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

[Richard Gildea]

Just to avoid any confusion between mine and Nat's responses, there are two
similarly named functions in miller.array, common_set and common_sets.

Thus the following two lines (note singular common_set):

f_obs = f_obs.common_set(f_calc)
f_calc = f_calc.common_set(f_obs)

is equivalent to the one-liner (note plural common_sets):

f_obs, f_calc = f_obs.common_sets(f_calc)

Cheers,

Richard


On 6 July 2012 12:04, Richard Gildea <rgildea at gmail.com> wrote:

> 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
>> _______________________________________________
>> cctbxbb mailing list
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>
>
>
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