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: [email protected]
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 <[email protected]>
Reply-To: Christopher Bahl <[email protected]>
To: [email protected]
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
