VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Jan 07 2008 - 15:44:15 CST

John:
Now that the link has been redirected, a new fantastic world, R, is offered
(and I can install it as a Debian package). Yes, I am in contact with Luis; I
asked his rmsd plugin, to apply to the trajectories on vmd; then comes R
cluster.
francesco

--- John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Francesco,
> I'd suggest emailing Luis Gracia (his email is listed at the bottom of
> the URL I sent) and query him about obtaining the required packages.
>
> Cheers,
> John Stone
> johns_at_ks.uiuc.edu
>
> On Mon, Jan 07, 2008 at 02:35:30AM -0800, Francesco Pietra wrote:
> > Hi
> >
> > I have installed Luis Gracia's plugin with no problems in Debian Linux.
> Only
> > after that I recognize that other software is needed (actually anticipated
> by
> > John's email). Therefore, I would be very grateful receiving information
> about
> > the software needed from users familiar with this plugin. My problem is the
> > common problem of choosing the most representative snapshot, or family of
> > snapshots' from a long MD (for a protein complex, thus two molecules
> involved:
> > a problem for definying atoms for rmsd?)
> >
> > The NMRCLUSTER link does not work (as stated by Luis).
> >
> > The Xcluster link brings to very expensive commercial software, which does
> not
> > fit my current plans. Otherwise, a web search for "xcluster" brings to
> > affordable sources, like
> http://genetics.stanford.edu/~sherlock/cluster.html.
> > Which one is the correct xcluster?
> >
> > The R link brings to some humanitarian associations for Africa
> > (http://www.cran.org/). To applaud, though not fitting my present needs.
> >
> > Thanks for helping
> >
> > francesco
> >
> >
> > --- John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > > Hi,
> > > If you have the other required packages installed, you might try
> > > out the "Cluster" VMD plugin by Luis Gracia at Cornell:
> > >
> http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/cluster/
> > >
> > > So far as I'm aware, his plugin doesn't care what file format the
> trajectory
> > > came from.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Sun, Jan 06, 2008 at 02:27:19AM -0800, Francesco Pietra wrote:
> > > > Is it possible to carry out a cluster analysis with VMD from Amber
> > > mdcrd/prmtop
> > > > files? I have combined the various trajectories into a single mdcrd of
> ca
> > > 90
> > > > MB.
> > > >
> > > > Thanks
> > > > francesco pietra
> > > >
> > > >
> > > >
> > >
> >
>
____________________________________________________________________________________
> > > > Never miss a thing. Make Yahoo your home page.
> > > > http://www.yahoo.com/r/hs
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
> >
> >
> >
> >
>
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> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

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