AMBER Archive (2002)

Subject: Re: residue cross-correlation

From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Tue Nov 12 2002 - 04:57:10 CST

Le Vendredi 8 Novembre 2002 16:00, Bimo Ario Tejo a écrit :
> Dear Amber users,
>
> I have to ask this question again because nobody helps me to answer it
> until now. Does anyone know how to analyse residue cross-correlation over a
> trajectory in Amber? I *really* need this analysis tool. If Amber can't do,
> please tell me how to do it using another package.
>
> Any help would be really appreciated.
>
> Regards,
> Bimo

I don't know what you mean by cross correlation, but if it fits my point of
view, here is one way to do it :
Monitor the distances between these residues (or any relevant parameter to
you), and use xmgrace to do the correlation.
In XmGrace, (available at http://plasma-gate.weizmann.ac.il/Grace/), you can
load the two sets independently, and then do a correlation by going in :
Data -> Transformations -> Evaluate expression, and in the dialog box that
appear, write this :
assuming your data file is like x, y :
copy s0 to s2 (apply)
s2.x=s0.y (apply)
s2.y=s1.y (apply)

Like this, you'll have the cross correlation you need.

Stef 

-- 
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Teletchéa Stéphane - CNRS UMR 8601
Lab. de chimie et biochimie pharmacologiques et toxicologiques
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tel : (33) - 1 42 86 20 86 - fax : (33) - 1 42 86 83 87
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