AMBER Archive (2003)

Subject: Re: AMBER: curves nomenclature

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 16 2003 - 17:29:01 CDT

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
speculation.)

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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