Re: [cctbxbb] Structure factor calculation weirdness

I meant to include in the previous email that I add the following lines to the loop over dmin in Graeme's script: gridding = structure.crystal_symmetry().gridding(d_min=dmin) print "gridding: ", gridding.n_real() giving the output: d_min: 5.0 gridding: (3, 3, 3) d_min: 2.5 gridding: (8, 8, 8) d_min: 1.7 gridding: (9, 9, 9) With so few grid points it is entirely unsurprising that the FFT is such a poor approximation of the direct summation in this case! Cheers, Richard On 7 December 2012 10:49, Richard Gildea wrote:

Hi Graeme,

When you pass algorithm=None to xray.structure.structure_factors() it is supposed determine dynamically whether direct summation or FFT is best suited. However in this case (I guess because of the tiny unit cell?), the algorithm for choosing which method clearly fails as in this case direct summation would undoubtedly be better than FFT:

(from cctbx_project/cctbx/xray/structure_factors/from_scatterers.py)

# rough estimate if ( 4*n_scatterers*self.space_group().order_p()*n_miller_indices < self.crystal_gridding().n_grid_points()): algorithm = "direct"

Maybe there should be some special handling for small unit cells here? I don't know if there is a reason why you would ever want to calculate structure factors via FFT for unit cells this tiny?

Cheers,

Richard

On 7 December 2012 09:21, Nicholas Sauter wrote:

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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

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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: [email protected] [ [email protected]] on behalf of Nathaniel Echols [ [email protected]] 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, wrote:

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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 _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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