PCAsuite is a c program which can be used to make eigenvector movies in
amber format:
http://mmb.pcb.ub.es/software/pcasuite/
Just my 2 rapidly-devaluing-eurocents. I'm not aware of any actual licence
for the code, gpl or otherwise, but I have an old version; maybe the
finished one is gpl or something.
Josh
On 22 May 2012 16:16, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
> On Tue, 22 May 2012 06:59:35 -0400
> "David A. Case" <case.biomaps.rutgers.edu> wrote:
>
> > On Tue, May 22, 2012, steinbrt.rci.rutgers.edu 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 IED uses Numeric which has been superseded by numpy since.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
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16740.html
>
> Hannes.
> --
> Scanned by iCritical.
>
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Received on Tue May 22 2012 - 07:30:04 PDT
