[cctbxbb] Getting r1_factor of miller arrays with different count of miller indices
Richard Gildea
rgildea at gmail.com
Fri Jul 6 12:39:29 PDT 2012
Actually, the R2-factor (or more commonly the wR2-factor) is calculated
using the squared differences in the intensities rather than the squared
differences in the amplitudes as I stated in my previous email. See also
section 2.7 in the SHELX manual.
Cheers,
Richard
On 6 July 2012 12:34, Richard Gildea <rgildea at gmail.com> wrote:
> 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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