[phenixbb] refinement / alpha_beta
Kay Diederichs
kay.diederichs at uni-konstanz.de
Tue Oct 5 11:30:30 PDT 2010
Dear Phenix developers,
I'd like to refine (using phenix.refine) a _very_ incomplete model
(obtained by molecular replacement with one subunit of the complete
structure) against the native amplitudes, with the goal to obtain
meaningful phases and figures_of_merit which should serve to find heavy
atom sites in derivative datasets.
If I "just refine" in phenix.refine, then the R-factors are in the 50s
and the program estimates the coordinate error to be very large. Thus I
would like to tell phenix.refine that the coordinates are actually quite
accurate, but that a lot of the model is simply missing.
I found
alpha_beta
free_reflections_per_bin= 140
number_of_macromolecule_atoms_absent= 225
n_atoms_included= 0
bf_atoms_absent= 15.0
final_error= 0.0
absent_atom_type= "O"
method= *est calc
estimation_algorithm= *analytical iterative
verbose= -1
interpolation= True
fix_scale_for_calc_option= None
number_of_waters_absent= 613
sigmaa_estimator
kernel_width_free_reflections= 100
kernel_on_chebyshev_nodes= True
number_of_sampling_points= 20
number_of_chebyshev_terms= 10
use_sampling_sum_weights= True
in the documentation but I have trouble understanding its meanings and
defaults - but I do think this should be used. Maybe I should switch to
method=calc and specify number_of_macromolecule_atoms_absent= as well as
bf_atoms_absent= ?
Can anyone advise me, please?
thank you,
Kay
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