<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-15"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
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>
<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>