I have  run into something that has me a bit puzzled.  When finishing up a structure we ended reprocessing the data to get nice statistics for deposition, I don’t want to get into that discussion.  Upon reprocessing the unit cell dimensions shifted slightly, 0.05 A or so.  The PDB file used had the unit cell from the original solution/refinement while the data set cell dimensions were different.  I ran the newly processed reflection data set through the reflection editor in order to transfer the Rfree set.  Now the really odd thing is that I ended up reprocessing a couple times and transferring over the Rfree set once more.  The cell dimensions on the final reflection file is from not the original reflection file/PDB but one that was used with an intermediate cutoff between the two, it is not the cell dimensions in the input reflection either.  Just for completeness the data were processed using XDS at SSRL.

My question is where does phenix.refine pick up the unit cell dimensions and were does the reflection file editor pick them up?

Best Regards

Len