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: NO MERGE ORIGINAL INDEX 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 doi:10.1107/S0907444913001121 and references there-in. eab 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]