Correlation of two maps after accounting for origin shifts with get_cc_mtz_mtz



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.


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


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


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


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.


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 \

Possible Problems

Specific limitations and problems:


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.

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