It is internally consistent, though not necessarily correct
On 7 Dec 2012, at 16:23, Alan Cheung wrote: > Related to this, I've always wondered what CC1/2 values mean for low > resolution. Not being mathematically inclined, I'm sure this is a naive > question, but i'll ask anyway - what does CC1/2=100 (or 99.9) mean? Does it > mean the data is as good as it gets? > > Alan > > > > On 07/12/2012 17:15, Douglas Theobald wrote: >> Hi Boaz, >> >> I read the K&K paper as primarily a justification for including extremely >> weak data in refinement (and of course introducing a new single statistic >> that can judge data *and* model quality comparably). Using CC1/2 to gauge >> resolution seems like a good option, but I never got from the paper exactly >> how to do that. The resolution bin where CC1/2=0.5 seems natural, but in my >> (limited) experience that gives almost the same answer as I/sigI=2 (see also >> K&K fig 3). >> >> >> >> On Dec 7, 2012, at 6:21 AM, Boaz Shaanan <bshaa...@exchange.bgu.ac.il> wrote: >> >>> Hi, >>> >>> I'm sure Kay will have something to say about this but I think the idea of >>> the K & K paper was to introduce new (more objective) standards for >>> deciding on the resolution, so I don't see why another table is needed. >>> >>> Cheers, >>> >>> >>> >>> >>> Boaz >>> >>> >>> Boaz Shaanan, Ph.D. >>> Dept. of Life Sciences >>> Ben-Gurion University of the Negev >>> Beer-Sheva 84105 >>> Israel >>> >>> E-mail: bshaa...@bgu.ac.il >>> Phone: 972-8-647-2220 Skype: boaz.shaanan >>> Fax: 972-8-647-2992 or 972-8-646-1710 >>> >>> >>> >>> >>> >>> ________________________________________ >>> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Douglas >>> Theobald [dtheob...@brandeis.edu] >>> Sent: Friday, December 07, 2012 1:05 AM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] refining against weak data and Table I stats >>> >>> Hello all, >>> >>> I've followed with interest the discussions here about how we should be >>> refining against weak data, e.g. data with I/sigI << 2 (perhaps using all >>> bins that have a "significant" CC1/2 per Karplus and Diederichs 2012). >>> This all makes statistical sense to me, but now I am wondering how I should >>> report data and model stats in Table I. >>> >>> Here's what I've come up with: report two Table I's. For comparability to >>> legacy structure stats, report a "classic" Table I, where I call the >>> resolution whatever bin I/sigI=2. Use that as my "high res" bin, with high >>> res bin stats reported in parentheses after global stats. Then have >>> another Table (maybe Table I* in supplementary material?) where I report >>> stats for the whole dataset, including the weak data I used in refinement. >>> In both tables report CC1/2 and Rmeas. >>> >>> This way, I don't redefine the (mostly) conventional usage of "resolution", >>> my Table I can be compared to precedent, I report stats for all the data >>> and for the model against all data, and I take advantage of the information >>> in the weak data during refinement. >>> >>> Thoughts? >>> >>> Douglas >>> >>> >>> ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^` >>> Douglas L. Theobald >>> Assistant Professor >>> Department of Biochemistry >>> Brandeis University >>> Waltham, MA 02454-9110 >>> >>> dtheob...@brandeis.edu >>> http://theobald.brandeis.edu/ >>> >>> ^\ >>> /` /^. / /\ >>> / / /`/ / . /` >>> / / ' ' >>> ' >>> >> >> > > -- > Alan Cheung > Gene Center > Ludwig-Maximilians-University > Feodor-Lynen-Str. 25 > 81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76999 > E-mail: che...@lmb.uni-muenchen.de
