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 1.5-20.0A.

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 free-R
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.

phenix.fmodel model.pdb reflection_data.mtz twin_law="l,-k,h" twin_fraction=0.3
generates twin data set (real type) with given twin law and fraction.