[phenixbb] Pseudotranslation issue

Gino Cingolani gino.cingolani at jefferson.edu
Fri Jun 7 03:38:49 PDT 2013

Dear Fulvio,
We just had a similar problem (further complicated by some twinning). Assuming that:
1. You collected enough data and 
2. You don't have a crazy number of molecules in the tetragonal asymmetric unit, 

I would advice to scale your data in P1 and do MR in P1. Then use conventional refinement + model building to bootstrap a better model (most likely your initial model isn't as good). Rosetta may help, too.

Then eventually go back to the tetragonal data with the improved search model and see if LLG and packing make sense.

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
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E-mail:   gino.cingolani at jefferson.edu
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)

Fulvio Saccoccia <fulvio.saccoccia at uniroma1.it> wrote:

>Dear phenixbb,
>     I have a data set collected at 2.2A resolution that I can integrate 
>in P4. Aimless, Phaser and Xtriage recognized a pseudotranslation  
>(34.6% of origin peak) at fractional coordinates 0.500 0.500 0.479  
>(ORTH   46.7   46.7   37.4). However labelit.index run with 
>sublattice_allow=true search did not detect the pseudotranslation 
>vector. So far, any attempts to phase by molecular replacement was 
>unsuccesfull and I suspect that it could be due to incorrect assignement 
>of space group:
>Now, some questions arise:
>1) does the pseudo translation exist or do not?
>2) if translational NCS is present, could it mimic a P41/P42/P43 space 
>3) in any case, any advices in order to properly deal with tNCS will be 
>of great help?
>I thank you in advance
>Best wishes
>Fulvio Saccoccia, PhD
>Sapienza University of Rome
>Dept. of Biochemical Sciences "A. Rossi Fanelli"
>Piazzale Aldo Moro, 5
>00185 Rome (Italy)
>phenixbb mailing list
>phenixbb at phenix-online.org
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