[phenixbb] R-merge

Nathaniel Echols nechols at lbl.gov
Wed May 29 14:44:18 PDT 2013

On Wed, May 29, 2013 at 2:37 PM, Mengbin Chen <mengbinc at sas.upenn.edu> wrote:
> I have R-merge values equal 0.000 from highest resolution shell (which
> corresponds to values larger than 1.000) in a data set processed by HKL2000,
> with redundancies higher than 10 (I know this may help in increasing
> R-merge). I am not sure if this is going to be a problem of Table 1 for the
> reviewers. Could you kindly drop me your suggestions?

Here is how to recalculate the statistics in Phenix:

1) in the "macros" tab of HKL2000, under "Scaling", type "no merge
original index"
2) re-run the scaling - you will get a new .sca file in a different
format, which contains unmerged (but scaled) intensities
3) in Phenix, run phenix.merging_statistics (under "Reflection tools"
in the GUI) with the unmerged .sca file as input

You can also input the unmerged data in the "Table 1" program in
Phenix (which just runs phenix.merging_statistics internally).


PS #1: You should probably email the HKL2000 developers in case they
don't already know about this bug.
PS #2: if you run xia2 instead, you automatically get both merged and
unmerged data!

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