[phenixbb] pseudo translational symmetry

Esko Oksanen esko.oksanen at helsinki.fi
Mon Jun 22 22:09:41 PDT 2009


  I had a similar problem some time ago. Though I had a translation  
vector leading to body centering, which is even worse for the  
refinement probably...I realised that half the reflections were very  
weak compared to the other half and didn't really contribute to the  
refinement target.  What I did was to separately refine against the  
weak (rigid body) and the strong reflections, which at least in my  
case helped. This is described in Oksanen et al. (2006) Acta Cryst D62  


On 23.6.2009, at 7.44, youssef ben ammar wrote:

> Hi all,
> I recently solved the structure of a protein containing 395aa using  
> phenix autosol. After autoBuild I got about 65% of the sequence  
> docked with 2 monomers in the ASU.
> After several refinement cycles the map has been improved and I  
> build manually the remaining amino acids. But the problem is that R  
> and Rfree didn't decrease below 0.28 and 0.33 respectively. I tried  
> with NCS restraints, TLS but without success.
> When I revised phenix autosol logs carefully, I found that in  
> xtriage the analyses of the Patterson function reveals a significant  
> off-origin peak that is 41.59 % of the origin peak, indicating  
> pseudo translational symmetry and no twin laws were found.
> The space group is P212121 (36.898, 59.45, 393.908, 90, 90, 90). The  
> basic statistics suggested 1 copy in the ASU (but the solution gave  
> 2 copies per ASU !!!). The same analysis done by ccp4i gave the same  
> solvent content and math. coef. in p21212 but with 2 copies per ASU.
> In xtriage I found this suggestion: If the observed pseudo  
> translationals are crystallographic the following spacegroups and  
> unit cells are possible:
> space group  P 21 21 2 (b-1/4,2*c,a)          operator    x, y+1/2,  
> z     unit cell of reference setting  (393.91, 36.90, 29.73,  90.00,  
> 90.00, 90.00)
> I am really stucked with the refinement and don't know how to deal  
> with this pseudo translation.
> Any help or suggestions are welcome.
> Thank you.
> Youssef
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