[cctbxbb] Getting r1_factor of miller arrays with different count of miller indices

[Richard Gildea]

Hi Jan,

You will need to get a matching set of indices for both arrays before
calculating the R1 factor. The simplest way to do this would be by calling
the miller.array.common_sets() function:

e.g. where f_obs and f_calc are two arrays that are not necessarily
matching sets of indices:

f_obs, f_calc = f_obs.common_sets(f_calc)

Hope that helps,

Richard

On 6 July 2012 11:59, Jan Marten Simons <marten at xtal.rwth-aachen.de> wrote:

> Hi,
>
> I'm facing a new challenge while working with cctbx:
>
> Imagine a set of (possibly incomplete) measured intesities, or integrated
> intensities from xrd powder patterns (I_obs) and a fitting crystal symmetry
> (xtal_symm). Now if I want to check if a given structure would generate the
> same intensities. (--> low R1) the following code exibits the problem:
>
> # -*- coding: utf-8 -*-
> from __future__ import division
> from cctbx import xray
> from cctbx import crystal
> from cctbx.array_family import flex
> from libtbx import Auto
>
> obs_file = "Test.hkl"              # in shelx hklf4 format
> xtal_symm = crystal.symmetry(
>     unit_cell=(4.000, 5.4321, 7.531, 90.0, 90.0, 90.0),
>     space_group_symbol="P mm2")
>
> trial_structure = xray.structure(
>   special_position_settings=crystal.special_position_settings(
>     crystal_symmetry=xtal_symm),
>   scatterers=flex.xray_scatterer([
>     xray.scatterer(
>       label="Si",
>       site=(0.0,0.0,0.0),
>       u=0.2)]))
>
> # load (integral) intensities from diffraction data
> from iotbx import reflection_file_reader
> rfl = reflection_file_reader.any_reflection_file("amplitudes="+obs_file,
>                                                   ensure_read_access=True)
> I_obs = rfl.as_miller_arrays(crystal_symmetry=xtal_symm,
>                               force_symmetry=False,
>                               merge_equivalents=True,
>                               base_array_info=None)[0]
> I_obs = I_obs.discard_sigmas()
> f_obs = I_obs.as_amplitude_array()
>
> f_calc = trial_structure.structure_factors(d_min=1.0).f_calc()
> f_calc.merge_equivalents()
>
> R1 = f_calc.r1_factor(f_obs, scale_factor=Auto,
> assume_index_matching=False)
>
> gives:
> "    assert other.indices().size() == self.indices().size()
> AssertionError                               "
>
>
> Is there some way to get the R1_factor for this kind of scenario?
>
> Cheers and thanks in advance,
> Jan
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