[phenixbb] phenix and weak data

Ed Pozharski epozh001 at umaryland.edu
Mon Dec 10 14:16:14 PST 2012


You are answering a different question, and the one I did not ask.  So
let me try again.

If you compare equation (4) in Lunin et al.(2002) (or equation (14) in
Lunin&Skovoroda,(1995)) and equation (14) in Murshudov et al.(1997) (or
equation(1) in Cowtan,(2005)), you will see that the beta replaces the
combination of the model error and experimental error.  An assumption
that beta is identical for every reflection in a given resolution shell
is absolutely necessary for the minimization with respect to alpha/beta
as outlined in appendix A of Lunin&Skovoroda.  Derivation of the
analytical expression breaks down if you introduce experimental errors
for individual reflections.

So as far as I am concerned, it appears that experimental errors are
simply neglected.  There must be a justification for this. It was my
understanding that this is based on the assumption that the model errors
overwhelm experimental errors, which is supposedly confirmed by showing
that sqrt(beta)>>sigf (which is a different story with its own

So, here is my point.

ML formalism as implemented in phenix does not "lump" experimental
errors into some combined value.  It simply ignores them because it
assumes that they are much smaller than model errors.  It is an
important distinction.



On Mon, 2012-12-10 at 13:08 -0800, Pavel Afonine wrote:
> Hi Ed,
> >>> I had always assumed that experimental sigmas were somehow lumped
> >> into the alpha and beta parameters (esp. given your discussion in
> >> section 2.3).  In principle they could be, right?
> >>
> >> Yes, they could be.
> > I would like clarification on this.  (...)
> >
> > Alpha/beta are calculated in individual resolution shells.  How can you
> > "lump" experimental variance that varies by two orders of magnitude for
> > individual reflections into a single parameter?
> I'm sorry for being unclear (often email happens to be a poor way to 
> express what you actually mean, unless you have heaps of time to write 
> it lawyer style. There is always a room for reader to imagine unsaid. 
> Sometimes it works, sometimes it doesn't.).
> Anyways, extending my phrase above to better reflect what I actually 
> meant: "Yes, they could be, to some extent (approximation). Surely, a 
> proper way is to have sigmas in the formula explicitly, as I stated in 
> previous email of that thread. Whether that makes any practically useful 
> difference is debatable, and yet to answer."
> > I also wonder if introducing experimental uncertainty into Lunin's ML
> > target is even possible without fundamentally altering it.
> It is possible, and depends how fundamentally you want to alter it.
> All the best,
> Pavel
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Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

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