Also there is nice program - Bio3D from Barry Grant,
currently at the University of Michigan. It displays various
maps and does pca analysis and produces pictures, etc.
Piotr
On Tue, 2012-05-22 at 07:28, Josh Berryman wrote:
> 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 IED uses Numeric which has been superseded by numpy since.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.
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue May 22 2012 - 10:30:10 PDT
