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

[Richard Gildea]

Hi Pavel,

Small molecule crystallographers often refer to the R-factor as the
R1-factor. The '1' just means that is calculated using the amplitudes
without squaring. An R2-factor would be obtained by replacing the
amplitudes by the squares of the amplitudes and taking the square root. See
for example equations 7 and 8 in this paper by David Watkin (
http://dx.doi.org/10.1107/S0021889808007279). The terminology R1 factor is
also used in the SHELX manual.

Cheers,

Richard

On 6 July 2012 12:23, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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> 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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