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Just to understand, what is your necessity for changing the CNS reflection file back to MTZ each time?
I didn't explain this very well. I have three problems: cells are not always isomorphous, reflections are not always scalable between datasets, and resolution limits are different. I need to preserve the FreeRflag from one file, but also extend it where necessary and *not* change the unit cell, change the resolution, or add reflections. I couldn't figure out a way to do this through ccp4i, so I did it directly through text files (although CNS now appears to have been the least appropriate format for this).
I didn't realize mtzutils could combine columns as well (only used it to change spacegroup before), so I'll try that instead. However, I suspect that CAD would do what I need if I used it from the command line instead of ccp4i - I probably should have tried that first.
Anyway, I managed to get something working without mixing up test and working sets - I just wasn't sure how f2mtz works. Sorry for the confusion.
