Re: AMBER: curves nomenclature

From: David A. Case <>
Date: Wed, 16 Jul 2003 15:29:01 -0700

On Wed, Jul 16, 2003, Sue Heavner wrote:

> This is not a question that directly relates to Amber but I think there are
> enough people who use Curves for DNA structural analysis to pose the
> question. In the section of the Curves output that reports sugar pucker,
> angles corresponding to what is generally considered O4'-endo (72-108 deg)
> are referred to as O1'-endo.

The atom that is now (pretty correctly) called O4' used to be called O1' in
the older literature. I think what you are seeing just an anachronism.

(If some one else gives a better answer, please believe them! Mine is a


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Jul 16 2003 - 23:53:01 PDT
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