[phenixbb] phenix.refine with simulated annealing

[Nathaniel Echols]

On Fri, Dec 17, 2010 at 4:56 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> This is a known bug that will be fixed in a newer version. A work-around for
> you is: locate and remove these lines from PDB file header:
>
> REMARK 3 TWINNING INFORMATION.
> REMARK 3 FRACTION: NULL
> REMARK 3 OPERATOR: NULL
>
> This structure (2VZ8) was refined using phenix.refine, and, believe me or
> not, phenix.refine would not put these lines if ML refinement target was
> used (which is the case for this model). Therefore I'm puzzled about how the
> above lines ended up in this PDB file. This reminds me to repeat once again:
> any post-refinement manipulation of a PDB file with refined mode is bad.

This may be the PDB's fault.  I recently submitted seven related
structures to the PDB, and two of them came back with these same
remark lines added for no apparent reason.  (It never occurred to me
to look for this until now - PDB deposition is painful enough without
proofreading the entire REMARK section.)

-Nat