Combine composite OMIT files from a set of parallel runs on different computers

If you run a composite OMIT job but it fails at the last step of combining files, or if you run all the individual omit boxes on different machines, you can still combine them all into one single composite omit map.

You can do this by copying all the individual mtz files with map coefficients for omit regions to a single directory.

Here is a script you can edit and use to combine omit maps representing different omit regions into one.

NOTE: you need to ensure that the OMIT regions are defined the same in the runs where you got your overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc files and this run. You ensure that with the n_xyz command that sets the grid. You can copy this from one of your resolve log files created when you ran your omit (i.e., AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0/resolve.log will have a line like "nu nv nw: 32 32 32 " and you copy those numbers).

 ------------------------------------
#!/bin/csh -f
# COMBINE OMIT SCRIPT
phenix.resolve << EOD
hklin exptl_fobs_phases_freeR_flags.mtz
labin FP=FP SIGFP=SIGFP
n_xyz 32 32 32  # YOU MUST SET THIS BASED ON THE nu nv nw in a resolve log
file.
solvent_content 0.85
no_build
ha_file NONE
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_2
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_3
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_4
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_5
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_6
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_7
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_8
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_9
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_10
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_11
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_12
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_13
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_14
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_15
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_16
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_17
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_18
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_19
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_20
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_21
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_22
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_23
combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_24
omit
EOD
# END OF COMBINE OMIT SCRIPT