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.
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?
Any comments?
Rasmus
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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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