> > As I remember r^-1/6 sum is used in all calculations, constraint lists,
> > etc. r^-1/6 average is used in (some of?) the menus and in the structure
> > viewer. I thought that was actually deliberate. The reason would be that
> > the r^-1/6 sum of a restraint to e.g. a methyl group would be clearly
> > shorter than the distance between any two individual protons. For a
> > methyl-methyl restraint it is even worse.
>
> why is that bad? what do you need the individual proton-proton
> distances for except for calculation the -1/6 sum? which is the
> quantitity that should be compared with the distance that is
> determined from the NOE.
The r^-1/6 sum assumes physical ambiguity, i.e. multiple contributions.
This is not always the case.
As an example, take a constraint between two non-stereospecifically
resolved prochiral methyl groups. Using a real structure, for 12LeuHdb* -
42ValHga*, the NOE sum is 1.850 and the NOE mean is 3.362. In this case
there is logical ambiguity and there really is only one contribution
between two methlys. Using an NOE sum here is misleading at best.
Also I might just want to do a seeminly simple thing and know an
approximation to a real distance. Say if comparing to a crystal structure.
Sure, we can have the default as NOE sum if that's what people are doing
most often. But Analysis should not be so restrictive and dictatorial to
assume that all people would only be interested in working in ARIA-space
at all times.
I think Igor's suggestion was a good one, and the two options will stay.
This also gives the opportunity to not be restricted to the NOE. There are
other kinds of distance relationships that are used in NMR, thinking
initially about solid state and HADDOCK-like constraints.
T.
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Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
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