Re: [AMBER] PCA analysis for side chain atoms and backbone atoms

From: Hannes Loeffler <>
Date: Wed, 26 Jan 2011 08:48:07 +0000

On Tue, 25 Jan 2011 20:31:03 +0100
Jorgen Simonsen <> wrote:

> Hi all,
> I would like to make a PCA using ptraj module with ambertools - I am
> not quite sure how the syntax is though.
> for the backbone selection I use the following syntax
> .N,CA,C
> is there any easier way to select side chains?
> for an analysis of the side chains will the following syntax make any
> sense?
> strip .N,CA,C
> matrix mwcovar name cc.matrix out cc.matrix
> analyze matrix cc.matrix out new.matrix

Just wondering. What exactly do you expect to see from a side chain
PCA? The side chains will mostly follow the backbone movements but
also have some independent movement of their own. The side chain modes
will be just somewhat weaker than their corresponding main chain
modes. Directions may also be slightly different.

Don't forget to also remove rotations and translations for the
selected atoms first.

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Received on Wed Jan 26 2011 - 01:00:03 PST
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