phenix.fem: compute Feature Enhanced Map (FEM)


The program reads PDB model, reflection data (Fobs or Iobs), experimental uncertainties and R-free flags, if available. Then it computes {2mFobs-DFmodel, Phase_model} map that is subject to FEM procedure.

Output is MTZ file with three sets of Fourier map coefficients:
  • 2mFoDFc,PHI2mFoDFc: usual {2mFobs-DFmodel, Phase_model} sigma-a weighted synthesis. No anisotropy correction or filling missing data.
  • ResolveDM,PHIResolveDM: Resolve density modified map coefficients
  • FEM,PHIFEM: Feature Enhanced Map

Command line usage examples

  1. Running with all defaults:

    % phenix.fem model.pdb data.mtz
  2. Specify data label:

    % phenix.fem data.mtz model.pdb label=Fobs
  3. Specify scattering dictionary (X-ray, electron, neutron):

    % phenix.fem model.pdb data.mtz scattering_label=neutron
  4. Some other settings and their defaults:
    • use_omit=True : use OMIT map
    • use_resolve=Auto : use Resolve DM as extra filter
    • use_max_map=True : use 'maximal synthesis'
    • file_name_prefix=fem : file prefix for output
    • For more settings run phenix.fem without arguments in the command line.


Graphical user interface is available

Additional information

Latest presentation of FEM methodology:

Publication in Computational Crystallography Newsletter (front page):


FEM: feature-enhanced map. P.V. Afonine, N.W. Moriarty, M. Mustyakimov, O.V. Sobolev, T.C. Terwilliger, D. Turk, A. Urzhumtsev, and P.D. Adams. Acta Cryst. D71, 646-666 (2015).

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