AMBER Archive (2003)

Subject: AMBER: curves nomenclature

From: Sue Heavner (sheavner_at_hsc.wvu.edu)
Date: Wed Jul 16 2003 - 14:34:13 CDT

Fellow Amber Users:
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. In all other cases, Curves seems to use designations pertaining to atom name i.e. C1' and not pertaining to position number. Thanks for any help. Sue

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