Agreed - but it wasn't entirely clear from the original question that
this was the purpose of the calculation. Assuming that is the case then
it surely behoves subscribers as far as possible to ask the right
questions, or at least explain their reasons for needing to perform the
calculation: it should not be assumed that others will understand what
you meant to say, as opposed to what you did say!
If restraints are to be included then a rough estimate is to say that
Nrestraints = Nparameters; a more precise estimate that I use is
Nrestraints = 0.96 Nparameters, so as you say you need to add that to
the reflection count. The rationale for this is that if 2 or more
restraints have the same or nearly the same effect, i.e. they are not
independent, then they should be counted as only 1 restraint, and if
there are more restraints than parameters (i.e. more equations than
unknowns) then they cannot all be independent, so Nparameters is the
maximum possible value of Nrestraints, counting only independent
restraints.
In that situation the model would be completely defined by the
restraints (and there would be no need for X-ray data!). In reality the
parameters of the model are undefined to the extent that the molecules
can freely translate & rotate (in general 6 params per molecule, or 3
for single atoms such as waters), and also for a protein the main-chain
phi & psi angles (and sometimes side-chain chi angles) are undefined.
So Nrestraints turns out to be slightly < Nparameters, in practice I've
found that 0.96 is a reasonable estimate. This is much easier than
trying to count individual bond length, angle, planar, torsion, B factor
(etc.) restraints.
Cheers
-- Ian
> -----Original Message-----
> From: Artem Evdokimov [mailto:[log in to unmask]]
> Sent: 29 August 2008 13:47
> To: Ian Tickle
> Subject: RE: [ccp4bb] Ratio of Number of Reflections to
> Number of restrained Parameters
>
> Angle/bond/planarity restraints (because they are
> experimentally determined
> from prior data) should count as observations.
>
> Artem
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On
> Behalf Of Ian
> Tickle
> Sent: Thursday, August 28, 2008 9:16 PM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Ratio of Number of Reflections to
> Number of restrained
> Parameters
>
> Hi Rajan
>
> You don't really need a program: e.g. if there are N non-H atoms
> refined, then there are 4N params (isotropic B) or 9N
> (aniso). TLS adds
> 19 params per group to the isotropic count. You count unique
> reflections.
>
> -- Ian
>
> > -----Original Message-----
> > From: [log in to unmask]
> > [mailto:[log in to unmask]] On Behalf Of Rajan Pillai
> > Sent: 29 August 2008 00:35
> > To: [log in to unmask]
> > Subject: Ratio of Number of Reflections to Number of
> > restrained Parameters
> >
> > Hi All,
> >
> > I was wondering if there is any program that calculates the
> > ratio of number of reflections (observation) to number of
> > restrained parameters. If not then how it can be calculated.
> > The number of reflections is it number of unique reflections
> > or number of the total reflections?
> >
> > Thanks,
> >
> > Rajan
> >
> >
>
>
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