I was under the impression that the differences arise due to XDS uses <font face="courier new, monospace" size="1">SIGNAL/NOISE >= -3.0</font> as the cutoff, thus allowing some negative reflections, while phenix use a strict cutoff of 0? Note, that the completeness in the high res. shell is lower in phenix than XDS (90.6 vs 99.7), a behavior I have seem several times solving different structures. XDS will show high completeness at high res. and then in phenix.refine it always drops.<br>
<br>Am I wrong thinking this?<br><br>Thanks for any insights!<br>-Bj�rn<br>-- <br>Bj�rn Panyella Pedersen<br>Macromolecular Structure Group<br>University of California, San Francisco<br><br><br><div class="gmail_quote">On Fri, Oct 19, 2012 at 8:15 AM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@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 class="im">On Fri, Oct 19, 2012 at 8:07 AM, Kay Diederichs<br>
<<a href="mailto:Kay.Diederichs@uni-konstanz.de">Kay.Diederichs@uni-konstanz.de</a>> wrote:<br>
> I just want to point out that one possible source of discrepancy between<br>
> I/sigma reported by a data processing program, and I/sigma reported by a<br>
> program that uses the relevant cctbx routine is the following: that cctbx<br>
> routine calculates the variance of merged data as max("internal variance",<br>
> "external variance") which is different from what the data processing<br>
> programs do (they calculate the "internal variance" - I hope I didn't get it<br>
> the wrong way round). SHELXC and SHELXL also calculate the variance of the<br>
> merged data like the data processing programs do.<br>
<br>
</div>Good point. �However, this particular CCTBX routine is only used when<br>
merging non-unique data, which would not be the typical input here (at<br>
least in the official release).<br>
<div class="im"><br>
> I dislike this "feature" of cctbx but I do not know if phenix.table_one<br>
> actually uses this routine for this purpose.<br>
<br>
</div>It does. �But I may change this, if I can be certain it won't screw<br>
things up for the small molecule folks. �I'm just not sure why it was<br>
written that way in the first place...<br>
<div class="HOEnZb"><div class="h5"><br>
-Nat<br>
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