phenix.fem: compute Feature Enhanced Map (FEM)

Description

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.

GUI

Graphical user interface is available

Additional information

Latest presentation of FEM methodology:

http://phenix-online.org/presentations/fem_06MAY2014.pdf

Publication in Computational Crystallography Newsletter (front page):

http://www.phenix-online.org/newsletter/CCN_2013_07.pdf

References

• 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).

List of all available keywords

• random_seed = 2679941
• use_omit = True Use composite OMIT protocol
• sharp = True
• use_unsharp_masking = True
• resolution_factor = 1./4
• signal_threshold = 0.5
• use_resolve = Auto
• use_max_map = True
• ignore_zero_occupancy_atoms = True
• job_title = None Job title in PHENIX GUI, not used on command line
• input
  • sequence = None
  • scattering_table = wk1995 it1992 *n_gaussian neutron electron
  • wavelength = None
  • energy = None
  • xray_dataScope of X-ray data and free-R flags
    • file_name = None
    • labels = None
    • high_resolution = None
    • low_resolution = None
    • outliers_rejection = True Remove basic wilson outliers , extreme wilson outliers , and beamstop shadow outliers
    • french_wilson_scale = True
    • sigma_fobs_rejection_criterion = None
    • sigma_iobs_rejection_criterion = None
    • ignore_all_zeros = True
    • force_anomalous_flag_to_be_equal_to = None
    • convert_to_non_anomalous_if_ratio_pairs_lone_less_than_threshold = 0.5
    • french_wilson
      • max_bins = 60 Maximum number of resolution bins
      • min_bin_size = 40 Minimum number of reflections per bin
    • r_free_flags
      • file_name = None This is normally the same as the file containing Fobs and is usually selected automatically.
      • label = None
      • test_flag_value = None This value is usually selected automatically - do not change unless you really know what you're doing!
      • ignore_r_free_flags = False Use all reflections in refinement (work and test)
      • disable_suitability_test = False
      • ignore_pdb_hexdigest = False If True, disables safety check based on MD5 hexdigests stored in PDB files produced by previous runs.
      • generate = False Generate R-free flags (if not available in input files)
      • fraction = 0.1
      • max_free = 2000
      • lattice_symmetry_max_delta = 5
      • use_lattice_symmetry = True
      • use_dataman_shells = False Used to avoid biasing of the test set by certain types of non-crystallographic symmetry.
      • n_shells = 20
  • pdb
    • file_name = None Model file(s) name (PDB)
  • monomers
    • file_name = None Monomer file(s) name (CIF)
  • maps
    • map_file_name = None A CCP4-formatted map
    • d_min = None Resolution of map
    • map_coefficients_file_name = None MTZ file containing map
    • map_coefficients_label = None Data label for complex map coefficients in MTZ file
• output
  • file_name_prefix = fem
  • column_root_label = FEM
  • gui_output_dir = None