[phenixbb] phenix.refine using anomalous concepts for neutron data?

Nathaniel Echols nechols at lbl.gov
Wed May 29 07:56:03 PDT 2013

On Wed, May 29, 2013 at 4:18 AM, Derek Logan
<derek.logan at biochemistry.lu.se> wrote:
> What's going on here? If I let phenix.refine decide automatically, it looks
> like it's reading in F+ and F- separately and regarding them as independent
> in the refinement. If I force "no anomalous" it merges them. However I can't
> work out whether in either case it has actually read FOBS instead of the
> Friedel mates.

Technically it's reading the merged amplitudes plus the anomalous
differences*, and reconstructing the original Friedel pairs from
these, hence "reconstructed amplitudes".  We generally recommend just
using the actual F+/F- (or I+/I-) instead of the reconstructed arrays,
but if you have the ISYM column it probably doesn't matter too much.
(And I realize that for neutron diffraction it's pointless either way,
but we try not to assume too much about what the user wants.)

(* By the way, does anyone actually understand why CCP4 programs
outputs DANO,SIGDANO as separate columns?  What programs actually use
this in preference to the Friedel pairs?)

> According to the SCALA manual the I+ and I- columns will
> always be written out even if the keyword ANOMALOUS OFF is used, so this is
> a potential pitfall for many.

I will add a warning to the GUI about this.

> In addition, phenix.refine seems to identify
> the neutron data first as xray.reconstructed_amplitude then as
> xray.amplitude even though the data are explicitly defined as neutron data
> in the GUI.

That's an implementation detail - Ralf wrote all of the code to handle
experimental observations with the assumption that it would be X-ray
data, which (at least) 99% of the time would be true.  It won't
actually make any difference to the way scattering is treated as long
as you select the neutron scattering table.  But perhaps we should add
a disclaimer to the log output...


More information about the phenixbb mailing list