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

[Ian Tickle]

Hi Nicolas

Sorry a correction to my first reply:

"Fs unlike intensiities cannot be non-negative by definition"

should of course read

"Fs unlike intensiities cannot be negative by definition"

Too many negatives!

Cheers

-- Ian


On Tue, 22 Jun 2021 at 11:43, Ian Tickle <ianjt05 at gmail.com> wrote:

>
> 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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