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 ' "

List of all available keywords

input_files
- mtz_in = None Input MTZ file with map coefficients
- map_coeff_labels = None If map coefficients cannot be identified automatically from your MTZ file, you can specify the label or labels for them. (Please separate labels with blank space, MTZ columns grouped together separated by commas with no blanks.) You can specify: map_coeff_labels (e.g., FWT,PHIFWT) amplitudes and phases (e.g., FP,SIGFP PHIB) or amplitudes, phases, weights (e.g., FP,SIGFP PHIB FOM)
- map_file = None Optional input CCP4-style map file. No mtz_in is needed if a map file is supplied
- ncs_in = None File with NCS operators to be applied to ncs_in This can be a .ncs_spec file from find_ncs, simple_ncs_from_pdb or find_ncs_from_density It can also be NCS formatted for resolve, including rotations, translations, and centers Note: you can alternatively supply a PDB file with pdb_in
- pdb_in = None Optional PDB file containing NCS to apply
output_files
- ccp4_map_out = ncs_average.ccp4 Output CCP4-style map file with NCS-averaged density
- ncs_mask_file = ncs_mask.ccp4 Output CCP4-style map file with NCS-mask
- map_coeffs_out = ncs_average.mtz Output MTZ file with map coefficients representing NCS-averaged density. Note: only applicable if input map is represented as map coefficients information with mtz_in. not applicable if map_in is used.
- log = ncs_average.log Output log file
- params_out = ncs_average_params.eff Parameters file to rerun ncs averaging
directories
- temp_dir = "temp_dir" Optional temporary work directory
- output_dir = "" Output directory where files are to be written
crystal_info
- high_resolution = None high-resolution limit for map calculation
- solvent_content = 0.5 solvent fraction
- wang_radius = 5 Smoothing radius for identification of solvent boundary
- use_pdb_in_as_mask = False Use pdb_in file as mask for NCS (if supplied)
- rad_mask = 4 mask radius around atoms in pdb_in.
- high_resolution_scale = 0.95 Resolution of output map coeffs will be high_resolution_scale* resolution of input map coeffs if high_resolution is None
- fraction_ncs_min = 0.05 If the fraction of the asymmetric unit occupied by the NCS related molecules is less than fraction_ncs_min it is ignored
- refine_ncs_operators = False Refine NCS operators
control
- verbose = False Verbose output
- raise_sorry = False Raise sorry if problems
- debug = False Debugging output
- dry_run = False Just read in and check parameter names
- coarse_grid = False Use coarse grid (saves on memory)
- 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' "