[cctbxbb] using scatterer flags?

Pavel Afonine pafonine at lbl.gov
Tue Apr 16 10:50:10 PDT 2013

I added "use" flag (at the time when I was adding all other scatterer 
flags) rather as a placeholder for a future use, so yes, indeed, 
currently it is not respected in fcalc and gradients calculation (though 
it should be respected!). Perhaps it's time to start using it...


On 4/15/13 11:58 AM, Richard Gildea wrote:
> Are the same scatterers contributing to f_calc for every calculation, 
> or will the scatterers that are contributing vary from calculation to 
> calculation? In the case of the former it might be simplest to create 
> a new copy of the xray_structure with only those scatterers.
> It looks the "use" flag isn't actually respected in the structure 
> factor or gradient calculations as far as I can tell. If you feel you 
> need something like this rather than creating new copies of the 
> xray_structure with only the scatterers you need or alternatively 
> setting the occupancy to zero, then this is probably something we can 
> add into the code. There is some code in cctbx/xray/scatterer_flags.h 
> for flags_set_grad_*() that will set a selection of gradients all at 
> once in C++, but I don't see an equivalent for set_use_*(). I suspect 
> that the overhead of looping through the scatterers to set flags in 
> Python would be small compared to the cost of calculating the 
> structure factors in the first place.
> Cheers,
> Richard
> On 15 April 2013 10:40, Jan Marten Simons <marten at xtal.rwth-aachen.de 
> <mailto:marten at xtal.rwth-aachen.de>> wrote:
>     Am Montag 15 April 2013 18:33:00 schrieb Jan Marten Simons:
>     > Hi,
>     >
>     > while working on a really fast way to calculate the structure
>     factors of a
>     > few millions of different modifications of a structure with only the
>     > selected scatterers contributing to f_calc ....
>     [...]
>     > (I think building a larger structure and working with
>     > selections might be faster than creating lots of different
>     structures
>     > containing only the desired scatterers, but I might be wrong on
>     this.)
>     I've found "flags" might be what I'm looking for. So if I could
>     set the "use"
>     flag for all scatterers at once and if it was taken into
>     consideration during
>     structure factor calculation then I think it would most likely be
>     the fastest
>     way to enable or disable the contribution of individual scatterers
>     to the
>     structure factors. Am I right on this and how would I best
>     interface with the
>     flags mechanism (from python)?
>     Cheers,
>     Jan
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