For the sake of a thought experiment we can assume the refinement
is implemented with infinite-precision arithmetic. And for actually
...
terms in the 2n'd derivative matrix are ignored?). Two ncs-related atoms
can move in agreement with the ncs-restraint without penalty from the
near-infinite n
chains when the ASU is made. At this point I
> guess the copies can bump and so apply a force on each other but that is a
> local, and likely to be perturbing, force.
>
> best wishes
> Martyn
>
> Martyn Symmons
> Cambridge
>
>
>
> --- On Thu, 23/9/10, Ian Tick
Ed Pozharski wrote:
On Wed, 2010-09-22 at 22:46 +0200, Gerard DVD Kleywegt wrote:
...constraints are just a special case of restraints in the limit
of infinite weights
If you impose "infinitely strong" NCS
restraints,
But "in the limit" means that the restrained refinement can be made to
ap
this point I guess the copies can
bump and so apply a force on each other but that is a local, and likely to be
perturbing, force.
best wishes
Martyn
Martyn Symmons
Cambridge
--- On Thu, 23/9/10, Ian Tickle wrote:
> From: Ian Tickle
> Subject: Re: [ccp4bb] Effect of NCS on estim
On Wed, 2010-09-22 at 22:46 +0200, Gerard DVD Kleywegt wrote:
> > ...constraints are just a special case of restraints in the limit
> > of infinite weights
> If you impose "infinitely strong" NCS
> restraints,
But "in the limit" means that the restrained refinement can be made to
approach the re
Hi Gerard & Pavel
Isn't this the proviso I was referring to, that one cannot in practice
use an infinite weight because of rounding errors in the target
function. The weight just has to be 'big enough' such that the
restraint residual becomes sufficiently small that it's no longer
significant.
I
I agree with Gerard. Example: it's unlikely to achieve a result of
rigid-body refinement (when you refine six rotation/translation
parameters) by replacing it with refining individual coordinates using
infinitely large weights for restraints.
Pavel.
On 9/22/10 1:46 PM, Gerard DVD Kleywegt wr
Hi Ian,
First, constraints are just a special case of restraints in the limit
of infinite weights, in fact one way of getting constraints is simply
to use restraints with very large weights (though not too large that
you get rounding problems). These 'pseudo-constraints' will be
indistinguishabl
Dear Ian,
many thanks for your explanations - they've changed my view! I was
always a bit puzzled by the supposedly contradictory transition between
restraints and constraints with increasing weight, which has been
clarified by their effect on the number of parameters, and not on the
number
Dirk,
Apologies, my last e-mail was incomplete, I meant to say that there
was one thing I should have added:
>From Table 2 in the paper the expected Rfree/Rwork ratio comes out as:
< Rfree / Rwork > = sqrt( (f+m') / (f-m') ) = sqrt( (x+1) / (x-1) )
where x = f / m' = no of X-ray data /
Dirk,
One thing I should have added:
The expected Rfree/Rwork ratio comes out as:
wrote:
> Hi Dirk
>
> First, constraints are just a special case of restraints in the limit
> of infinite weights, in fact one way of getting constraints is simply
> to use restraints with very large weights (thoug
Hi Dirk
First, constraints are just a special case of restraints in the limit
of infinite weights, in fact one way of getting constraints is simply
to use restraints with very large weights (though not too large that
you get rounding problems). These 'pseudo-constraints' will be
indistinguishable
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 p
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
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 an
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