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"