[phenixbb] r_work and r_free from an .mtz file containing Fobs and Fcalc

Pavel Afonine pafonine at lbl.gov
Mon Jul 1 14:05:22 PDT 2019

Hi Andre,

no problems, please send me sample files that I can use as an example, 
and I will send you back a working script that does what you want. 
Please allow me 0-3 days to do this, depending when I get the files.


On 7/1/19 12:43, Andre LB Ambrosio wrote:
> Dear Pavel, thank you very much for this.
> Yes, that is indeed the case; mostly for educational purposes, myself 
> along with some undergraduate students are trying to perform a couple 
> of non-usual streamlined analyses on .mtz files, such as calculating 
> Unitary SF or validating r_values upon symmetry expansion.
> However, I have zero programming skills in python or any other 
> languages, hence this request.
> Therefore, it would be extremely helpful and appreciated if you could 
> write such a code for us. There is no need for the code to write any 
> output file, just calculate r_work and r_free from Fobs and Fcalc from 
> an input .mtz.
> We thank you again for your attention and time.
> Best wishes,
> Andre.
> Em seg, 1 de jul de 2019 às 15:15, Pavel Afonine <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> escreveu:
>     Hi Andre,
>     > Can Phenix calculate r_work and r_free from a .mtz file
>     containing FP
>     > and FC_ALL (from PDB_REDO), without inputing the matching .pdb file?
>     if it is still actual... No, there is no user-available tool to do
>     this
>     in Phenix, AFAIK. Simply because it isn't clear what it is useful for
>     unless you are doing some custom experimenting (and if that's the
>     case
>     you probably can do it yourself anyway!).
>     I can write a few lines of cctbx based script to do this. Literally,
>     this is under 10 lines of trivial python code. Let me know!
>     Pavel
> -- 
> Andre LB Ambrosio

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