Calculating a simple NCS averaged map

If you already have map coefficients in an MTZ file and have identified your NCS with phenix.find_ncs and just want to calculate the average density in all your NCS copies, you can use phenix.ncs_average. In most cases this can be run automatically by passing the name of the MTZ file and the ncs_spec file with NCS information.

The output of phenix.ncs_average is a CCP4-style map file.

These simple NCS averaged maps can be accurate maps for cases with high NCS symmetry and they are useful for evaluating what an NCS density modified map should be expected to look like.

If you want to see the region that is being averaged, you can run phenix.ncs_average like this (notice the double and single quotes, both are necessary):

phenix.ncs_average  ncs_map_coeffs.mtz ncs.ncs_spec resolve_command_list=" 'ncs_mask_file ncs_mask.ccp4' "

If you want to specify the region to be averaged, you can do this by supplying a PDB file and the mask will be around atoms in that file. Note: the mask you supply is an overall mask around ALL the areas to be averaged, not just a single asymmetric unit of NCS.

phenix.ncs_average ncs_map_coeffs.mtz ncs.ncs_spec resolve_command_list=" 'ncs_mask_file ncs_mask.ccp4' 'model model_defining_mask.pdb' 'use_model_mask' 'rad_mask 5 ' "

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