[phenixbb] refining with f' and f" values

Nathaniel Echols nechols at lbl.gov
Thu Nov 1 09:49:27 PDT 2012

On Thu, Nov 1, 2012 at 8:43 AM, Subhani Bandara <ramssb17 at gmail.com> wrote:
> Then I merged only Intensity+-, sigma+- from reflection file ( as
> amplitudes) with Rfree flags of mtz file and used it with ML as target
> function. Then refinement started  with high Rfree value (41% compared to
> 16% for current model)  and ended up with 48% Rfree. But when I checked the
> map, occupancies of metals at general positions are matching with that of
> ligands.
> Am I merging the correct data arrays? Are there anymore suggestions for
> this.

After inspection of the file containing anomalous data*, it's obvious
that these are still the intensities, only mislabeled as amplitudes.
When you're converting the intensities, you need to change the option
"Output diffraction data as", and not "Force observation type" - the
first one actually does the numerical conversion to get amplitudes,
the second leaves the values alone but changes the data type in the
MTZ file.  Which I guess is what happened in your case.  Actually
running the conversion results in a dataset that reproduces your
R-factors and has huge anomalous difference map peaks for the metals;
I will send you this file separately.


(* For the record: under "Reflection tools" there is a program called
"Compare datasets", which will visualize pseudo-precession planes
through reciprocal space for a pair of datasets, showing only those
reflections in common.  This makes it very easy to spot when something
is wrong - the attached images show the difference between actual
amplitudes [1], and intensities mislabeled as amplitudes [2].)
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