Re: [phenixbb] Table 1 stastics

= -3.0 as the cutoff, thus allowing some negative reflections, while

I was under the impression that the differences arise due to XDS uses SIGNAL/NOISE 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. Am I wrong thinking this? Thanks for any insights! -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group University of California, San Francisco On Fri, Oct 19, 2012 at 8:15 AM, Nathaniel Echols wrote:

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I just want to point out that one possible source of discrepancy between I/sigma reported by a data processing program, and I/sigma reported by a program that uses the relevant cctbx routine is the following: that cctbx routine calculates the variance of merged data as max("internal variance", "external variance") which is different from what the data processing programs do (they calculate the "internal variance" - I hope I didn't get it the wrong way round). SHELXC and SHELXL also calculate the variance of

On Fri, Oct 19, 2012 at 8:07 AM, Kay Diederichs wrote: the

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merged data like the data processing programs do.

Good point. However, this particular CCTBX routine is only used when merging non-unique data, which would not be the typical input here (at least in the official release).

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I dislike this "feature" of cctbx but I do not know if phenix.table_one actually uses this routine for this purpose.

It does. But I may change this, if I can be certain it won't screw things up for the small molecule folks. I'm just not sure why it was written that way in the first place...

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb