[phenixbb] phenix.fmodel: a command line tool to compute structure factors from a model (Fcalc or Fmodel).

[Pavel Afonine]

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
   }
 }