[phenixbb] Experimental Data Question

Nathaniel Echols nechols at lbl.gov
Sat Jul 16 09:23:23 PDT 2011

On Sat, Jul 16, 2011 at 9:00 AM, Yuri <yuri.pompeu at ufl.edu> wrote:
> It looks like phase_and_build only takes reflections input as F SIGF. I had
> to use a reflection converter as I had a .sca file with I SIGI data.

Okay, this probably means that the reflection file converter added new
R-free flags - or if not, phase_and_build certainly would have.  As a
result, you've run a refinement with one set of flags, then rebuilding
(which includes more refinement) with another set of flags.  I'd
recommend starting back with phase_and_build again, using the model
from the first refinement, but this time with the "_data.mtz" file
that came with it for your reflections.  Then use those reflections
with all subsequent refinements.

(This isn't always necessary - if your refinement still has a way to
go, one round with simulated annealing can help de-bias R-free - but
it's the most conservative approach.  If you decide to continue with
the existing model, however, use the R-free flags that phase_and_build
used - either reflections.mtz if it has them, or exptl_fobs...mtz
[making sure *not* to use the "experimental" phases it contains].)


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