[phenixbb] refinement with translational ncs

[Jorge Iulek]

Dear Esko,


     Thank you for your input. I must also look into these papers.


Jorge



On 1/27/21 10:02 AM, Esko Oksanen wrote:
> Dear Jorge,
>
> 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 
> (https://doi.org/10.1107/S0907444906031519) and since then there is a 
> nice paper summarising the effects of pseudosymmetry 
> (https://doi.org/10.1107/S090744490705531X).
>
> HTH,
> Esko
> *_____________________*
> *
> *
> *Esko Oksanen, PhD*
> Instrument Scientist - Neutron Macromolecular Crystallography
>
> European Spallation Source ERIC
> P.O Box 176, SE-221 00 Lund, Sweden
> Visiting address: Odarslövsvägen 113 224 84 Lund Sweden
> Switchboard: +46 46 888 00 00
> Phone: +46 721 79 20 36
> E-mail: esko.oksanen at ess.eu <mailto:esko.oksanen at esss.se>
>
> www.ess.eu <http://www.esss.se/>
>
>
>
>
>
>
>
>
>> On 27 Jan 2021, at 11:46, Jorge Iulek <iulek at uepg.br 
>> <mailto:iulek at uepg.br>> 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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