phenix.map_box: extract box with model and map around selected atoms


The program carves out a box with model and map around selected atoms. Resulting map is output in three files: map coefficients in MTZ, and maps in CCP4 and X-plor formatted files.

Contact author

For questions, bug reports, feature requests: Pavel Afonine (

Usage examples

  1. Using map defined in MTZ file as Fourier map coefficients. Box is defined by selected atoms in residues from 1 to 10 in chain A

    phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10"

  2. Using CCP4 formatted map

    phenix.map_box model.pdb map.ccp4 selection="resname LIG"

  3. Extract unique part of a map. You can extract just the unique part of a map (unique based on map symmetry). This map is masked around high density. It will normally only have positive density and lower density parts of even the unique part are truncated. Note that if you want to sharpen the map, you must sharpen it before you extract the unique part. You should not sharpen a map file created with extract_unique because the extract_unique function creates a map that has been set to zero over much of the map and this interferes with auto-sharpen.

    phenix.map_box map.ccp4 extract_unique=True symmetry.ncs_spec resolution=3


  1. By default the output map will superimpose on the input map (keep_origin=True). The output map is normally smaller than the input map. For example, the input map might go from (0,0,0) to (100,100,100) and the output map might include only grid points from (50,50,50) to (100,100,100). The origin of the output map in this case will be (50,50,50). If the two maps are displayed, the region from (50,50,50) to (100,100,100) will be the same for the two maps. Not that anything outside of this range is meaningless for the output map.
  2. The cell dimensions of the output map will be the dimensions of the part that is cut out. In the above example, if the starting unit cell was (200,200,200) then be output map will have a unit cell of (100,100,100).

List of all parameters