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CCP4BB  June 2012

CCP4BB June 2012

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Subject:

Re: Death of Rmerge

From:

Leonid Sazanov <[log in to unmask]>

Reply-To:

Leonid Sazanov <[log in to unmask]>

Date:

Fri, 1 Jun 2012 20:45:02 +0100

Content-Type:

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Hi, as we reported in our paper in Table 1 (actually Supplementary Table 1), at the end of Scaling 2, completeness in the outer shell after aniso truncation was 54%. Whilst 96% completeness and I/sigma 0.8 is of course before aniso truncation. I/sigma after truncation would be higher, but it is not clear to me how to calculate that number exactly, since aniso truncation is done post data scaling. One could of course re-process images in Mosflm with applied aniso limits and then scale data, but that would not be exactly the same.

From many trials with strongly anisotropic data we found that for map calculation and refinement it is best to cut data anisotropically where F/sigma is approaching 2.5-2.7 in each direction, as long as completeness in the outer shell remains above 50% or so. Usually the highest useful resolution is also where the correlation coefficient between random half-data-set estimates of intensities in SCALA falls below about 0.5 (as advocated by Phil Evans, I think). CC seems to be less affected by anisotropy (in this case it reached 0.5 at 3.0 angstrom, which was another criterion to cut data at 3.0).

HTH.
Leo



>>>>>>>>>>>>
I am little curious about the anisotropically truncated data for 3RKO:

    Percent Possible(All)  	96.0
Mean I Over Sigma(Observed) 	0.8

In the supplementary table of the nature paper it was made clear that this 
3.16-3.0A, I/sigmaI=0.8 and Rmerge=1.216 shell was the outer shell of the 
anisotropically truncated data. The authors did also report the 
isotropically truncated resolution to be 3.2A with I/sigmaI=1.3 and 
Rmerge=73%.

The authors also stated in the main text that

"the best native data set was anisotropically scaled and truncated to 3.4 Å, 
3.0 Å and 3.0 Å resolution, where the F/σ ratio drops to ~2.6–2.8 along 
the a*, b* and c* axes, respectively (scaling 2, Supplementary Table 1)"

My question is, is the I/sigmaI=0.8 a consequence of many reflections with 
nearly 0 I/sigmaI being included in the calculation? Then what does the 96% 
completeness mean? Does it mean that 96% completeness in the spherical shell 
of 3.16-3.0A was achieved, by including a great number of I=0 reflections?


Zhijie

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