-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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:
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 zero. 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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