Dear Eiso,
In answer to your questions:
The problem with the r^-1/6 sum is that it does not correspond to any
distance. It is what the distance would have been if there had been only
one proton. That is the correct value to compare to the distance
constraint (which also does not correspond to any real distance in cases
with multiple assignment). But if I want to get an idea about what is
going on, it is nice to have at least the option of finding out how far
away things are in reality. Tim had an example with prochiral methyl
groups: r^-1/6 average 4.2A, r^-1/6 sum 1.8A. Now, if those methyl groups
were really 1.8A apart they would be in van der Waals contact. They are
not.
By all means use r^-1/6 sum as the default, I would say, but leave r^-1/6
average as an alternative for tables and display. What you use for your
dynamics calculations is another matter.
Yours,
Rasmus
---------------------------------------------------------------------------
Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Thu, 9 Nov 2006, eiso wrote:
> Rasmus Fogh wrote:
> > Dear All,
> >
> > 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.
>
> >
> > Consider a methyl-methyl restraint. The distance limit is 5A, the r^-1/6
> > average is ca. 5.5A, which would also be the approximate distance between
> > the centroids, the shortest proton-proton distance is 5.2A and the r^-1/6
> > sum comes out as 4.2A (I have not done the math, these are guesses). How
> > should this situation be represented in an overview table?
> >
>
> why do you want to look at individual proton distances of a methyl group?
> there's no point. use the r^-1/6 sum of the protons that make up the resonance.
>
> Eiso
>
>
> > Any comments?
> >
> > Rasmus
> >
> > ---------------------------------------------------------------------------
> > Dr. Rasmus H. Fogh Email: [log in to unmask]
> > Dept. of Biochemistry, University of Cambridge,
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
> >
> > On Thu, 9 Nov 2006, Brian Smith wrote:
> >
> >
> >>On Thu, 9 Nov 2006, Eiso AB wrote:
> >>
> >>
> >>>Is there any sensible use for the r^-1/6 average? (I don't think so)
> >>>
> >>>And this is already more then ten years ago....
> >>>So please get rid of it.
> >>
> >>I'm happy to second that suggestion.
> >>
> >>--
> >>Dr. Brian O. Smith ---------------------- B Smith at bio gla ac uk
> >> Division of Biochemistry & Molecular Biology,
> >> Institute Biomedical & Life Sciences,
> >>Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
> >>Tel: 0141 330 5167/6459/3089 Fax: 0141 330 8640
> >>
> >
> >
>
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