[phenixbb] refinement / alpha_beta
Frank von Delft
frank.vondelft at sgc.ox.ac.uk
Tue Oct 5 22:21:00 PDT 2010
I believe incomplete models is one thing the Buster developers claim
their program is good at.
(Sorry, not a phenix answer.)
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.
> 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
>> 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,
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
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