Author(s)

• density_outside_model: Tom Terwilliger

Purpose

This routine takes a model and map coefficients and returns new map coefficients with density set to zero near the atoms in the model

Usage

The main uses of phenix.density_outside_model are:

• Creating a map where all the parts of the map that have been explained by a model are removed.

How density_outside_model works:

Density_outside_model calculates a map from the map coefficients. Then all map values at points near an atom in the model are set to zero. Then a new set of map coefficients is calulated and written out.

Optionally the model can be trimmed so that that the last n_trim residues in each segment of the model are not included.

Output files from density_outside_model

density_removed.mtz: An MTZ file with your new map coefficients.

Examples

Standard run of density_outside_model:

Running density_outside_model is easy. From the command-line you can type:

phenix.density_outside_model pdb_in=mask_pdb.pdb \
   map_coeffs.mtz

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all available keywords

• density_outside_model
  • input_files
    • pdb_in = None Input PDB file marking region to remove from map
    • 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)
  • output_files
    • mtz_out = density_removed.mtz Output MTZ file in sg p1 with density_removed of density
    • log = density_removed.log Output log file
    • params_out = density_removed_params.eff Parameters file to rerun density_removed
  • directories
    • temp_dir = "temp_dir" Optional temporary work directory
    • output_dir = "" Output directory where files are to be written
  • density_removed_region
    • density_removed_model_radius = 2.5 If density_removed_type is model, then flat density will replace actual density inside of region within density_removed_model_radius of an atom in pdb_in (after application of any selections specified with atom_selection.
    • include_hetatm = True If True, then include HETATM atoms in input PDB file in defining region to be included
    • atom_selection = None Any selection specified with atom_selection is applied to input model before using the model.
    • n_trim = 0 Trim all ends of segments by n_trim residues before calculating density
    • density_removed_as_map = False Return modified density as map (alternative is map coeffs).
    • chain_type = PROTEIN chain type (PROTEIN RNA DNA)
  • 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
    • 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' "