[phenixbb] refinement with translational ncs
Jorge Iulek
iulek at uepg.br
Sun Jan 31 04:55:33 PST 2021
Thanks, Pavel, I will read and study the paper.
Jorge
On 1/27/21 5:04 PM, Pavel Afonine wrote:
> 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
>>
>>
>>
>>
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>
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