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

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu