[phenixbb] pseudo-merohedral twinning

[Jon Schuermann]

Tongqing,

As for the twinning... 2% is nothing and within error of saying no 
twinning. What twin test gave you the 2% twin fraction?

What was the Rsym for the data processed in P222? How many molecules do 
you have in the AU? What is the sequence identity of your search model 
to your protein? Did you look at the density to see if there are missing 
molecules you have not accounted for? Did you try MR in the other 7 
possible SG/permutations in primitive orthorhombic?

I would ignore the 'twinning' and move forward since that is probably 
not your problem. If you have checked all the other SG/permutations in 
orthorhombic and you have tried to refine but saw nothing out of the 
ordinary in the maps, then you could reprocess in P2 and check all the 
possible permutations (using Pointless) to see if one gives you a lower 
Rsym. In that case you could have twinning and/or NCS issues, but I 
wouldn't jump into that until you have exhausted all your options 
orthorhombic.

Jon Schuermann

-- 
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439

email: schuerjp at anl.gov
Tel: (630) 252-0682
Fax: (630) 252-0687


On 12/06/2011 02:58 PM, Zhou, Tongqing (NIH/VRC) [E] wrote:
> Hi Pavel,
>
> I just collected a 2.85 A dataset  with space group P212121, MR went well, however, the refinement was not fine: (eg: Rigid body r=48%, it won't go down anymore). I then ran xtriage, it turned out the my data was pseudo-merohedral twinned. The twin fraction is ~0.02.  Twin_law=k,h,-l. It there a way to de-twin the data and then do the refinement or just use the twin_law="k,h,-l" at the command line? Is there a way to specify twin_fraction in the paramenter file?
>
> Also re-processed data in P41212 or P43212, the ~25% Rsym indicated the data should still be in  P222.
>
> Thanks,
>
>
> Tongqing
>
> Tongqing Zhou, Ph.D.
> Staff Scientist
> Structural Biology Section
> Vaccine Research Center, NIAID/NIH
> Building 40, Room 4607B
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-- 
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439

email: schuerjp at anl.gov
Tel: (630) 252-0682
Fax: (630) 252-0687