d" is a Python style formatting descriptor
------------------------------------------------------------------------------- 
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
   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