[cctbxbb] map grid sizes

Nicholas Sauter nksauter at lbl.gov
Tue Feb 18 17:34:13 PST 2020


Possibly because the "Fast" aspect of the "FFT" requires the map size to
have a prime factorization of small factors, generally combinations of
powers of 2, 3, 5, 7, and 11, in order for the algorithm to work.  Here's
some basic documentation from the web:
http://www.fftw.org/fftw2_doc/fftw_3.html

Nick

Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713


On Tue, Feb 18, 2020 at 9:43 AM GEORGE N PHILLIPS <george.phillips at wisc.edu>
wrote:

> I am confused about grid sizes of maps.
>
> When i specify a grid size for an fft_map  but then pull the numpy array
> out for direct manimpulation, it's always 2 larger in the last dimension.
>
> Why is it not the same size?  Any help appreciated.
>
> George
>
>
> y# Now make initial (smoothed) map using random phases with Fobs
> f_obs_B = f_obs1.apply_debye_waller_factors( b_iso=biso_init)
> phases =
> f_obs_B.random_phases_compatible_with_phase_restrictions(deg=False)
> phases_data = phases.data()
> e_map_coeff = f_obs_B.phase_transfer(phase_source = phases_data)
> e_map = e_map_coeff.fft_map(crystal_gridding = crystal_gridding,
> symmetry_flags = maptbx.use_space_group_symmetry)
> print("cgridding", crystal_gridding.n_real())
> # pick initial envelope
> e_map_array = e_map.real_map().as_numpy_array()
> print("e_map", e_map_array.shape)
>
>
> cgridding (90, 90, 80)
> e_map (90, 90, 82)
>
> George N. Phillips, Jr., Ph.D.
> Professor Emeritus
> University of Wisconsin-Madison
> 433 Babcock Dr. Madison, Wi 53706
> Phone 713 348 6951 (Houston)
>
>
>
>
>
>
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