[phenixbb] P3 pseudotranslation

[Randy Read]

Hi,

It seems that you're using an old version of Phaser that predates the implementation of corrections for translation NCS (tNCS).  When tNCS is not accounted for, Phaser has been known to give incorrect solutions.  In particular, the TFZ score for the second molecule is generally rather misleading, because any molecule in the same orientation related by the NCS translation will account for the modulation of the data introduced by the interference between the contributions of the two copies; even if the solution is wrong, accounting for the modulation explains a lot of the features of the data.

So I would suggest installing the recent Phenix release and running a job looking for two copies of the monomer, to see if you get the same solution or a different one.  Another advantage is that this version of Phaser will give you intensity statistics corrected for the statistical effects of tNCS, which can help to detect twinning in the presence of tNCS.

Best wishes,

Randy Read

On 14 Jan 2013, at 05:07, Ethayathulla A.S wrote:

> Hello
> 
> I am trying to solve a structure with P3 Pseudotranslation at 3.5A. The 3.5 dataset have cell of 150,150,200 and 5A dataset have smaller cell 150,150, 100. The data can be scaled in P321, p3221,p3121 with similar rsym (6 (54).  Pointless gave me Spacegroups as P3221 or P3121 as soln. I tried Phenix.xtriage it showed me 40% Pseudotranslation peak ( 0,0,0.5) for 3.5A dataset as the c-axis is double that of 5A data. According to cell content analysis it can be dimer in 3.5A and monomer for 5A dataset. So I tried MR with both datasets with homology model build using similar fold protein. I got solns for dimer with LLGs with 1000's in P3221,P3121,P321 with 3.5A dataset. There were 28 solutions
> 
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>     SOLU SET  RFZ=2.0 TFZ=8.2 PAK=0 LLG=259 TFZ==11.3 LLG=1181 TFZ==28.4 (   SOLU SPAC P 32 2 1)
> 
>    SOLU 6DIM ENSE partial EULER 94.4 2.7 25.5 FRAC -0.07 -1.07 -0.81 BFAC -1.00
> 
>    Solution #2 annotation (history):
> 
>    SOLU SET  RFZ=2.0 TFZ=8.2 PAK=0 LLG=225 LLG=1066 (   SOLU SPAC P 31 2 1)
> 
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> So I refined the solns. of P3221, p321 it refined to 44/54 after that it doesn’t go down. The 0.5 Pseudotranslated molecule can been as symmetry molecule along c-axis. The packing looks very good. I have attached the image of it with native patt map. I deleted one monomer and refined to check the solution I could see clearly see the other molecule.  I could see 2n+1 odd reflections to be weak.
> 
> To check whether two fold can be due to twinning due to pseudotranslation I could not observe it. So I tried to see check whether the it can be P32 merohedral twinning with pseudotranslation with  twinning of 0.36 (h,-h-k,-l) from yeates server. I try to use the dimer of P3212 and try for alternative spacegroup which yield me unique soln in P32. I refined the molecule four molecule which yielded me 46/49 and when I apply twinning fraction the r-factor decreases to 40/45.
> 
> Similarly for 4.5A dataset I used dimer of 3.4 dataset dimer which yield me solution in P32 but cannot refine it gets struck for 45/50.I tried to use the dimer with 5A dataset I get unique solu and refine with merohedral twinning the r/freeR goes to 38/57.
> 
>  
> How I can check whether it is P32 merohedral twinning with Pseudotranslated or P3221. Also the patterson analysis another peak of height 4% ( 0.050, 0.102, 0.495 ) :    4.452 . Is it significant ?
> 
> Any suggestion will be helpful
> 
>  
> 
> Thank you
> 
> Abdul
> 
> 
>  
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>  Patterson analyses from phenix.xtriage
> 
>  Frac. coord.        :    0.000    0.000    0.500
> 
>  Distance to origin  :  103.157
> 
>  Height (origin=100) :   40.427
> 
>  p_value(height)     :    2.740e-04
> 
> The full list of Patterson peaks is:
> 
>   x      y      z            height   p-value(height)
> 
> ( 0.000, 0.000, 0.500 ) :   40.427   (2.740e-04)
> 
> ( 0.050, 0.102, 0.495 ) :    4.452   (9.782e-01)
> 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
> 
> -- 
> ***********************************************
> Dr. A.S. Ethayathulla
> Dept of biophysics
> AIIMS, new delhi
> ***********************************************
> <patt-pack1.jpg><self-rot.jpg>_______________________________________________
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk

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