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

[Pavel Afonine]

Hi,

can anyone tell me what's r1_factor and how it is different from 
classical text-book definition of R-factor, for example:

http://en.wikipedia.org/wiki/R-factor_(crystallography)

(or for those who doesn't trust wiki: page 147 in Blundell&Johnson (1976))

?

Are there r2_factor, r3_factor, ..., etc ?

Thanks,
Pavel

On 7/6/12 12:09 PM, Richard Gildea wrote:
> 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 
> <mailto: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 <mailto: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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>
>
>
>
>
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