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Hi Gregers,<br>
<br>
this is confusing I agree, thanks for pointing this out!<br>
<br>
phenix.maps applies a correction to bulk-solvent mask to not fill
bulk-solvent into internal "bulk-solvent free" voids in protein; it
reports R-factors after this correction is done. Other tools also do
this correction for the purpose of map calculation but they do not
report corresponding R-factors (after such correction).<br>
<br>
I will review this to make reported output clearer.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 7/31/14, 12:08 AM, Gregers Rom
Andersen wrote:<br>
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<p class="MsoNormal">Dear bb<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have encountered a quite significant
difference between Rfree reported by phenix.maps, refine and
reciprocal_space_arrays. I have used default values in the
GUI, and don’t find differences in reflections statistics
reported in the phenix.maps log that could explain the
difference. I have another example also, but with a smaller
difference between phenix.maps and phenix.refine. Both are
quite large structures with maximum resolution between 3.5 and
4. Any explanation?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">phenix.maps<o:p></o:p></p>
<p class="MsoNormal">-------------------------------------------------------------------------------<o:p></o:p></p>
<p class="MsoNormal">Bulk solvent correction and anisotropic
scaling:<o:p></o:p></p>
<p class="MsoNormal">|--(resolution: 3.68 - 29.45 A,
n_refl.=22769 (all), 10.16 % free)------------|<o:p></o:p></p>
<p class="MsoNormal">|
|<o:p></o:p></p>
<p class="MsoNormal">| r_work= 0.2550 r_free= 0.2823 coordinate
error (max.-lik. estimate): 0.60 A |<o:p></o:p></p>
<p class="MsoNormal">|
|<o:p></o:p></p>
<p class="MsoNormal">| x-ray target function (ml) for work
reflections: 6.433959 |<o:p></o:p></p>
<p class="MsoNormal">|-----------------------------------------------------------------------------|<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">phenix.reciprocal_space_arrays<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">|--(resolution: 3.68 - 29.45 A,
n_refl.=22769 (all), 10.16 % free)------------|<o:p></o:p></p>
<p class="MsoNormal">|
|<o:p></o:p></p>
<p class="MsoNormal">| r_work= 0.2741 r_free= 0.3045 coordinate
error (max.-lik. estimate): 0.69 A |<o:p></o:p></p>
<p class="MsoNormal">|
|<o:p></o:p></p>
<p class="MsoNormal">| x-ray target function (ml) for work
reflections: 6.492710 |<o:p></o:p></p>
<p class="MsoNormal">|-----------------------------------------------------------------------------|<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">phenix.refine, strategy=none 1 macrocycle<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">|--(resolution: 3.68 - 29.45 A,
n_refl.=22769 (all), 10.16 % free)------------|<o:p></o:p></p>
<p class="MsoNormal">|
|<o:p></o:p></p>
<p class="MsoNormal">| r_work= 0.2741 r_free= 0.3045 coordinate
error (max.-lik. estimate): 0.69 A |<o:p></o:p></p>
<p class="MsoNormal">|
|<o:p></o:p></p>
<p class="MsoNormal">| x-ray target function (ml) for work
reflections: 6.492702 |<o:p></o:p></p>
<p class="MsoNormal">|-----------------------------------------------------------------------------|<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">gregers<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Professor Gregers Rom Andersen<o:p></o:p></p>
<p class="MsoNormal">Department of Molecular Biology and
Genetics<o:p></o:p></p>
<p class="MsoNormal">Aarhus University<o:p></o:p></p>
<p class="MsoNormal">Gustav Wiedsvej 10C DK8000 Aarhus C<o:p></o:p></p>
<p class="MsoNormal">phone +45 871 55507 fax +45 861 23178<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">email <a class="moz-txt-link-abbreviated" href="mailto:gra@mb.au.dk">gra@mb.au.dk</a><o:p></o:p></p>
<p class="MsoNormal"><o:p></o:p><br>
</p>
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