[phenixbb] r-free flag cell constant mismatch

Pavel Afonine pafonine at lbl.gov
Wed Jun 1 11:23:54 PDT 2016

Hi Wolfram,

you can take Fobs from A and R-free-flags from B and write them into MTZ 
file and use that file for refinement. To make sure you can actually to 
it I repeated all steps myself.

A: m1.pdb, m1.mtz

B: m2.pdb, m2.mtz (different unit cell parameters, different free-R 
flags, different resolution)

Load both MTZ files into Phenix -> Reflection tools -> Reflection file 
editor .

Then copy Fobs from m1.mtz and R-free-flags from m2.mtz from All input 
arrays to Output arrays.

Then, Output options check "Disable unit cell isomorphism check", then 
hit "Run".

This will create MTZ file ready for refinement.

Let me know if you have questions or problems!


On 6/1/16 05:53, wtempel wrote:
> Dear Phenix experts,
> our project involves crystals *A* and *B*, which are nearly 
> isomorphous and of a protein’s complexes with two different small 
> molecules, respectively. *A* diffracts better than *B*.
> The r-free flag from *A* was “attached” to *B*‘s input reflections 
> with the CCP4 |cad| command and is still associated to *B*‘s slightly 
> different cell dimensions. Would/should this be reason enough for 
> |refine| to throw an error? The error message suggests changing the 
> |refinement.input.symmetry_safety_check| setting. Can this setting be 
> changed in the GUI?
> Thank you.
> Wolfram Tempel

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