[phenixbb] phenix.fmodel: a command line tool to compute structure factors from a model (Fcalc or Fmodel).
Pavel Afonine
PAfonine at lbl.gov
Wed Jan 27 12:36:51 PST 2010
Starting PHENIX nightly build version 1.6-295 (2010-01-27), a new
command line tool
phenix.fmodel
is available. This is a replacement for "phenix.pdbtools --f-model"
command, which is not available anymore.
phenix.fmodel is a comprehensive tool to compute structure factors from
a model. For more information and usage examples simply run phenix.fmodel .
Pavel.
P.S. Below is the result of running phenix.fmodel:
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:
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.
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
scattering_table = wk1995 it1992 *n_gaussian neutron
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
}
output {
format = *mtz cns
label = FMODEL
type = real *complex
file_name = None
}
anomalous_scatterers {
group {
selection = None
f_prime = 0
f_double_prime = 0
}
}
More information about the phenixbb
mailing list