..and Rmerg seems to be meaningless for judging data quality? ----- Original Message ----- From: "Klaus Fütterer" <k.futte...@bham.ac.uk> To: "Andrea Edwards" <edwar...@stanford.edu> Sent: Thursday, June 13, 2013 8:49:13 AM Subject: Re: [ccp4bb] Concerns about statistics
Seems you are reviewing a paper at present. If this is indeed the case, it is fair to ask the authors to supply CC1/2 for their data or to rationalise their hi-res cut-off in light of that stats. For older papers, you can't obviously do that. As always in stats, there is no sharp line. My personal take is: I/sig > 1.5 in the high res shell with at least 85% completeness (at that cut-off). 15 years ago, I would have said I/sigI > 3 with at least 75% completeness, from which you can see how arbitrary the figures are. The merit of the Karplus & Diederichs paper is to demonstrate changes in the electron density map in relation to cut-offs. Klaus ======================================================================= Dr. Klaus Fütterer Deputy Head of School Undergraduate Admissions Room 717, Biosciences Tower School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: k.futte...@bham.ac.uk Birmingham, B15 2TT, UK W: http://tinyurl.com/futterer-lab ======================================================================= On 13 Jun 2013, at 16:44, Andrea Edwards wrote: In this case, the author should report a correlation coefficient along with the other standard statistics (I/sigI, Rmerg, Completeness, redundancy, ect.)? What about Rpim instead of Rmerg? and if Rpim is reported, what should be the criteria for resolution cutoff? Also, if this paper is the "new standard" how should we regard statistic reported in the literature? Or.. more importantly, how do we go about reviewing current literature that does not report this statistic? ----- Original Message ----- From: "Klaus Fütterer" < k.futte...@bham.ac.uk > To: "Andrea Edwards" < edwar...@stanford.edu > Sent: Thursday, June 13, 2013 8:27:33 AM Subject: Re: [ccp4bb] Concerns about statistics The commonly accepted answer is in Linking crystallographic model and data quality. Karplus PA, Diederichs K. Science . 2012 May 25;336(6084):1030-3. doi: 10.1126/science.1218231. Best wishes, Klaus Fütterer ======================================================================= Dr. Klaus Fütterer Deputy Head of School Undergraduate Admissions Room 717, Biosciences Tower School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: k.futte...@bham.ac.uk Birmingham, B15 2TT, UK W: http://tinyurl.com/futterer-lab ======================================================================= On 13 Jun 2013, at 16:15, Andrea Edwards wrote: Hello group, I have some rather (embarrassingly) basic questions to ask. Mainly.. when deciding the resolution limit, which statistics are the most important? I have always been taught that the highest resolution bin should be chosen with I/sig no less than 2.0, Rmerg no less than 40%, and %Completeness should be as high as possible. However, I am currently encountered with a set of statistics that are clearly outside this criteria. Is it acceptable cut off resolution using I/sig as low as 1.5 as long as the completeness is greater than 75%? Another way to put this.. if % completeness is the new criteria for choosing your resolution limit (instead of Rmerg or I/sig), then what %completeness is too low to be considered? Also, I am aware that Rmerg increases with redundancy, is it acceptable to report Rmerg (or Rsym) at 66% and 98% with redundancy at 3.8 and 2.4 for the highest resolution bin of these crystals? I appreciate any comments. -A
