[phenixbb] on Phenix's "Generate "Table 1" for journal"

Edward A. Berry BerryE at upstate.edu
Sat Mar 21 10:31:28 PDT 2015

I completely agree with Pavel Afonine's advice.
For one question that you might not find in Rupp's BMC or other textbook:

> then how can I get the R-merge, R-meas,CC1/2 and CC*?

If you have a recent version of HKL, these values are in the scalepack log-file.

If you are using an older version of HKL, then you need to re-run the scaling step with:


and then use phenix.merging_statistics to print these statistics from the unmerged .sca file
The unmerged .sca does not have cell param, so supply them like:

phenix.merging_statistics /path/to/your/unmerged.sca \
  cell="72.394    85.188   294.019    90.000    90.000    90.000" \
  n_bins=30 high_resolution=2.2

If you have refined with phenix.refine you can also calculate correlation
statistics between model and data (CC_free, CC_work) with phenix.cc_star:

phenix.cc_star /path/to/your/unmerged.sca  \
  /path/to/your/refinement/prefix_066.mtz n_bins=30

For the meaning of these statistics, see:
Acta Cryst. (2013). D69, 1215–1222
and references there-in.


On 03/21/2015 08:25 AM, Smith Liu wrote:
> Dear All,
> With the Phenix refine PDB and mtz file, I just prepared a "Table 1" for journal with Phenix. Here I find something special, which I hope I can get your advice.
> First, for the "Total reflections" and "Multiplicity", they are empty (no data given). Wil you please tell me why?
> Secondly, it writes, "Statistics for the highest-resolution shell are shown in parentheses". Suppose my crystal resolution is 2.5-45.6, then the the highest-resolution value should be 2.5, rather than 45.6, right?
> In addition, what is the diffrence between highest-resolution shell in the Table 1 and highest-resolution bin in the "Results" of Phenix refine?
> What is R-merge, R-meas,CC1/2 and CC*? I can get these data from MOSFLM output mtz file. But is my images were processe by HKL, which I have no experience, then how can I get the R-merge, R-meas,CC1/2 and CC*?
> I am looking forward to getting your reply.
> Smith
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