AMBER Archive (2004)

Subject: Re: AMBER: Alignment tensor for Sander RDCs

From: David A. Case (case_at_scripps.edu)
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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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