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

[Nicolas Foos]

Hi Ian, 

Thank you for your answer. 
I definitely agree with you, I know that and I am actually working with the Fs (especially to being able to use buster). 
My question was actually a more general point of view about that, like opening a discussion about the influence of the negative intensity and about the different existing way to deal with them. 

Cheers, 

Nicolas 


De: "Ian Tickle" <ianjt05 at gmail.com> 
À: "Nicolas Foos" <nicolas.foos at ibs.fr> 
Cc: "buster-discuss" <buster-discuss at globalphasing.com> 
Envoyé: Mardi 22 Juin 2021 13:04:29 
Objet: Re: [buster-discuss] two questions : one about negative reflections and one about Simulated annealing 


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 < [ mailto:ianjt05 at gmail.com | 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 | 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 < [ mailto:ianjt05 at gmail.com | ianjt05 at gmail.com ] > wrote: 

BQ_BEGIN


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 | 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 < [ mailto:nicolas.foos at ibs.fr | nicolas.foos at ibs.fr ] > wrote: 

BQ_BEGIN


BQ_BEGIN

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 
[ mailto:buster-discuss at globalphasing.com | buster-discuss at globalphasing.com ] 
[ https://www.globalphasing.com/mailman/listinfo/buster-discuss | https://www.globalphasing.com/mailman/listinfo/buster-discuss ] 
BQ_END


BQ_END


BQ_END


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.globalphasing.com/pipermail/buster-discuss/attachments/20210622/96acc5b6/attachment.html>