[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
       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
          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,


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