[phenixbb] How should we estimate the "uncertainty" of the occupancy of an atom?

Peter Zwart PHZwart at lbl.gov
Wed Feb 11 20:08:51 PST 2015

Dear All,

How meaningful are the second derivative based estimates obtained via full
matrix inversion when the gradient is not 0 (i.e. when not in the minimum)?
I can understand that when you are working with high-resolution data and
your R-value is close to 0, things could work, but what happens when around
a more challenging 2A?

If you are interested in the uncertainty of the occupancy, I recommend not
doing any refinement, but just generate a list of occupancies and B-values
for the atom of interest and compute the (free) likelihood for each model.
Subsequent normalisation of the neg-exponent of these values, should
provide you with an answer that could be just as believable as any other
method around.  A little bit of python scripting should do the trick quite

Both the full matrix inversion and the suggestion above probe the steepness
of the data-agreement hole the structure is sitting in. Pavels suggestion
explores the spread of local minima around the starting configuration. I am
not sure what method is more appropriate, perhaps it is instructive to know
what problem you are trying to solve.


On 11 February 2015 at 16:13, Masaki UNNO <unno19 at mx.ibaraki.ac.jp> wrote:

> Dear all
> Thank you very much for your suggestions.
> I will try making a number of models in which the atom has different
> occupancies (e.g. 0.1-1.0). Then, I will refine them by restraining the
> B-factors.
> Actually, our structure contains some reaction intermediates not only the
> substrate. So I would like to estimate the ratio.
> Best regards
> Masaki
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
> Sent: Thursday, February 12, 2015 6:36 AM
> To: Dale Tronrud; phenixbb at phenix-online.org
> Subject: Re: [phenixbb] How should we estimate the "uncertainty" of the
> occupancy of an atom?
> Hi Dale,
> > P.S. I'll look up the paper you reference but my university does not
> > subscribe to acta Cryst and getting those papers takes time.
> it is open access:
> http://phenix-online.org/papers/wd5073_reprint.pdf
> All the best,
> Pavel
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P.H. Zwart
Staff Scientist
Berkeley Center for Structural Biology, Science lead
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
SASTBX:  http://sastbx.als.lbl.gov
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
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