[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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