Dear CCP4ers,
I'm not convinced, that thin shells are sufficient: I think, in
principle, one should omit thick shells (greater than the diameter of
the G-function of the molecule/assembly that is used to describe NCS-
interactions in reciprocal space), and use the inner thin layer of
these thick shells, because only those should be completely
independent of any working set reflections. But this would be too
"expensive" given the low number of observed reflections that one
usually has ...
However, if you don't apply NCS restraints/constraints, there is no
need for any such precautions.
Best regards,
Dirk.
Am 07.02.2008 um 16:35 schrieb Doug Ohlendorf:
It is important when using NCS that the Rfree reflections be
selected is
distributed thin resolution shells. That way application of NCS
should not
mix Rwork and Rfree sets. Normal random selection or Rfree + NCS
(especially 4x or higher) will drive Rfree down unfairly.
Doug Ohlendorf
-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Eleanor Dodson
Sent: Tuesday, February 05, 2008 3:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] an over refined structure
I agree that the difference in Rwork to Rfree is quite acceptable at
your resolution. You cannot/ should not use Rfactors as a criteria for
structure correctness.
As Ian points out - choosing a different Rfree set of reflections can
change Rfree a good deal.
certain NCS operators can relate reflections exactly making it hard to
get a truly independent Free R set, and there are other reasons to
make
it a blunt edged tool.
The map is the best validator - are there blobs still not fitted?
(maybe
side chains you have placed wrongly..) Are there many positive or
negative peaks in the difference map? How well does the NCS match
the 2
molecules?
etc etc.
Eleanor
George M. Sheldrick wrote:
Dear Sun,
If we take Ian's formula for the ratio of R(free) to R(work) from his
paper Acta D56 (2000) 442-450 and make some reasonable
approximations,
we can reformulate it as:
R(free)/R(work) = sqrt[(1+Q)/(1-Q)] with Q = 0.025pd^3(1-s)
where s is the fractional solvent content, d is the resolution, p is
the effective number of parameters refined per atom after allowing
for
the restraints applied, d^3 means d cubed and sqrt means square root.
The difficult number to estimate is p. It would be 4 for an isotropic
refinement without any restraints. I guess that p=1.5 might be an
appropriate value for a typical protein refinement (giving an R-
factor
ratio of about 1.4 for s=0.6 and d=2.8). In that case, your R-factor
ratio of 0.277/0.215 = 1.29 is well within the allowed range!
However it should be added that this formula is almost a
self-fulfilling prophesy. If we relax the geometric restraints we
increase p, which then leads to a larger 'allowed' R-factor ratio!
Best wishes, 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. +49-551-39-2582
*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [EMAIL PROTECTED]
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