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
Usage examples:
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.
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 1.520.0A.
phenix.fmodel model.pdb high_resolution=1.5 algorithm=direct
is similar to "1)" but the Fcalc are computed using direct summation algorithm.
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 freeR
flags with 10% of test reflections. This is a typical command to simulate Fobs.
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.
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 }.
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.
phenix.fmodel model.pdb reflection_data.mtz data_column_label="FOBS,SIGMA"
similar to "7)", where the specific data array is selected.
See below for complete list of available parameters.
Parameters to compute Fmodel:
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
}
}
