Hi Peter,

you suggest to calculate "the (free) likelihood".. May I ask: specifically likelihood of what you are suggesting to calculate and what is "free" in this context? I guess I'm just lost in jargon, sorry!

Thanks,
Pavel

On 2/11/15 8:08 PM, Peter Zwart wrote:

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 easily.

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.

HTH

P

 

On 11 February 2015 at 16:13, Masaki UNNO <unno19@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@phenix-online.org
[mailto:phenixbb-bounces@phenix-online.org] On Behalf Of Pavel Afonine
Sent: Thursday, February 12, 2015 6:36 AM
To: Dale Tronrud; phenixbb@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
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Lawrence Berkeley National Laboratories
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Cell: 510 289 9246
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