[phenixbb] pseudo-translational symmetry refinement

[Paul Adams]

Hi,

    the presence of this level of translational NCS (which you should  
be able to see from the arrangement of your molecules) is likely to  
lead to some issues with refinement. You will have sets of strong and  
very weak reflections. In this case you are likely to see poorer R- 
factors than you otherwise might expect at the same resolution (as  
there will be a lot of noise associated with the very weak  
reflections). However, you don't say what the R-factors are though.

   Cheers,
	Paul

On Apr 29, 2008, at 2:08 PM, a a wrote:

> Dear all:
> We have a set of crystal data having psuedo-translational symmetry  
> when examined with xtriage:
> ---------------------------------------------------------------------- 
> ---------
> Twinning and intensity statistics summary (acentric data):
>
> Statistics independent of twin laws
>   - <I^2>/<I>^2 : 2.519
>   - <F>^2/<F^2> : 0.724
>   - <|E^2-1|>   : 0.854
>   - <|L|>, <L^2>: 0.504, 0.337
>        Multivariate Z score L-test: 1.854
>        The multivariate Z score is a quality measure of the given
>        spread in intensities. Good to reasonable data are expected
>        to have a Z score lower than 3.5.
>        Large values can indicate twinning, but small values do not
>        necessarily exclude it.
>
>
> No (pseudo)merohedral twin laws were found.
>
>
> Patterson analyses
>   - Largest peak height   : 67.742
>    (corresponding p value : 4.897e-06)
>
>
> The analyses of the Patterson function reveals a significant off- 
> origin
> peak that is 67.74 % of the origin peak, indicating pseudo  
> translational symmetry.
> The chance of finding a peak of this or larger height by random in a
> structure without pseudo translational symmetry is equal to the  
> 4.8972e-06.
> The detected tranlational NCS is most likely also responsible for  
> the elevated intensity ratio.
> See the relevant section of the logfile for more details.
> The results of the L-test indicate that the intensity statistics
> behave as expected. No twinning is suspected.
>
> ---------------------------------------------------------------------- 
> ---------
> The structure was solved by auto-sad at 2.7A. However, the r-factor  
> can not be lowered by phenix.refine (TLS+ADP+rigid). Is there any  
> manipuliations we can do to deal with this situation?
> Thanks,
>
> Zhiyong Ren,
> MD Anderson Cancer Center
>
>
>
>
>        
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-- 
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
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BLDG 64R0121
Berkeley, CA 94720, USA.
--