[phenixbb] pseudo-merohedral twinning

Phzwart phzwart at gmail.com
Tue Dec 6 16:06:39 PST 2011


I recommend to skip p2 and go to p1 immediately.

HTH
Peter

Sent from my iPhone

On Dec 6, 2011, at 3:29 PM, Gino Cingolani <Gino.Cingolani at jefferson.edu> wrote:

> Tongqing,
> 
> most likely you have a pseudo-merohedral P21 cell.
> The higher symmetry (orthorhombic) is due to a two fold twinning axis. 
> Your real space group could be primitive monoclinic (P21),
> with b-angle close to 90, or a=c (....and there's a third condition for 
> pseudo-merohedral twinning that I can't remember).
> 
> My suggestion to you.... go back to your data; scale them as P21, 
> check the b-angle and a,c unit cell axes; then run X-triage. 
> If you detect pseudo-merohedral twinning, try MR in P1 and refine in P1.
> Then, eventually de-twin appropriately.
> 
> Good luck!
> 
> Gino
> 
> 
> 
> 
> ******************************************************************************
> Gino Cingolani, Ph.D.
> Associate Professor
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> 
> 
> ---- Original message ----
>> Date: Tue, 06 Dec 2011 17:17:56 -0600
>> From: phenixbb-bounces at phenix-online.org (on behalf of Jon Schuermann <schuerjp at anl.gov>)
>> Subject: Re: [phenixbb] pseudo-merohedral twinning  
>> To: phenixbb at phenix-online.org
>> 
>> 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
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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
>> 
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