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

Peter Zwart PHZwart at lbl.gov
Wed Feb 11 22:29:50 PST 2015

```i actually mean the log-likelihood, which is the target function typically
optimized in phenix.refine. If you compute the log likehood for the
test/free set instead, one might overcome bias issues, if any are present.

P

On 11 February 2015 at 21:56, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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> 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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>
>
>
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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
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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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