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

Pei-Chun Lin pclin at hotmail.com
Mon Dec 14 07:15:17 PST 2009

Hi, Tom and Nat

After reading your replies, I found out that I misunderstand some precesses. Your answers make it much clear.


> From: NEchols at lbl.gov
> Date: Sat, 12 Dec 2009 15:58:36 +0000
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] How to extend R-free set to higher resolution by new	phenix-1.5.2
> 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.
> Correct.
> 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.
> -Nat
> (* Plus Hendrickson-Lattman coefficients from experimental phasing, if you have them.)
> --------------------
> Nathaniel Echols
> Lawrence Berkeley Lab
> 510-486-5136
> NEchols at lbl.gov
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