AMBER Archive (2004)

Subject: Re: AMBER: Alignment tensor for Sander RDCs

From: David A. Case (
Date: Fri Apr 02 2004 - 11:46:24 CST

On Fri, Apr 02, 2004, tim wrote:
> How does Sander calculate the alignment tensor for it's RDCs
> calculations? I ask because it seems to be somewhat different from the
> way PALES does...

The two calculations are completely different, in both input and output.

PALES estimates the alignment tensor from the structure, based on a physical
model for how the alignment is taking place. It does not need any RDC's
as input.

Sander fits the alignment tensor to the observed RDC's, by minimizing a
chi-square function (or similar error function). It does not require any
physical model for what is causing the alignment in the first place.

...hope this helps....dac


================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to