 |
 |
Hi Douglas, Using two Table Is is a good way to show the difference between the two cut-offs, but I assume you will only discuss one of the models in your paper. IMO you only need to deposit the high res model, so there should be no problems with resolution conflicts in the PDB file. The annotators will probably help you if there is a problem with Rmerge > 1.00. As for the title of your paper: nobody forces you to put a resolution in it if it causes to much of a stir. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > Boaz Shaanan > Sent: Friday, December 07, 2012 12:21 > To: [log in to unmask] > Subject: Re: [ccp4bb] refining against weak data and Table I stats > > 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: [log in to unmask] > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: CCP4 bulletin board [[log in to unmask]] on behalf of Douglas > Theobald [[log in to unmask]] > Sent: Friday, December 07, 2012 1:05 AM > To: [log in to unmask] > 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 > > [log in to unmask] > http://theobald.brandeis.edu/ > > ^\ > /` /^. / /\ > / / /`/ / . /` > / / ' ' > '