Hi Pavel,<div><br></div><div>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 (<a href="http://dx.doi.org/10.1107/S0021889808007279">http://dx.doi.org/10.1107/S0021889808007279</a>). The terminology R1 factor is also used in the SHELX manual.</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Richard</div><div><br><div class="gmail_quote">On 6 July 2012 12:23, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
can anyone tell me what's r1_factor and how it is different from
classical text-book definition of R-factor, for example:<br>
<br>
<a href="http://en.wikipedia.org/wiki/R-factor_(crystallography)" target="_blank">http://en.wikipedia.org/wiki/R-factor_(crystallography)</a><br>
<br>
(or for those who doesn't trust wiki: page 147 in
Blundell&Johnson (1976))<br>
<br>
?<br>
<br>
Are there r2_factor, r3_factor, ..., etc ?<br>
<br>
Thanks,<br>
Pavel<div><div class="h5"><br>
<br>
On 7/6/12 12:09 PM, Richard Gildea wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">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.�
<div><br>
</div>
<div>Thus the following two lines (note singular common_set):</div>
<div><br>
</div>
<div>f_obs = f_obs.common_set(f_calc)</div>
<div>f_calc = f_calc.common_set(f_obs)</div>
<div><br>
</div>
<div>is equivalent to the one-liner (note plural common_sets):</div>
<div><br>
</div>
<div>f_obs, f_calc = f_obs.common_sets(f_calc)</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Richard</div>
<div><br>
<br>
<div class="gmail_quote">On 6 July 2012 12:04, Richard Gildea <span dir="ltr"><<a href="mailto:rgildea@gmail.com" target="_blank">rgildea@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Jan,
<div><br>
</div>
<div>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:</div>
<div>
<br>
</div>
<div>e.g. where f_obs and f_calc are two arrays that are not
necessarily matching sets of indices:</div>
<div><br>
</div>
<div>f_obs, f_calc = f_obs.common_sets(f_calc)</div>
<div><br>
</div>
<div>Hope that helps,</div>
<div><br>
</div>
<div>Richard</div>
<div>
<div>
<div>
<div><br>
<div class="gmail_quote">On 6 July 2012 11:59, Jan
Marten Simons <span dir="ltr"><<a href="mailto:marten@xtal.rwth-aachen.de" target="_blank">marten@xtal.rwth-aachen.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I'm facing a new challenge while working with
cctbx:<br>
<br>
Imagine a set of (possibly incomplete) measured
intesities, or integrated<br>
intensities from xrd powder patterns (I_obs) and
a fitting crystal symmetry<br>
(xtal_symm). Now if I want to check if a given
structure would generate the<br>
same intensities. (--> low R1) the following
code exibits the problem:<br>
<br>
# -*- coding: utf-8 -*-<br>
from __future__ import division<br>
from cctbx import xray<br>
from cctbx import crystal<br>
from cctbx.array_family import flex<br>
from libtbx import Auto<br>
<br>
obs_file = "Test.hkl" � � � � � � �# in shelx
hklf4 format<br>
xtal_symm = crystal.symmetry(<br>
� � unit_cell=(4.000, 5.4321, 7.531, 90.0, 90.0,
90.0),<br>
� � space_group_symbol="P mm2")<br>
<br>
trial_structure = xray.structure(<br>
�
special_position_settings=crystal.special_position_settings(<br>
� � crystal_symmetry=xtal_symm),<br>
� scatterers=flex.xray_scatterer([<br>
� � xray.scatterer(<br>
� � � label="Si",<br>
� � � site=(0.0,0.0,0.0),<br>
� � � u=0.2)]))<br>
<br>
# load (integral) intensities from diffraction
data<br>
from iotbx import reflection_file_reader<br>
rfl =
reflection_file_reader.any_reflection_file("amplitudes="+obs_file,<br>
� � � � � � � � � � � � � � � � � � � � � � � �
� ensure_read_access=True)<br>
I_obs =
rfl.as_miller_arrays(crystal_symmetry=xtal_symm,<br>
� � � � � � � � � � � � � � �
force_symmetry=False,<br>
� � � � � � � � � � � � � � �
merge_equivalents=True,<br>
� � � � � � � � � � � � � � �
base_array_info=None)[0]<br>
I_obs = I_obs.discard_sigmas()<br>
f_obs = I_obs.as_amplitude_array()<br>
<br>
f_calc =
trial_structure.structure_factors(d_min=1.0).f_calc()<br>
f_calc.merge_equivalents()<br>
<br>
R1 = f_calc.r1_factor(f_obs, scale_factor=Auto,
assume_index_matching=False)<br>
<br>
gives:<br>
" � �assert other.indices().size() ==
self.indices().size()<br>
AssertionError � � � � � � � � � � � � � � � "<br>
<br>
<br>
Is there some way to get the R1_factor for this
kind of scenario?<br>
<br>
Cheers and thanks in advance,<br>
Jan<br>
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