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<p>Dear Esko,</p>
<p><br>
</p>
<p> Thank you for your input. I must also look into these papers.</p>
<p><br>
</p>
<p>Jorge<br>
</p>
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<div class="moz-cite-prefix">On 1/27/21 10:02 AM, Esko Oksanen
wrote:<br>
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Dear Jorge,
<div class=""><br class="">
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<div class="">With significant translational pseudosymmetry, at
least close to a pseudo-centerering vector, will inevitably lead
to higher R-values. Basically the R-value isn’t a very good
indicator of the structure correctness any more and the expected
values for an acentric structure are no longer really valid. I
had a somewhat similar case long ago (<a
href="https://doi.org/10.1107/S0907444906031519" class=""
moz-do-not-send="true">https://doi.org/10.1107/S0907444906031519</a>)
and since then there is a nice paper summarising the effects of
pseudosymmetry (<a
href="https://doi.org/10.1107/S090744490705531X" class=""
moz-do-not-send="true">https://doi.org/10.1107/S090744490705531X</a>).</div>
<div class=""><br class="">
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<div class="">HTH,</div>
<div class="">Esko</div>
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<blockquote type="cite" class="">
<div class="">On 27 Jan 2021, at 11:46, Jorge Iulek <<a
href="mailto:iulek@uepg.br" class=""
moz-do-not-send="true">iulek@uepg.br</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Dear all,<br class="">
<br class="">
<br class="">
I have a dataset at 2.98 A resolution, images
processed to CC_1/2 at circa 50% in the last resolution
shell, tetramer in the asymmetric unit, local
(rotational) symmetry 222. Xtriage indicates a peak in
the Patterson function at 20% height of origin peak, at
fractional coordinates of 0.0000 0.0000 0.3177. Space
group is P21.<br class="">
<br class="">
I am aware that this brings problems to refinement
, as even stated at xtriage output "Translational
pseudo-symmetry is very likely present in these data.
Be aware that this will change the intensity statistics
and may impact subsequent analyses, and in practice may
lead to higher R-factors in refinement.", and so I can't
lower my R and R-free below ~31 and 36 % , respectively.<br
class="">
<br class="">
At phenix.refine, setting "tncs_correction = True"
brings little benefit (what does this actually do?
points to references are welcome). I wonder nevertheless
if some strategy might help in on lowering these R's
and, of course, allow me to build a better model (in
spite of the resolution). I tried some combinations of
other types of ncs and tls groups, with little success.
Particularly, it seems that the refinement of ADPs are a
kind of unstable (what I would understand come from the
- partial - modular nature of the intensities - due to
tncs - and these - ADP - would be reflected by the
intensity fall-off with resolution). What about refining
ADPs only to a zone which is not affect by data
modulation? How to do that? Any other ideas?<br class="">
<br class="">
Thanks,<br class="">
<br class="">
<br class="">
Jorge<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
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