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Hi Nat,<br>
<br>
it is all published. Below are the papers that I used in phenix.refine
to code maximum-likelihood target, phase and coordinate errors
estimates. The complete list of relevant papers will include those by
Randy Read, G. Bricogne, and others.<br>
<br>
Alpha/Beta and phase error estimation algorithms, ML target formula:<br>
V.Yu., Lunin & T.P., Skovoroda. Acta Cryst. (1995). A51, 880-887.
"R-free likelihood-based estimates of errors for phases calculated from
atomic models"<br>
<br>
Formula for coordinate error estimation:<br>
V.Y., Lunin, P.V. Afonine & A.G., Urzhumtsev. Acta Cryst. (2002).
A58, 270-282. "Likelihood-based refinement. I. Irremovable model errors"<br>
<br>
P. Afonine, V.Y. Lunin & A. Urzhumtsev. J. Appl. Cryst. (2003). 36,
158-159. "MLMF: least-squares approximation of likelihood-based
refinement criteria"<br>
<br>
Paper suggesting to use TEST reflections in Alpha/Beta estimation:<br>
A.G. Urzhumtsev, T.P. Skovoroda & V.Y. Lunin. J. Appl. Cryst.
(1996). 29, 741-744. "A procedure compatible with X-PLOR for the
calculation of electron-density maps weighted using an
R-free-likelihood approach"<br>
<br>
<blockquote cite="mid:E934E9EB-5FBE-4A3A-A5A6-812B48592FA4@lbl.gov"
type="cite">
<pre wrap="">they will influence the
final phases calculated in phenix.refine, but those will still be
biased towards the refined model.
</pre>
</blockquote>
<br>
No, because the estimates are done using TEST reflections that are not
supoosed to be used in any step of structure solution and refinement.<br>
<br>
Pavel.<br>
<br>
<br>
On 6/11/09 10:20 AM, Nathaniel Echols wrote:
<blockquote cite="mid:E934E9EB-5FBE-4A3A-A5A6-812B48592FA4@lbl.gov"
type="cite">
<pre wrap="">On Jun 10, 2009, at 9:18 PM, Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">you can get it using phenix.refine. Just type from the command line:
phenix.refine model.pdb data.mtz strategy=none
main.number_of_macro_cycles=1
and hit Enter. Look for the numbers towards the end of log file or
output to the screen (after bulk solvent correction and scaling is
reported done).
</pre>
</blockquote>
<pre wrap=""><!---->
I've never been able to understand the math involved, but isn't the
phase error calculated by phenix.refine is based on the estimates of
model error (and incompleteness) used for maximum likelihood
calculations, not an evaluation of the original experimental phases?
If experimental phase restraints were used (which is the default for
phenix.refine, and I assume AutoBuild too), they will influence the
final phases calculated in phenix.refine, but those will still be
biased towards the refined model.
-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
<a class="moz-txt-link-abbreviated" href="mailto:NEchols@lbl.gov">NEchols@lbl.gov</a>
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</pre>
</blockquote>
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