[phenixbb] refinement / alpha_beta

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Tue Oct 5 22:21:00 PDT 2010


  Hi Kay

I believe incomplete models is one thing the Buster developers claim 
their program is good at.

(Sorry, not a phenix answer.)
phx





On 06/10/2010 06:08, Pavel Afonine wrote:
> Hi Kay,
>
> the coordinate error is estimated from alpha/beta parameters, and 
> alpha/beta parameters are estimated using test set of Fobs and Fcalc 
> computed from your current model. So, if your model is poor (severely 
> incomplete) then it obviously gets reflected on Fcalc and you get what 
> you get.
>
> I guess a way around would be to use an a priori knowledge about the 
> missing structure (amount and location) and incorporate it into alpha 
> and beta but this is not implemented.
>
> I played with computing (as opposed to estimation) of alpha and beta 
> (the parameters you refer to below) but it never worked good in my 
> hands, although may be I didn't try hard.
>
> I guess it is a nice project to spend a few weeks/a moths on but there 
> is no quick solution right now, sorry.
>
> Pavel.
>
>
> On 10/5/10 11:30 AM, Kay Diederichs wrote:
>> 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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>
>
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