AMBER Archive (2006)

Subject: Re: AMBER: rms in principal component analysis

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 18 2006 - 10:30:51 CST

On Tue, Jan 17, 2006, Lydia wrote:
>
> Would someone please tell me that if the rms fitting is actually needed
> here in the pca analysis?

It *is* needed: pca analysis (in cartesian coordinates) is not much good for
analyzing overall rotations. If the structure is rotating, the average
structure becomes pretty meaningless. So, you want to remove all overall
translation and rotation before proceeding.

...good luck...dac

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