[buster-discuss] two questions : one about negative reflections and one about Simulated annealing

[Ian Tickle]

Hi Nicolas

I should have included a link to the StarAniso webserver in case you are
not aware of it:

https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi

There you can get a lot more information (and maybe even submit your data
to it!).

Cheers

-- Ian


On Tue, 22 Jun 2021 at 11:36, Ian Tickle <ianjt05 at gmail.com> wrote:

>
> Hi Nicolas
>
> As far as I know, Buster doesn't have a Simulated Annealing option, but
> maybe the Buster developers will have more to say on that.
>
> On your second question, there's an important step between getting the
> merged intensities and performing the refinement with Buster.  Again as far
> as I know Buster only uses amplitudes (Fs) as input.  Fs unlike
> intensiities cannot be non-negative by definition.  So we need to convert
> all the merged intensities including negative ones to positive Fs.  This is
> usually done by French & Wilson Bayesian estimation:
>
>
> https://warwick.ac.uk/fac/sci/statistics/staff/academic-research/french/publications/bayes_impact_french_wilson.pdf
>
> Also see the reference to the original 1978 paper cited there.
>
> This algorithm, or a modification of it, is implemented, among others, in
> the Truncate, CTruncate and StarAniso programs.  For example, StarAniso
> computes the Fs using a very accurate numerical method instead of using
> table look-ups, and takes into account the effect of anisotropy on the
> Bayesian prior.
>
> Best wishes
>
> -- Ian
>
>
> On Tue, 22 Jun 2021 at 10:29, Nicolas Foos <nicolas.foos at ibs.fr> wrote:
>
>> Dear buster users and developers,
>>
>> I have two questions : one simple : is it possible to perform a simulated
>> annealing using buster. I didn't see anything like that in the manual, but
>> maybe I miss it.
>>
>> The second question : how autoBuster handle the negative reflections
>> present in the data file ?
>> - Does it ignore them ?
>> - Does it fill them ?
>> - Does it set them to zero ?
>> What's you opinion about that point, should we use them or not. I would
>> be glad to have your opinion about that point.
>>
>> To let you know a bit more : I am working on time resolve project. The
>> Data were originally collected in XFEL, then processed using CrystFel. And
>> then based on Fo(state1)-Fo(state2) difference map calculation, I did an
>> extrapolation to refine the model. The data which generates my questions
>> are the Extrapolated ones.
>>
>> I am fully open to any comments.
>>
>> All the best,
>>
>> Nicolas Foos
>>
>> _______________________________________________
>> buster-discuss mailing list
>> buster-discuss at globalphasing.com
>> https://www.globalphasing.com/mailman/listinfo/buster-discuss
>
>
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