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

Dale Tronrud detBB at daletronrud.com
Thu Feb 12 12:36:56 PST 2015

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On 2/11/2015 1:35 PM, Pavel Afonine wrote:
> 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

   Thanks.  I recall this paper.  It is just an example of what you
have been describing, repeated refinements, and what I have been
(slightly) criticizing.

   Repeated refinements are very useful in probing the confidence that
you can place in the details of a model, if you can't perform a proper
error analysis.  This tool's main usefulness is to inform you about
the aspects of your model which are not nailed down by your data and
restraints.  Basically it gives you a set of models which your target
function cannot distinguish between. It does not tell you how fast the
target function rises when you move away from the minimum, but does
tell you when the parameters can change without changing the value of
the target function.  i.e. it tells you where the second derivative is

   This is very useful information because you shouldn't be paying
much attention to a side chain that forms a bush in the repeated
refinements but should pay attention to a side chain that always comes
up with the same conformation.  The degree of clustering of that
single conformer is not equal to the SU of those parameters, however.

   Since the paper used simulated data it is unfortunate that the
analysis was not extended to a higher resolution where the
distribution of the repeated refinements could be compared to
traditionally calculated SUs.  Maybe a follow up paper is in order.

Dale Tronrud
> All the best, Pavel
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