[phenixbb] How to correct translational psuedosymmetry

Randy Read rjr27 at cam.ac.uk
Mon Aug 12 05:45:55 PDT 2013


Unless you can grow a different crystal form, you'll just have to be aware of the potential difficulties from having translational non-crystallographic symmetry (tNCS).  A peak height of less than 50% of the origin won't cause as much trouble as if you had, say, a peak of 80% of the origin, but it can lead to difficulties nonetheless.

You haven't mentioned whether this is a molecular replacement or experimental phasing case.  If it's molecular replacement, recent versions of Phaser can cope pretty well with tNCS, first characterising it and then taking account of it while placing pairs of copies.  For SAD phasing, Phaser also accounts for tNCS but that treatment could probably be a bit more robust.  

One possibility when the translation is nearly a centering operator, as in your case, is to assume the translation is exact, reindex the data, and start by solving the structure in the approximate space group.  Xtriage will tell you what space group you would get and how to reindex, if you wanted to try that approach.  After getting a solution, then you have to work out how to break the symmetry to get the true structure in a lower symmetry space group.

Good luck!

Randy Read

On 11 Aug 2013, at 17:22, Appu kumar <appu.kumar9 at GMAIL.COM> wrote:

> Dear all,
>                    I have processed a protein-DNA complex data with imosflm. Phenix.xtriage suggest that the is a off origin peak of hight 41.702 hight at fractional coordiantes of 0.500 0.021 0.500 with distance of 40.019 from origin. I am new to such kind of problem, so would you please suggest me how to solve the psuedosymmetry problem encountered in data process. The present unit cells are  55.41 109.72 66.61 90 98.74 90 in space group P1211 with p_value is 3.116e-04. Your help would be much appreciated
> Thank you 
> Appu
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Randy J. Read
Department of Haematology, University of Cambridge
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