[ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ]
if i provide the test set .mtz (flag = "1") in refinement separately from the data .mtz, it looks like reflection_file_converter.py does not flag the work set as "0", if the work set lacks such a flag -- is that right?
I think that's true. Nat wrote a more comprehensive tool for generating R-free flags, which are included in recent nightly builds. I'm pretty sure Nat generates the flags for all possible reflections.
i.e. when providing the test set, it looks like all observed data must be in the test set, however the work set has flag "0".
Hm... not sure I understand, but try Nat's new tools first. It is easiest through the GUI, but there's also a command-line version, phenix.reflection_file_editor. Ralf