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Re: [ccp4bb] question about processing data |
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CCP4bb navigationCCP4bb <-- 2008 <-- March 2008 <-- 17 March 2008Subject: Re: question about processing data From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA Date: 2008-03-17 > Hi all, > > I have always been wondering... for a data set diffracting to say 2.15 > Angstrom but in the highest resolution shell (2.25-2.15) the > completeness is 74%, should I use merge all the data and call it a 2.15 > A dataset or I should cut the data set to say 2.25 A where the highest > resolution shell has better completeness (>85%)? What is an acceptable > completeness value for the highest resolution shell? > > Thank you. > > Best, > Melody Hi Melody, This reply is not aimed at you directly as this situation seems to have become systemic in the field. So thanks for bringing it up! We can have a long, and mostly aimless, discussion on what resolution you should claim for your data set but DON'T throw away good data to make the statistics look better. At high resolution the statistics are supposed to get worse! What matters is if the data still contain useful information. The fact that 26% of the data is missing does not normally mean that anything is wrong with the 74% that you did measure. Perhaps you used a square detector and didn't place it close enough to capture the full resolution, or perhaps your diffraction pattern is anisotropic. The only reason to throw out data is if they are too inaccurate for your purpose. When your data is used for phasing, especially anomalous phasing, there is reason to focus on data quality, but I see far too many native data sets that make poor use of the diffraction potential of the crystal. I thought this was due to people not properly collecting the data, but now it seems that people are simply throwing away good data because they don't like the statistics. So my advice; if your high resolution shell data has poor completeness then check why this happened. If you did not collect the data properly then let it be a lesson for the next data collection trip. If it resulted from some issue of the crystal then decide if the measured data is messed up as well. If not then use all the data you trust, which means there is useful signal (I/SigI >1.5 or >2.0 depending who you talk to) and no problems leading to systematic errors or outliers. Bart ============================================================================== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================== CCP4bb navigationCCP4bb <-- 2008 <-- March 2008 <-- 17 March 2008 |
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