[phenixbb] differences in refinement stats between phenix-dev-2219 and -1.9-1692
pafonine at lbl.gov
Tue Dec 15 17:06:39 PST 2015
Could you please send me the entire set of inputs and outputs for this
refinement run (using dev-2247)? Please send files off-list.
On 12/15/15 16:17, Ezequiel Noguera wrote:
> 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
> 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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