[cctbxbb] map grid sizes

Pavel Afonine pafonine at lbl.gov
Tue Feb 18 10:05:58 PST 2020


Hi George,

map gridding is automatically defined such so it is compatible with FFT 
requirements.

Instead of

e_map_array = e_map.real_map()

try

e_map_array = e_map.real_map_unpadded()

Pavel

On 2/13/20 13:41, GEORGE N PHILLIPS 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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