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Merging two models with density_outside_model

How density_outside_model works:
Output files from density_outside_model
Standard run of density_outside_model:
Possible Problems
Specific limitations and problems:
Additional information
List of all density_outside_model keywords


  • density_outside_model: Tom Terwilliger


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


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.


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 \

Possible Problems

Specific limitations and problems:


Additional information

List of all density_outside_model keywords

Legend: black bold - scope names
        black - parameter names
        red - parameter values
        blue - parameter help
        blue bold - scope help
        Parameter values:
          * means selected parameter (where multiple choices are available)
          False is No
          True is Yes
          None means not provided, not predefined, or left up to the program
          "%3d" is a Python style formatting descriptor
      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)
      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
      temp_dir= "temp_dir" Optional temporary work directory
      output_dir= "" Output directory where files are to be written
      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)
      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' "