The routine auto_sharpen will automatically identify optimal sharpening/blurring/map adjustment for the input map and will write out an optimized version of the map.
Auto-sharpen adjusts the resolution dependence of the map to maximize the clarity of the map. You can choose to use map kurtosis or the adjusted surface area of the map which is the default for this purpose.
The auto-sharpen tool works best at resolutions of about 4.5 A or better. At lower resolutions it may be unable to distinguish variations in the quality of the map as the sharpening is varied.
You can also choose to specify the sharpening/blurring parameters for your map and they will simply be applied to the map. For example you can apply a sharpening B-value (b_sharpen) to sharpen the map, or you can specify a target overall B-value (b_iso) to obtain after sharpening.
Normally phenix.auto_sharpen will determine the optimal sharpening by examining the density in a box cut out of your map, then apply this to the entire map.
You can choose to apply autosharpening locally if you want. In this case the auto-sharpening parameters are determined in many boxes cut out of the map, and corresponding sharpened maps are calculated. The map that is produced is a weighted map where the density at a particular point comes most from the sharpened map based on a box near that point.
You can identify the sharpening parameters using two half-maps if you want. The resolution-dependent correlation of density in the two half-maps is used to identify the optimal resolution-dependent weighting of the map. This approach requires a target resolution which is used to set the overall fall-off with resolution for an ideal map. That fall-off for an ideal map is then multiplied by an estimated resolution-dependent correlation of density in the map with the true map (the estimation comes from the half-map correlations).
You can identify instead the sharpening parameters using your map and a model. This approach requires a guess of the RMSD between the model and the true model. The resolution-dependent correlation of model and map density is used as in the half-map approach above to identify the weighting of Fourier coefficients.
You can use phenix.auto_sharpen with a crystallographic map (represented as map coefficients).
Most crystallographic maps have the origin at the corner of the map ( grid point [0,0,0]), while most cryo-EM maps have the orgin in the middle of the map. An output map with the origin shifted to the corner of the map is optionally written out.
sharpened_map_coeffs.mtz: Sharpened map, shifted to place the origin on grid point (0,0,0) and sharpened, represented as map coefficients.
where my_map.map is a CCP4, mrc or other related map format, and you specify the nominal resolution of the map.
Maps produced with the extract-unique option of map_box should not be sharpened with auto-sharpen. These maps are closely masked around the density of a single molecule and are set to zero in much of the map, so the information about noise in the map that normally is available is missing and auto-sharpen does not work properly.
Automated map sharpening by maximization of detail and connectivity. T.C. Terwilliger, P.V. Afonine, Sobolev, OV, and P.D. Adams. bioRxiv (2018).
pdb_file = None If a model is supplied, the map will be adjusted to maximize map-model correlation. This can be used to improve a map in regions where no model is yet built.
ncs_file = None File with NCS information (typically point-group NCS with the center specified). Typically in PDB format. Can also be a .ncs_spec file from phenix. Created automatically if symmetry is specified.
seq_file = None Sequence file (unique chains only, 1-letter code, chains separated by blank line or greater-than sign.) Can have chains that are DNA/RNA/protein and all can be present in one file.
sharpened_map_file = sharpened_map.ccp4 Sharpened input map file. In the same location as input map.
shifted_sharpened_map_file = None Input map file shifted to place origin at 0,0,0 and sharpened.
output_directory = None Directory where output files are to be written applied.
resolution = None Optional nominal resolution of the map.
solvent_content = None Optional solvent fraction of the cell.
box_in_auto_sharpen = False Use a representative box of density for initial auto-sharpening instead of the entire map. Default is False.
density_select_in_auto_sharpen = True Choose representative box of density for initial auto-sharpening with density_select method (choose region where there is high density). Normally use False for X-ray data and True for cryo-EM.
soft_mask = True Use soft mask (smooth change from inside to outside with radius based on resolution of map).
local_sharpening = None Sharpen locally using overlapping regions. NOTE: Best to turn off local_aniso_in_local_sharpening if NCS is present. If local_aniso_in_local_sharpening is True and NCS is present this can distort the map for some NCS copies because an anisotropy correction is applied based on local density in one copy and is transferred without rotation to other copies.
local_aniso_in_local_sharpening = None Use local anisotropy in local sharpening. Default is True unless NCS is present.
max_box_fraction = 0.5 If box is greater than this fraction of entire map, use entire map. Default is 0.5.
k_sharpen = 10 Steepness of transition between sharpening (up to resolution ) and not sharpening (d < resolution). Note: for blurring, all data are blurred (regardless of resolution), while for sharpening, only data with d about resolution or lower are sharpened. This prevents making very high-resolution data too strong. Note 2: if k_sharpen is zero or None, then no transition is applied and all data is sharpened or blurred.
search_b_min = None Low bound for b_iso search. Default is -100.
search_b_max = None High bound for b_iso search. Default is 300.
search_b_n = None Number of b_iso values to search. Default is 21.
residual_target = None Target for maximization steps in sharpening. Can be kurtosis or adjusted_sa (adjusted surface area). Default is adjusted_sa.
sharpening_target = None Overall target for sharpening. Can be kurtosis or adjusted_sa (adjusted surface area). Used to decide which sharpening approach is used. Note that during optimization, residual_target is used (they can be the same.) Default is adjusted_sa.
require_improvement = None Require improvement in score for sharpening to be applied. Default is True.
region_weight = None Region weighting in adjusted surface area calculation. Score is surface area minus region_weight times number of regions. Default is set automatically. A smaller value will give more sharpening.
sa_percent = None Percent of target regions used in calulation of adjusted surface area. Default is 30.
n_bins = None Number of resolution bins for sharpening. Default is 20.