We recently had this problem in our lab.
No matter what we tried, we could not get convert2mtz (or any other program) to
work properly. We were probably doing something wrong with the fortran....?
Depending on how far along you are, you can try using phenix.refine. Just
input your model and the .cv file and phenix will export a new .cv file with
Free-R flags intact.
One more options:
"Reflection file editor" from PHENIX GUI can convert most of any known
reflection data formats into MTZ. You will also have options to rename
labels, create r-free-flags, combine multiple input files (in different
formats) into one MTZ, and more.
Pavel.
