[phenixbb] Refining anomalous groups
pafonine at lbl.gov
Sat Jan 12 10:13:48 PST 2013
> There's probably no reason why it needs to be this hidden - it seems
> very safe so far, but until we've had more chances to test it we
> prefer to minimize the number of features that can potentially break.
My understanding is that this option will select all atoms that are
heavier than some defined value, and then it will refine f' and f'' for
them. This may mean that you will be refining f' and f'' for atoms that
were not anomalously scattering; that is you will be refining parameters
that do not need to be refined. While this may be harmless (though
someone needs to prove it) I believe it is suboptimal: 1) runtime wise,
and 2) unnecessary refined parameters may mop up other model errors.
Analogy could be: refining occupancy of fully occupied atoms.
>> Will be the event of refinement of anomalous dispersion parameters f' and f"
>> recorded in PDB file?
> I am not sure whether phenix.refine includes anything in the headers -
It does output it like this:
REMARK 3 ANOMALOUS SCATTERER GROUPS DETAILS.
REMARK 3 NUMBER OF ANOMALOUS SCATTERER GROUPS : 2
REMARK 3 ANOMALOUS SCATTERER GROUP : 1
REMARK 3 SELECTION: name BR
REMARK 3 fp : -0.8792
REMARK 3 fdp : 5.8029
REMARK 3 ANOMALOUS SCATTERER GROUP : 2
REMARK 3 SELECTION: name CO
REMARK 3 fp : 0.0000
REMARK 3 fdp : 0.0000
but does not read.
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