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

{{phil:phenix.command_line.density_outside_model}}