Merging two models with density_outside_model



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:

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 available keywords