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Hi Kay<br>
<br>
I believe incomplete models is one thing the Buster developers claim
their program is good at. <br>
<br>
(Sorry, not a phenix answer.)<br>
phx<br>
<br>
<br>
<br>
<br>
<br>
On 06/10/2010 06:08, Pavel Afonine wrote:
<blockquote cite="mid:4CAC0441.3090307@lbl.gov" type="cite">
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Hi Kay,<br>
<br>
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.<br>
<br>
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.<br>
<br>
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. <br>
<br>
I guess it is a nice project to spend a few weeks/a moths on but
there is no quick solution right now, sorry.<br>
<br>
Pavel.<br>
<br>
<br>
On 10/5/10 11:30 AM, Kay Diederichs wrote:
<blockquote cite="mid:4CAB6EC6.7000606@uni-konstanz.de"
type="cite">Dear Phenix developers, <br>
<br>
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. <br>
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. <br>
I found <br>
�� alpha_beta <br>
����� free_reflections_per_bin= 140 <br>
����� number_of_macromolecule_atoms_absent= 225 <br>
����� n_atoms_included= 0 <br>
����� bf_atoms_absent= 15.0 <br>
����� final_error= 0.0 <br>
����� absent_atom_type= "O" <br>
����� method= *est calc <br>
����� estimation_algorithm= *analytical iterative <br>
����� verbose= -1 <br>
����� interpolation= True <br>
����� fix_scale_for_calc_option= None <br>
����� number_of_waters_absent= 613 <br>
����� sigmaa_estimator <br>
�������� kernel_width_free_reflections= 100 <br>
�������� kernel_on_chebyshev_nodes= True <br>
�������� number_of_sampling_points= 20 <br>
�������� number_of_chebyshev_terms= 10 <br>
�������� use_sampling_sum_weights= True <br>
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= ? <br>
<br>
Can anyone advise me, please? <br>
<br>
thank you, <br>
<br>
Kay <br>
<br>
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