So I guess a consequence of what you say is that since in cases where there
is no solvent the R values are often better than the precision of the actual
measurements (never true with macromolecular crystals involving solvent),
perhaps our real problem might be modelling solvent?
Alternatively/additionally, I wonder whether there also might be more
variability molecule-to-molecule in proteins, which we may not model well
either.
JPK
----- Original Message -----
From: "George M. Sheldrick" <[email protected]>
To: <[email protected]>
Sent: Thursday, October 28, 2010 4:05 AM
Subject: Re: [ccp4bb] Against Method (R)
It is instructive to look at what happens for small molecules where
there is often no solvent to worry about. They are often refined
using SHELXL, which does indeed print out the weighted R-value based
on intensities (wR2), the conventional unweighted R-value R1 (based
on F) and <sigmaI>/<I>, which it calls R(sigma). For well-behaved
crystals R1 is in the range 1-5% and R(merge) (based on intensities)
is in the range 3-9%. As you suggest, 0.5*R(sigma) could be regarded
as the lower attainable limit for R1 and this is indeed the case in
practice (the factor 0.5 approximately converts from I to F). Rpim
gives similar results to R(sigma), both attempt to measure the
precision of the MERGED data, which are what one is refining against.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Wed, 27 Oct 2010, Ed Pozharski wrote:
On Tue, 2010-10-26 at 21:16 +0100, Frank von Delft wrote:
> the errors in our measurements apparently have no
> bearing whatsoever on the errors in our models
This would mean there is no point trying to get better crystals, right?
Or am I also wrong to assume that the dataset with higher I/sigma in the
highest resolution shell will give me a better model?
On a related point - why is Rmerge considered to be the limiting value
for the R? Isn't Rmerge a poorly defined measure itself that
deteriorates at least in some circumstances (e.g. increased redundancy)?
Specifically, shouldn't "ideal" R approximate 0.5*<sigmaI>/<I>?
Cheers,
Ed.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
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