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

Running with all defaults:
% phenix.fem model.pdb data.mtz
Specify data label:
% phenix.fem data.mtz model.pdb label=Fobs
Specify scattering dictionary (X-ray, electron, neutron):
% phenix.fem model.pdb data.mtz scattering_label=neutron
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
- use_experimental_phases = False
- xray_dataScope of X-ray data and free-R flags
  - file_name = None
  - labels = None
  - high_resolution = None
  - low_resolution = None
  - twin_law = 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
    - required = True Specify if free-r flags are must be present (or else generated)
    - 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