Re: [phenixbb] pseudo-merohedral twinning

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 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 Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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Date: Tue, 06 Dec 2011 17:17:56 -0600 From: [email protected] (on behalf of Jon Schuermann ) Subject: Re: [phenixbb] pseudo-merohedral twinning To: [email protected]

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: [email protected] Tel: (630) 252-0682 Fax: (630) 252-0687

On 12/06/2011 02:58 PM, Zhou, Tongqing (NIH/VRC) [E] wrote:

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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 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ****************************************************************** _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- 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: [email protected] Tel: (630) 252-0682 Fax: (630) 252-0687

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