[phenixbb] How to extend R-free set to higher resolution by new phenix-1.5.2

Nathaniel Echols NEchols at lbl.gov
Sat Dec 12 07:58:36 PST 2009

On Dec 12, 2009, at 3:36 PM, Thomas C. Terwilliger wrote:
> I think reflection_file_editor will only copy arrays (or columns) of data,
> and not merge several columns of data into one.


Assuming you just want to combine the new data and old test set, based on what Tom said, you will need the old data file with R-free flags, and either the Scalepack file (if you want to keep your intensities, and/or you have anomalous data) or exptl_fobs_phases_freeR_flags.mtz (if you're happy with non-anomalous amplitudes).  The output arrays should be the R-free and the new amplitudes or intensities*, which will probably be labeled 'F,SIGF' or 'i_obs,sigma' or something similar.  Everything else should work automatically - the extend R-free option is on by default.  If the program gives you an error, please email me (not the list!) the files and I'll see if I can figure out what is breaking.  It might be worth trying the latest nightly build too (currently dev-249), because there have been many improvements and new features in that program.


(* Plus Hendrickson-Lattman coefficients from experimental phasing, if you have them.)

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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