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 <[email protected]> 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: [email protected] > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: CCP4 bulletin board [[email protected]] on behalf of Douglas > Theobald [[email protected]] > Sent: Friday, December 07, 2012 1:05 AM > To: [email protected] > 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 > > [email protected] > http://theobald.brandeis.edu/ > > ^\ > /` /^. / /\ > / / /`/ / . /` > / / ' ' > ' >
