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.
Dear All
one thing I remembered from what Gerard pointed out was the difference
in the XPLOR/CNS formalism between strict and restrained which is not a
continuum. Restrained was obviously when you had multiple copies and they were
restrained with a weight (which was like a force
I think you could answer this by performing the following thought experiment:
1. Refine the structure to convergence using strict NCS constraints.
2. Switch to using the equivalent 'infinite-in-the-limit weight'
restraints, keeping everything else as is continue refinement of the
output from
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
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
Dirk,
One thing I should have added:
The expected Rfree/Rwork ratio comes out as:
Rfree/Rwork sqrt((f+m')/(f-m'))
On Mon, Sep 20, 2010 at 12:22 PM, Ian Tickle ianj...@gmail.com wrote:
Hi Dirk
First, constraints are just a special case of restraints in the limit
of infinite weights, in fact
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 /
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
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
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 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
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
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