On Wed, Aug 8, 2012 at 11:19 AM, Pavel Afonine
<Fobs> or "F/SigF and DF/SigDF" are derived from Fobs(+) and Fobs(-) with some information lost. That is you cannot restore the original Fobs(+) and Fobs(-) from <Fobs> or from "F/SigF and DF/SigDF". phenix.refine restores Fobs(+) and Fobs(-) from "F/SigF and DF/SigDF" for internal use making an arbitrary decision about the sign. phenix.refine cannot handle "F/SigF and DF/SigDF" and has no reason to do this.
Does XDS (or xdsconv) not include the ISYM column? In some files, we get a combination of columns like this: F SIGF DANO SIGDANO ISYM which is the same thing, but the ISYM column indicates how the DANO is applied to the Friedel mates, meaning that we can reconstruct the original F+ and F-. There's nothing wrong with using these data in Phenix - without ISYM, however, the DANO is useless. -Nat