Thank you for your valuable suggestions..it really helped me a lot..
On Fri, Aug 15, 2014 at 8:38 PM, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: > I should make the estimation in Aimless more robust, and curve fitting > sounds like a good idea (but what function?). Outliers are a difficult > problem, but anyway I think you should look at the curve and not just the > number estimated. I would look at I/sigI as well, and anisotropy to decide > the resolution. However, the final cutoff should probably be based on > refinement, and also I don't think the exact cutoff makes a huge difference > (see http://www.ncbi.nlm.nih.gov/pubmed/23793146) > > Phil > > On 15 Aug 2014, at 15:54, Ed Pozharski <pozharsk...@gmail.com> wrote: > > > Same here. Ultimately, the KD test must be used in the end to finalize > the resolution (keeping in mind recently discussed issues of effective > resolution given data completeness). I just want to add that at least some > versions of aimless report overestimated resolution based on CC1/2 cutoff > when outliers are present (e.g. due to ice rings or salt diffraction). It > seems that aimless just picks the highest resolution bin where cc1/2> 0.5 > even if some lower resolution bins are below 0.5 as well. I have written a > script for more robust automated evaluation of these curves. In a > nutshell, it fits CC1/2 (d) curve to 1/(1+exp (-x)) and returns the > resolution at midpoint. I'm pretty sure that theoretical CC1/2 (d) > dependence is different from this, but it seems good enough for a rough > estimate. > > > > > > Sent on a Sprint Samsung Galaxy S® III > > > > > > > > > > > > > > > > > > -------- Original message -------- > > From: Roger Rowlett > > Date:08/14/2014 5:44 PM (GMT-05:00) > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] CC-half value ?? > > > > Exactly. Aimless will give you suggested resolution cutoffs based on CC > 1/2 in the log file. > > > > Roger Rowlett > > > > On Aug 14, 2014 5:04 PM, "conan仙人指路" <conan_...@hotmail.com> wrote: > > Hi Faisal, > > > > CC-half standard is valuable in evaluating the cut-off of highest > resolution. Sometimes even if I/sigI is close to 1 and completeness is not > as high, if CC-half is still significant, it may be worth incorporate the > extra high-res shell data and extend the resolution. Again, if only the > reliability and unbias are carefully confirmed, and the apparent > significant CC-half is not due to an artifact of some other factors like > ice ring etc. > > (Ref: Karplus PA and Diederichs K. 2012 Science 336, 1030-1033 > https://www.pubmed.com/pubmed/22628654) > > > > It has yet to be appreciated by most population of the crystallography > society, unlike the I/sigI, completeness, Rsym. In particular, Rsym has > gradually less a direct measurement of the data quality and or determinant > of resolution cut-off. > > > > Best, > > Conan > > > > Hongnan Cao, Ph.D. > > Department of Biochemistry > > Rice University > > > > Date: Fri, 15 Aug 2014 01:39:48 +0530 > > From: faisaltari...@gmail.com > > Subject: [ccp4bb] CC-half value ?? > > To: CCP4BB@JISCMAIL.AC.UK > > > > Dear all > > > > How CC-half value of a data set determines the maximum resolution limit > during data processing ?? Although much we know about the Rsym and I/Isig > values of the highest resolution shell while processing the data, what are > the parameters we need to check related to CC-half values ?? > > > > -- > > Regards > > > > Faisal > > School of Life Sciences > > JNU > > > -- Regards Faisal School of Life Sciences JNU
