[cctbxbb] Structure factor calculation weirdness

[Nicholas Sauter]

Graeme,

Just as a general ballpark figure, for protein work the difference
between approximate FFT structure factors and the exact direct sum
figures is on the order of 1%.

Nick

On Fri, Dec 7, 2012 at 8:29 AM,  <Graeme.Winter at diamond.ac.uk> wrote:
> Bing! Bet Nat's hit this in one.
>
> There may be a resolution dependence for 'F' but F001 (say) should not change, and should not go from 0 to non-0 no matter what. Direct summation much better here...
>
> Presumably for a protein structure the effects of gridding will also be much less significant.
>
> Thanks,
>
> Graeme
> ________________________________________
> From: cctbxbb-bounces at phenix-online.org [cctbxbb-bounces at phenix-online.org] on behalf of Nathaniel Echols [nechols at lbl.gov]
> Sent: 07 December 2012 15:46
> To: cctbx mailing list
> Subject: Re: [cctbxbb] Structure factor calculation weirdness
>
> On Fri, Dec 7, 2012 at 7:36 AM,  <Graeme.Winter at diamond.ac.uk> wrote:
>> Some confusion here at diamond – it seems that the amplitude of F(hkl)
>> depends on dmin
>
> Yes, because it's using the FFT method, which means it first does map
> sampling on a grid whose dimensions will partly depend on the
> resolution.  I'm not sure if there is resolution dependence for the
> scattering factors (I thought so, but I don't really know details),
> but I tried using direct summation and the resolution effect
> disappears.
>
>   f_calc = structure.structure_factors(
>     algorithm="direct",
>     d_min = dmin).f_calc()
>
> For your toy example the speed difference isn't noticeable - for a
> protein structure it will be considerable.
>
> -Nat
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-- 
Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Physical Biosciences Division
Lawrence Berkeley National Laboratory
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