[phenixbb] Reliable twinning fraction estimation
Xiao Lei
xiaoleiusc at gmail.com
Wed Dec 10 14:13:13 PST 2014
Hi Tom,
Thank you very much for your advice, I just tried Xtriage analysis of the
data scaled as P1, the Wilson moment is 1.554, this result shows that the
dataset is nearly perfect twinned.
I paste the part of the log file of xtriage below.
Analyses of the absences table indicates a number of likely space group
candidates, which are listed below. For each space group, the number of
absent violations are listed under the '+++' column. The number of present
violations (weak reflections) are listed under ''. The last column is a
likelihood based score for the particular space group. Note that
enantiomorphic spacegroups will have equal scores. Also, if absences were
removed while processing the data, they will be regarded as missing
information, rather then as enforcing that absence in the space group
choices.

 space group  n absent  <Z>_absent  <Z/sigZ>_absent  +++    score


 P 1  0  0.00  0.00  0  0 
0.000e+00 

Wilson ratio and moments
Acentric reflections
<I^2>/<I>^2 :1.554 (untwinned: 2.000; perfect twin 1.500)
<F>^2/<F^2> :0.878 (untwinned: 0.785; perfect twin 0.885)
<E^2  1> :0.557 (untwinned: 0.736; perfect twin 0.541)
Xiao
On Wed, Dec 10, 2014 at 1:24 PM, Terwilliger, Thomas Charles <
terwilliger at lanl.gov> wrote:
> Hi Xiao,
>
> 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 lowersymmetry space groups (you can always get
> the Wilson moments in P1 and that will often be a good indicator).
>
> All the best,
> Tom T
>
> On Dec 10, 2014, at 1:37 PM, Xiao Lei wrote:
>
> > Dear All,
> >
> > I have a xray dataset of a proteinDNA 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 Ltest 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.
> >
> > Xiao
> > <p312_phenix_refine.png><P312_estimated
> twin_fraction.png><P312_Britton_plot.pdf><P312_Ltest.png>_______________________________________________
> > phenixbb mailing list
> > phenixbb at phenixonline.org
> > http://phenixonline.org/mailman/listinfo/phenixbb
>
>
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