Re: AMBER: Alignment tensor for Sander RDCs

From: David A. Case <>
Date: Fri, 2 Apr 2004 09:46:24 -0800

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            |
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Received on Fri Apr 02 2004 - 18:53:00 PST
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