[phenixbb] Reliable twinning fraction estimation
Terwilliger, Thomas Charles
terwilliger at lanl.gov
Wed Dec 10 13:24:02 PST 2014
Here are some things to check before concluding whether the data are twinned:
1. What are the Wilson moments (2 for untwinned 1.5 for perfect twin)?
2. Is it possible you have the wrong space group? If the data are overmerged then you could get this result. Perhaps your space group is really P31 or something like that? What are your merging statistics? Try an analysis with data in lower-symmetry space groups (you can always get the Wilson moments in P1 and that will often be a good indicator).
All the best,
On Dec 10, 2014, at 1:37 PM, Xiao Lei wrote:
> Dear All,
> I have a x-ray dataset of a protein-DNA complex to 2.8 A resolution with space group P312 checked by phenix xtriage for twinning. The estimated twin fraction from the output of xtriage is: 0.115 (Britton analysis); 0.119 (H test) and 0.022 (maximum likelihood method). However, the L-test graph in xtriage shows my observed data almost perfectly overlay with theoretical perfect twin data. In addition, when I tried to use phenix to do refinement with twin law -h,-k,l, the log file shows my twin fraction estimation is 0.49, which is very high and much bigger than Britton analysis and H test estimation.
> As far as my understanding is that if a twin fraction is lower than 15%, I still have hope to solve the structure (molecular replacement in this case) with reasonable R value, but if the twin fraction is 0.49, which is almost a perfect twin, which makes detwin impossible and refinement will stall at high R values (in my case, R free start: 0.4199; R work start: 0.4121; and R free final: 0.4038 and R work final: 0.3640 after running phenix refinement with twin law -h, -k, l).
> My question: which twin fraction estimation is more reliable? is my data almost perfectly twined?
> I attached the graphs of L test, Britton analysis and twin estimation from phenix xtriage and part of log file from phenix refine here.
> Many thanks in advance.
> <p312_phenix_refine.png><P312_estimated twin_fraction.png><P312_Britton_plot.pdf><P312_Ltest.png>_______________________________________________
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