[phenixbb] differences in refinement stats between phenix-dev-2219 and -1.9-1692

Ezequiel Noguera back_noguera at yahoo.com.ar
Tue Dec 15 16:17:08 PST 2015

Hi Pavel,I made a mistake with the output from phenix.reduce, now it works well. In my first attempt, the output from phenix.reduce was a file whose only content was: "USER  MOD reduce.3.24.130724 H: found=0, std=0, add=0, rem=0, adj=0". It was solved when I renamed the input pdb. I took erroneously the first file as an input for phenix.refine and it produced an error (obviously). Now I repeated the refinement following exactly your instructions. I got the same results (as expected). 
 version: dev-2247
  Final: r_work = 0.1755 r_free = 0.2044 bonds = 0.030 angles = 0.598
  version: 1.9-1692
 Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321

    El Martes, 15 de diciembre, 2015 22:07:15, Pavel Afonine <pafonine at lbl.gov> escribió:

  Hi Ezequiel
        phenix.reduce doesn't work well in my hands. I used "automatically add H's" in the phenix GUI instead.         
 "automatically add H's" in the phenix GUI uses phenix.reduce to add H. The machinery that actually add H is exactly the same.
       PS: phenix.reduce reads my file, but it output a pdb file with the added H's with "0" in the second column (and "new" in the last  column)
 Does this create any problem?

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