Hi Ian,
Am 19.09.10 15:25, schrieb Ian Tickle:
Hi Florian,
Tight NCS restraints or NCS constraints (they are essentially the same
thing in effect if not in implementation) both reduce the effective
parameter count on a 1-for-1 basis.
Restraints should not be considered as being added to the pool of
X-ray observations in the calculation of the obs/param ratio, simply
because restraints and X-ray observations can in no way be regarded as
interchangeable (increasing the no of restraints by N is not
equivalent to increasing the no of reflections by N). This becomes
apparent when you try to compute the expected Rfree: the effective
contribution of the restraints has to be subtracted from the parameter
count, not added to the observation count.
I always understood the difference between constraints and restraints
such, that a constraint reduces the number of parameters by fixing
certain parameters, whereas restraints are target values for parameters
and as such can be counted as observations, similarly to the Fobs, which
are target values for the Fcalc (although with different weights). I
don't see what is wrong with this view. Do I misunderstand something?
Best regards,
Dirk.
The complication is that a 'weak' restraint is equivalent to less than
1 parameter (I call it the 'effective no of restraints': it can be
calculated from the chi-squared for the restraint). Obviously no
restraint is equivalent no parameter, so you can think of it as a
continuous sliding scale from no restraint (effective contribution to
be subtracted from parameter count = 0) through weak restraint (0<
contribution< 1) through tight restraint (count ~=1) to constraint
(count = 1).
Cheers
-- Ian
On Sat, Sep 18, 2010 at 9:23 PM, Florian Schmitzberger
<schmitzber...@crystal.harvard.edu> wrote:
Dear All,
I would have a question regarding the effect of non-crystallographic
symmetry (NCS) on the data:parameter ratio in refinement.
I am working with X-ray data to a maximum resolution of 4.1-4.4 Angstroem,
79 % solvent content, in P6222 space group; with 22 300 unique reflections
and expected 1132 amino acid residues in the asymmetric unit, proper 2-fold
rotational NCS (SAD phased and no high-resolution molecular replacement or
homology model available).
Assuming refinement of x,y,z, B and a polyalanine model (i.e. ca. 5700
atoms), this would equal an observation:parameter ratio of roughly 1:1. This
I think would be equivalent to a "normal" protein with 50 % solvent content,
diffracting to better than 3 Angstroem resolution (from the statistics I
could find, at that resolution a mean data:parameter ratio of ca. 0.9:1 can
be expected for refinement of x,y,z, and individual isotropic B; ignoring
bond angle/length geometrical restraints at the moment).
My question is how I could factor in the 2-fold rotational NCS for the
estimate of the observations, assuming tight NCS restraints (or even
constraint). It is normally assumed NCS reduces the noise by a factor of the
square root of the NCS order, but I would be more interested how much it
adds on the observation side (used as a restraint) or reduction of the
parameters (used as a constraint). I don't suppose it would be correct to
assume that the 2-fold NCS would half the number of parameters to refine
(assuming an NCS constraint)?
Regards,
Florian
-----------------------------------------------------------
Florian Schmitzberger
Biological Chemistry and Molecular Pharmacology
Harvard Medical School
250 Longwood Avenue, SGM 130
Boston, MA 02115, US
Tel: 001 617 432 5602
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
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