VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 13 2006 - 10:00:51 CDT

Ravi,
  In order to have VMD find rmsdtt automatically, it either needs to be
put into the vmd/plugins/noarch/tcl/ directory, or you need to put it in
your own local directory, and then use a command like this added to your
.vmdrc to tell VMD to use it:
  lappend auto_path /my/favorite/directory
  vmd_install_extension rmsdtt rmsdtt_tk_cb "Analysis/RMSD Trajectory Tool"

The final version of VMD 1.8.4 includes Luis' rmsdtt plugin already, so you
won't have to do this next time... :)

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 13, 2006 at 04:32:50AM -0700, Ravinder Abrol wrote:
>
> Thanks John.
> I have VMD 1.8.4b7 for Windows and I didn't find rmsdtt in the extensions.
> But I downloaded it and put it in the plugins folder .../plugins/WIN32. I
> still cannot find rmsdtt in extensions. The only way I can run rmsdtt is
> by using the TkConsole to go to the plugins folder where I saved the
> rmsdtt plugin and typing rmsdtt.
> Is there an easier way and how do I make it appear in the Extensions?
> Thanks,
> Ravi
>
> --------------------------------------
> On Mon, 10 Apr 2006, John Stone wrote:
>
> >
> > You could use RMS fitting to align all of the frames with the first one
> > to eliminate the drift. The "rmsdtt" plugin by Luis Gracia will do this
> > for you quite easily, or you can use a Tcl script to do this yourself with
> > the 'measure fit' command etc.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Apr 07, 2006 at 07:26:52PM -0700, Ravinder Abrol wrote:
> > > Hi All,
> > > I have a long trajectory in which the protein shows a slow but visible
> > > drift. I want to save its movie without the drift by using move on each
> > > frame to align it to the first frame. How can I do this?
> > > Thanks,
> > > Ravi
> > >
> > > --
> > > ________________________________________________
> > >
> > > Ravinder Abrol
> > > 139-74, Beckman Institute
> > > Division of Chemistry and Chemical Engineering
> > > Caltech, Pasadena, CA 91125
> > > Phone: 1.626.395.8143
> > > Fax: 1.626.585.0917
> > > Email: abrol_at_wag.caltech.edu
> > > ________________________________________________
> > >
> >
> >
>
> --
> ________________________________________________
>
> Ravinder Abrol
> 139-74, Beckman Institute
> Division of Chemistry and Chemical Engineering
> Caltech, Pasadena, CA 91125
> Phone: 1.626.395.8143
> Fax: 1.626.585.0917
> Email: abrol_at_wag.caltech.edu
> ________________________________________________ 

-- 
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