Re: [AMBER-Developers] Visualizing ptraj eigenvectors

From: Hannes Loeffler <>
Date: Tue, 22 May 2012 15:16:58 +0100

On Tue, 22 May 2012 06:59:35 -0400
"David A. Case" <> wrote:

> On Tue, May 22, 2012, wrote:
> > I am trying to compute PCA-eigenvectors from an MD trajectory and
> > would like to visualize them.
> >
> > So I do something like:
> >
> > {read and rmsfit trajectory}
> > matrix covar name m1 .CA
> > analyze matrix m1 vecs vecs.out
> > analyze modes displ file vecs.out out displ.out
> >
> > Now, if I'm not mistaken, displ.out will contain the coordinate
> > changes that I would like to visualize, but how do I load them into
> > e.g. VMD? I know the IED program from UCSD could show amber
> > vectors, but it's fickly to install and I wondered if there is a
> > more recent option to do that.
> Re-directing to Amber-developers: it would be great if difficulties
> with IED could be resolved, most likely by someone who wants the
> solution. There are some improvements beyond installation needed,
> mainly in having a nice interface to control the visual amplification
> of the modes. I'll see if an undergrad with python experience can
> look at this, but anyone else is free to jump in.

One problem is that VMD requires the exact Python version it was built
with. I believe John Stone has given up providing pre-built Python
packages with the binary releases of VMD. The other problem is that
IED uses Numeric which has been superseded by numpy since. There is a
partial port at

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Received on Tue May 22 2012 - 07:30:04 PDT
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