2010/10/21 Vinson LIANG
Dear all,
Recently I deposited a structure to PDB. However, I was told
The R value of SF check are different from your reported value.
R work in SF check = 0.2859 your reported R work = 0.1474 Also there are no R free flags in your sending files, but you reported R free value in your all deposition.
However, when I tried to run the same file with refmac5, error came with "Free R label has not been set". I guess phenix.refine gives Rree-R label that other program could not recognize.
I've never heard of this happening before; I think what Phenix does is pretty standard (usually "FreeR_flag" or something similar), except that it uses 1 to mark the test set and 0 for everything else, which confuses Refmac. However, if the PDB is also getting such a different value of R-free, there may be something else wrong. It almost sounds like you kept re-refining against the unflagged reflections from data processing and re-assigned R free each time instead of using the same test set. Please send us the output of this command: phenix.mtz.dump data.mtz (replacing "data.mtz" with whatever your file is actually called.) -Nat