phenix.fmodel: a tool to compute structure factors, Fmodel:

Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s^2/4) * Fmask) where:

• Fmodel - total model structure factor (complex value)
• AnisoScale = -ht*A(-1)*b_cart*A(-1)th/4
• h - column vector with Miller indices
• A - orthogonalization matrix
• b_cart - anisotropic scale matrix
• t and (-1) denotes transposition and inversion operations
• scale - overall scale factor
• Fcalc - structure factors calculated from atomic model
• k_sol and b_sol - Flat Bulk solvent model parameters
• Fmask - structure factors calculated from bulk solvent mask

1. phenix.fmodel model.pdb high_resolution=1.5 will result in a file containing complete set of Fmodel = Fcalc computed from atomic model up to 1.5A resolution.

2. phenix.fmodel model.pdb scale=2 k_sol=0.35 b_sol=50 b_cart="1 2 3 0 4 7" high_res=1.5 low_res=10 will result in a file containing complete set of Fmodel computed using the above formula in resolution range 1.5-20.0A.

3. phenix.fmodel model.pdb high_resolution=1.5 algorithm=direct is similar to "1)" but the Fcalc are computed using direct summation algorithm.

4. phenix.fmodel model.pdb high_res=1.5 format=cns label=FOBS type=real r_free=0.1 will result in CNS formatted file containing complete set of amplitudes of Fmodel = Fcalc computed up to 1.5A resolution, labelled as FOBS, and free-R flags with 10% of test reflections. This is a typical command to simulate Fobs.

5. phenix.fmodel model.pdb high_res=1.5 scattering_table=neutron will result in a file containing complete set of Fmodel = Fcalc computed from atomic model up to 1.5A resolution using neutron scattering table.

6. phenix.fmodel model.pdb parameters.txt will result in a structure factor file, where Fmodel were computed using parameters defined in parameters.txt file. The parameters.txt file can contain all or any subset of parameters listed below. Note, that each { must have a matching one }.

7. phenix.fmodel model.pdb reflection_data.mtz will result in a file containing a set of Fmodel = Fcalc that will match the set of Miller indices of the data in reflection_data.mtz file.

8. phenix.fmodel model.pdb reflection_data.mtz data_column_label="FOBS,SIGMA" similar to "7)", where the specific data array is selected.

high_resolution = None
low_resolution = None
r_free_flags_fraction = None
add_sigmas = False
add_random_error_to_amplitudes_percent = None
scattering_table = wk1995 it1992 *n_gaussian neutron
pdb_file = None
reference_file = None
data_column_label = None
fmodel {
  k_sol = 0.0
  b_sol = 0.0
  b_cart = 0 0 0 0 0 0
  scale = 1.0
}
structure_factors_accuracy {
  algorithm = *fft direct
  cos_sin_table = False
  grid_resolution_factor = 1/3.
  quality_factor = None
  u_base = None
  b_base = None
  wing_cutoff = None
  exp_table_one_over_step_size = None
}
mask {
  use_asu_masks = True
  solvent_radius = 1.11
  shrink_truncation_radius = 0.9
  grid_step_factor = 4.0
  verbose = 1
  mean_shift_for_mask_update = 0.1
  ignore_zero_occupancy_atoms = True
  ignore_hydrogens = True
  n_radial_shells = 1
  radial_shell_width = 1.3
}
random_seed = None
output {
  format = *mtz cns
  label = FMODEL
  type = real *complex
  file_name = None
  job_title = None
}
anomalous_scatterers {
  group {
    selection = None
    f_prime = 0
    f_double_prime = 0
  }
}