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

Pavel Afonine pafonine at lbl.gov
Wed Feb 11 21:56:18 PST 2015

```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 at mx.ibaraki.ac.jp
> <mailto: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>
>     [mailto: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
>     <mailto: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
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