I'm not arguing to exclude high resolution reflections. I just think
that authors shouldn't claim to have a 1.3 angstrom structure if they
have 0.5 I/sigma and 90% Rsym in the high resolution shell.
-Chris
--
Christopher Bahl
Department of Biochemistry
Dartmouth Medical School
7200 Vail Building, Rm 408
Hanover, NH 03755-3844 USA
phone: (603) 650-1164
fax: (603) 650-1128
e-mail: [log in to unmask]
Engin Ozkan wrote:
> I have to agree with Ed Pozharski here. It has been shown that it can
> be valid to use I/sigma levels as low as ~1 for refinement (Ling,
> Read, et al, Biochemistry 1998; Delabarre, Brunger, Acta Cryst D,
> 2006). I am bothered more when I see I/sigma cutoffs of >4, where Rsym
> is <30% in the high resolution bin. It makes me think the authors
> might be hiding something, or stuck with the ancient notions of a
> not-to-be-exceeded, sacred Rsym value. Just because the reader might
> not read the statistics table does not mean legitimate data should be
> discarded during refinement.
>
> At the end, it is what inferences you make from your model that
> determine your claim of resolution limit (2.5 or 2.6 A!) to be much
> relevant. And I do agree with not making too much of the resolution
> limit, and presenting your statistics plainly and clearly in a table
> (probably not buried in supplementary table 3).
>
> Engin
>
> P.S. Oh well, the thread is hijacked now.
> -------- Original Message --------
> Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
> Date: Fri, 11 Dec 2009 16:58:07 -0500
> From: Christopher Bahl <[log in to unmask]>
> Reply-To: Christopher Bahl <[log in to unmask]>
> To: [log in to unmask]
>
>
>
> I think that when a model's resolution is clearly stated in a paper,
> many readers still assume the pre-maximum likelihood definition (i.e.
> high I/sigma, low Rsym in the high resolution shell). I've never seen a
> paper where the I/sigma was given in the abstract after stating a
> resolution. This can potentially mislead the average reader's
> perception of the "actual" resolution (if it exists). It is my opinion
> that authors should not proclaim a resolution for their structure if
> they aren't employing the same stringency that has classically guided
> the limits of resolution. Just leave that sentence out and let the
> statistics table do the talking.
>
> -Chris
>
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