[phenixbb] refinement with translational ncs
Pavel Afonine
pafonine at lbl.gov
Wed Jan 27 11:04:29 PST 2021
Hi Jorge,
"tncs_correction = True" is functional, somewhat tested and overall
supposed to work. However, we have not done any large scale systematic
tests to evaluate what exactly benefits are.
As to "what does this actually do?" -- this option treats the presence
of tNCS as described here:
https://doi.org/10.1107/S0907444912045374
Pavel
On 1/27/21 02:46, Jorge Iulek wrote:
> Dear all,
>
>
> 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.
>
> 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.
>
> 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?
>
> Thanks,
>
>
> Jorge
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
More information about the phenixbb
mailing list