<div dir="ltr"><div>Thanks to all, and especially Nat for finding out the cause (different formula for R-factor calculation in sftools and phenix)!<br></div>All the best, Simon<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 13, 2014 at 5:16 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Interesting.. I use this formula to calculate R-factor between two
data sets when I cannot choose which one to call "Fobs" and which
one to call "Fcalc". But clearly, this is not exact what we call
R-factor.<br>
<br>
Pavel<br>
<br>
<div>On 10/13/14 2:02 PM, Nathaniel Echols
wrote:<br>
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<blockquote type="cite">
<div dir="ltr">On Mon, Oct 13, 2014 at 11:54 AM, Nathaniel Echols
<span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span>
wrote:<br>
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote"><span>
<div>In the default phenix.refine output MTZ, the
"F-obs" column will not be scaled to F-model.
My guess is that your input data have already
been placed on an absolute scale based on the
Wilson statistics, so the results are reasonably
close, but when I tried using the same commands
on an XFEL dataset I got an R-factor of 192.</div>
</span></div>
</div>
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<div><br>
</div>
<div>Okay, this statement is at least partially incorrect -
your data are clearly on the correct scale in the
phenix.refine output file, but the data in the file I used
are not. (I'm going to blame this on the weirdness of
certain XFEL data.)</div>
<div><br>
</div>
<div>However, I did eventually figure out the problem:
SFTOOLS is using a different formula for the R-factor. If
you give it the command "correl help", it will include
this:</div>
<div><br>
</div>
<div>
<div> RFACT Rfactor in percent</div>
<div> ( 200*Sum|col1-col2|/sum(col1+col2) )</div>
</div>
<div><br>
</div>
<div>Which disagrees with our source code, and the Rupp
textbook, and Kay's wiki, and Wikipedia, all of which use
sum(col1) as the denominator (assuming col1 == F-obs, but
in our code it's written more generally). In other words:
the R-factors from SFTOOLS cannot be meaningfully compared
to the R-factors from refinement.</div>
<div><br>
</div>
<div>-Nat</div>
</div>
</div>
</div>
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