Nucleic acid notation within Toolchest

From: Rebecca Ann Perlow <>
Date: Mon 19 Feb 2001 13:59:59 -0800

Dear AMBER users,
I noticed that the MD Toolchest analysis program outputs the helix tosion
angles of the "left hand" strand differently from those of the "right hand
strand. The definition, ex., of alpha for the first strand is different than
that for the second. After reading the original paper by the Beveridge
group, I understand the rationale for this, but was wondering whether this
poses a problem for directly comparing the results of MD simulations with
structural information from NMR and crystallographic studies. Would it be
better to display these angles using the conventional definitions, in order
to make the results easier to compare with output from other analyses?
Does anyone have any comments on this issue?
Thanks in advance.
-Rebecca Perlow

Rebecca Ann Perlow
New York University
Department of Biology
100 Washington Square East
New York, New York 10003
tel: (212)998-8228

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Received on Mon Feb 19 2001 - 13:59:59 PST
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