[phenixbb] R-free problem with phenix.refine

Nathaniel Echols nechols at lbl.gov
Thu Oct 21 06:49:15 PDT 2010

2010/10/21 Vinson LIANG <lwg_conrad_1983 at yahoo.com.cn>:
> 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.)


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