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. The maps are calculated from map coefficients supplied by the user in two mtz files.

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 compatible with space-group symmetry that maximizes the correlation of the two maps. This shift is applied to the second map and the correlation of the maps is calculated.

Several parameters can be set by the user to define how the correlations are calculated. By default, maps are calculated using all the reflections present (to the specified high-resolution limit, if any) in each mtz file.

If you specify

use_only_refl_present_in_mtz_1=True

Then the map calculated using your second mtz file will only include reflections that were present in your first mtz file. This removes the effects of missing reflections on the correlation.

If you specify

scale=True

then get_cc_mtz_mtz scales the amplitudes from the second input mtz file to those in the first input mtz, including an overall B factor and a scale factor. This reduces effects of differences in overall B factors between the two mtz files on the correlation.

If you specify

keep_f_mag=False

then get_cc_mtz_mtz uses amplitudes from the first input mtz file and phases and figure of merit from both to do the correlation. This has the effect of removing effects due to differences in amplitudes on the correlation, and focusing on differences in phases and figures of merit.

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 (and optionally FOM) are, in this format:

phenix.get_cc_mtz_mtz map_coeffs_1.mtz  map_coeffs_2.mtz \
labin_1="FP=2FOFCWT PHIB=PH2FOFCWT"  labin_2="FP=2FOFCWT PHIB=PH2FOFCWT"

Possible Problems

Specific limitations and problems:

• Versions of phenix.get_cc_mtz_mtz up to 1.3-final used a different set of defaults, with the values,

scale=True
keep_f_mag=False
use_only_refl_present_in_mtz_1=True

These defaults were changed after version 1.3-final in order to make the results independent of the order of the mtz files and to make the default be to get the correlation of maps without manipulation.

List of all available keywords

• 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
  • map_in_1 = None CCP4 or MRC-style map file for file 1 (instead of mtz_1)
  • map_in_2 = None CCP4 or MRC-style map file for file 2 (instead of mtz_2)
  • resolution = None high-resolution limit for map calculation
  • low_resolution = None low-resolution limit for map calculation
  • offset_suffix = offset Suffix for output version of mtz file 2 or map_in_2, offset to maximize correlation with mtz file 1
  • temp_dir = "temp_dir" Temporary work directory
  • output_dir = "" Output directory where files are to be written
  • gui_output_dir = None
  • keep_f_mag = True If you set keep_f_mag=False then get_cc_mtz_mtz uses amplitudes from the first input mtz file and phases and fom from both to do the correlation. If you specify keep_f_mag=True then the amplitudes from both files are included.
  • scale = False If you set scale=True then get_cc_mtz_mtz scales the amplitudes from the second input mtz file to those in the first input mtz, including an overall B factor and a scale factor.
  • use_only_refl_present_in_mtz_1 = False You can specify that only reflections present in your first mtz file are used in the comparison. Note that this means that the order of the files will have an effect on the correlation coefficient
  • any_offset = False You can search for a match with any offset even though this is not allowed by space-group symmetry
  • fix_xyz = False You can get map-map correlation with no translations Does not apply to mtz-mtz comparisons
  • 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
  • resolve_command_list = None You can supply any resolve command here NOTE: for command-line usage you need to enclose the whole set of commands in double quotes (") and each individual command in single quotes (') like this: resolve_command_list="'no_build' 'b_overall 23' "
  • job_title = None Job title in PHENIX GUI, not used on command line