VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Jan 07 2008 - 12:08:27 CST

Hi Luis:
I would be happy to try itrajcomp plugin.
Thanks
francesco

--- Luis Gracia <lug2002_at_med.cornell.edu> wrote:

> Hi Francesco and the vmd community,
>
> Thanks for pointing out the broken R link. I just updated the the
> webpage. CRAN is the Comprehensive R Archive Network, and I type the
> wrong ULR. Well, I am glad it ended up in a humanitarian org, and not in
> other place in internet.
>
> The xcluster from standord has nothing to do Xcluster from Shroedinger
> (I know expensive, but we are fortunate to have it here).
>
> It is a pitty that NMRcluster cannot be found in internet anymore. You
> might want to contant the authors, the paper is still easy to find in
> pubmed.
>
> As of using ptraj, as suggested by Carlos Simmerling, it is an option. I
> have never used it for clustering and I don't remember it has an option,
> but certainly it can help you get the rmsd. You will probably need
> additional software for that. I am trying to get the paper he points
> out, but something is wrong the the web right now.
>
> My plugin won't help you do the clustering, it is only useful for
> visualizing the results: nice coloring of clusters and options to
> show/hide whole clusters or individual structures. If you need the
> itrajcomp plugin to calculate the rmsd let me know, I have no problem
> sharing it.
>
> Best,
>
> Luis Gracia
>
> Francesco Pietra said the following on 01/07/2008 05:35 AM:
> > 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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