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
> <[log in to unmask]> 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
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Germany
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