perhaps a second table in which certain statistics (Rsym, I/sigma,
CC0.5) are given as a function of, say, 10 bins of resolution would be
more useful than the same table twice at different resolution cutoffs.
then editors, reviewers and ultimately readers can decide for
themselves what resolution to call your structure.
completeness and multiplicity could be included also in this table if
they vary significantly with resolution (i.e. data in corners of
square detectors)
Quoting Robbie Joosten:
> 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/
>>
>> ^\
>> /` /^. / /\
>> / / /`/ / . /`
>> / / ' '
>> '
>
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: [log in to unmask]
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