Discussions of I/sigma(I) or less-than cutoffs have been going on for at least
35 years. For example, see Acta Cryst. (1975) B31, 1507-1509. I was taught by
my elders (mainly Lyle Jensen) that less-than cutoffs came into use when
diffractometers replaced film methods for small molecule work, i.e., 1960s. To
compare new and old structures, they needed some criterion for the electronic
measurements that would correspond to the fog level on their films. People
settled on 2 sigma cutoffs (on I which mean 4 sigma on F), but subsequently,
the cutoffs got higher and higher, as people realized they could get lower and
lower R values by throwing away the weak reflections. I'm unaware of any
statistical justification for any cutoff. The approach I like the most is to
refine on Fsquared and use every reflection. Error estimates and weighting
schemes should take care of the noise.
Ron
On Thu, 3 Mar 2011, Ed Pozharski wrote:
On Thu, 2011-03-03 at 09:34 -0600, Jim Pflugrath wrote:
As mentioned there is no I/sigmaI rule. Also you need to specify (and
correctly calculate) <I/sigmaI> and not <I>/<sigmaI>.
A review of similar articles in the same journal will show what is
typical
for the journal. I think you will find that the <I/sigmaI> cutoff
varies.
This information can be used in your response to the reviewer as in,
"A
review of actual published articles in the Journal shows that 75% (60
out of
80) used an <I/sigmaI> cutoff of 2 for the resolution of the
diffraction
data used in refinement. We respectfully believe that our cutoff of 2
should be acceptable."
Jim,
Excellent point. Such statistics would be somewhat tedious to gather
though, does anyone know if I/sigma stats are available for the whole
PDB somewhere?
On your first point though - why is one better than the other? My
experimental observation is while the two differ significantly at low
resolution (what matters, of course, is I/sigma itself and not the
resolution per se), at high resolution where the cutoff is chosen they
are not that different. And since the cutoff value itself is rather
arbitrarily chosen, then why <I/sigma> is better than <I>/<sigma>?
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
