[cctbxbb] solvent mask

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Mon Oct 15 09:56:41 PDT 2007


Hi Celine,

> I have a question about solvent mask in cctbx. I generated a mask using
 
> the mask manager. Then I am calculating the structure factors from the 
> mask (using mask_manager.structure_factors() ). If I am trying to redo
 a 
> map from the calculated structure factors (outside the cctbx and I hope
 
> without any scaling), I get a map with a mean density of zero,

That's because the F000 is missing. Without the F000, the mean of an FFT map
will always be exactly zero. -- This is a general feature of discrete
Fourier transforms.

> So I wonder what is exactly this 
> matrix.col(fft_manager.n_real()).product() doing?

That's the number of grid points in the map. The FFT introduces
this as a scale factor which we are taking out. -- Again, the number of
grid point issue is a general feature of discrete Fourier transforms.

> And how do I generate
 
> structure factors for a mask without any scaling?

I'm guessing the scaling is not the problem, but just the absence of F000,
which you can get as map_of_coeff[0]. I think it will also work if you
give an array of Miller indices including (0,0,0).

We could add suppress_scaling to the signature of the .structure_factors()
method, but the scale is rather arbitrary anyway, so I don't think this will
be very useful.

Ralf






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