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! Pavel 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