<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Maia,<br>
<br>
yes, we discussed it with Engin a few months ago, agreeing that
automatic NCS detection in phenix.refine should be enhanced by making
use of maps (for example), and automatic taking care of outliers.<br>
<br>
Pavel.<br>
<br>
<br>
On 6/26/09 2:38 PM, Maia Cherney wrote:
<blockquote cite="mid:4A453FD4.8090303@ualberta.ca" type="cite">
<pre wrap="">Hi Pavel,
Thank you for your letter. You mentioned "unless it is highly systematic
and consistent observation .."
Yes, it is highly systematic and consistent for these data. I continue
to refine this structure with both strategies (with and without ncs).
Weights optimization keeps the same difference between Rfee factors
(improves both). I liked the suggestion by Engin to keep the ncs, but
remove some offending residues from the ncs restraints. (There are such
residues that have slightly different conformations and they get moved
out of density by the ncs restraints).
Maia
Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Maia,
I would add a couple of comments too:
1)
</pre>
<blockquote type="cite">
<pre wrap="">I am wondering why the ncs refinement gives me a better Rfree (21.0%)
</pre>
</blockquote>
<pre wrap="">Because by using NCS you added some "observations", therefore you
improved the data-to-parameters ratio, which in turn reduced degree of
overfitting.
The fact that the R-factor dropped (and not increased) probably suggests
that you selected NCS groups correctly.
2)
</pre>
<blockquote type="cite">
<pre wrap="">the ncs refinement gives me a better Rfree (21.0%)
than without ncs (21.7%).
</pre>
</blockquote>
<pre wrap="">Here is another stream of thought...
The target for restrained coordinate (and similarly for B-factor)
refinement looks like this (in phenix.refine):
T_total = wxc_scale * wxc * T_xray + wc * T_geometry
where the relative target weight wxc is determined as wxc ~ ratio of
gradient's norms:
Brünger, A.T., Karplus, M. & Petsko, G.A. (1989). Acta Cryst. A45,
50-61. "Crystallographic refinement by simulated annealing: application
to crambin"
Brünger, A.T. (1992). Nature (London), 355, 472-474. "The free R value:
a novel statistical quantity for assessing the accuracy of crystal
structures"
Adams, P.D., Pannu, N.S., Read, R.J. & Brünger, A.T. (1997). Proc. Natl.
Acad. Sci. 94, 5018-5023. "Cross-validated maximum likelihood enhances
crystallographic simulated annealing refinement"
Before wxc scale is computed, the structure is subject of a short
molecular dynamics run - this is where the random component comes into
play.
Now, having said this, we know that if you run, for example, 100
identical phenix.refine runs, where the only difference between each run
is the random seed, you will get 100 slightly different refinement
results. The spread in R-factors depends on resolution, and if I
remember correctly, for a structure at ~2A resolution I was getting
delta_R~ from 0.1 to 2%. It can be higher at lower resolution, and
smaller at higher resolution.
The NCS term goes into T_geometry, which in turn means that it changes
(somehow) the weight. This may explain the difference in R-factors and,
I would say, the one less then 1% I would consider insignificant (unless
it is highly systematic and consistent observation, and unless it is not
made weight independent).
To make it less arbitrary I would suggest to run two refinement jobs
using "optimize_wxc=true optimize_wxu=true", one with NCS and the other
one without using NCS. I'm sure I suggested this a month or two ago.
Pavel.
_______________________________________________
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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<pre wrap=""><!---->
_______________________________________________
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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
</body>
</html>