[cctbxbb] Structure factor calculation weirdness

Graeme.Winter at diamond.ac.uk Graeme.Winter at diamond.ac.uk
Fri Dec 7 08:29:27 PST 2012

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.


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

  f_calc = structure.structure_factors(
    d_min = dmin).f_calc()

For your toy example the speed difference isn't noticeable - for a
protein structure it will be considerable.

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