Correlation of two maps after accounting for origin shifts with get_cc_mtz


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Correlation of two maps after accounting for origin shifts with get_cc_mtz_mtz

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

Author(s)

get_cc_mtz_mtz: Tom Terwilliger

Purpose

get_cc_mtz_mtz is a command line tool for adjusting the origin of a map so that the map superimposes on another map, and obtaining the correlation of the two maps.

Usage

How get_cc_mtz_mtz works:

get_cc_mtz_mtz calculates maps based on the supplied mtz files, then uses RESOLVE to find the origin shift that maximizes the correlation of the two maps. This shift is applied to the second map and the correlation of the maps is calculated.

Output files from get_cc_mtz_mtz

offset.log: Log file for correlation calculation.

Examples

Standard run of get_cc_mtz_mtz:

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

phenix.get_cc_mtz_mtz map_coeffs_1.mtz  map_coeffs_2.mtz

If you want (or need) to specify the column names from your mtz file, you will need to tell get_cc_mtz_mtz what FP and PHIB are, in this format:

phenix.get_cc_mtz_mtz map_coeffs_1.mtz  map_coeffs_2.mtz \
labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT"

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all get_cc_mtz_mtz 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
------------------------------------------------------------------------------- 
get_cc_mtz_mtz
   mtz_1= None MTZ file 1 with coefficients for a map
   mtz_2= None MTZ file 2 with coefficients for a map
   labin_1= "" Labin line for MTZ file 1 with map coefficients. This is
            optional if get_cc_mtz_mtz 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_2= "" Labin line for MTZ file 2 with map coefficients. This is
            optional if get_cc_mtz_mtz 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
   resolution= 0. high-resolution limit for map calculation
   temp_dir= "temp_dir" Optional temporary work directory (must exist if you
             specify it)
   output_dir= "" Output directory where files are to be written