VMD-L Mailing List

From: Ravinder Abrol (abrol_at_wag.caltech.edu)
Date: Thu Apr 13 2006 - 14:07:31 CDT

Thanks John.
It works nicely. Now I know how to make the other plugins appear
in Extensions as well.
Ravi

On Thu, 13 Apr 2006, John Stone wrote:

>
> 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
> > ________________________________________________
>
> 

-- 
________________________________________________
 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
________________________________________________