VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 31 2005 - 12:40:51 CST

Wen,
  Can you double-check and make sure that there's not an 'rmsdtt' item
in your VMD extensions menu? I just tested here with the same procedure
you used, and it worked fine for me. If you don't get any error messages
when VMD starts up, then it should be showing up in the VMD extensions
menu somewhere.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 31, 2005 at 11:53:10AM -0500, Wen Li wrote:
> Dear Dr. Stone,
>
> Thanks for your quick response. I typed "package require rmsdtt" in vmd
> console, and it showed "1.0". I really appreciate your effort.
>
> Wen
>
> On Thu, 31 Mar 2005, John Stone wrote:
>
> >
> > Wen,
> > What do you see if you just type "package require rmsdtt" at the VMD
> > command prompt with that .vmdrc in place etc?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Mar 31, 2005 at 11:24:18AM -0500, Wen Li wrote:
> > > Hello Everyone,
> > >
> > > I am trying to add "RMSDTT" plugin for VMD by doing the following that
> > > results in loss of the VMD Main window without showing any error message
> > > and rmsdtt can not be found in Extensions. When I remove .vmdrc in
> > > /home/liw, the little window comes back. The following is what I did, and I
> > > was hoping that you could help me to find what is the problem, thanks!
> > >
> > > In as SGI:
> > >
> > > 1. mkdir
> > > /usr/local/spider/vmd/vmd-1.8.3/vmd-1.8.3b4/plugins/IRIX6_64/tcl/rmsdtt
> > >
> > > 2. in the rmsdtt dir, add file pkgIndex.tcl which contains:
> > > package ifneeded rmsdtt 1.0 [list source [file join $dir rmsdtt.tcl]]
> > >
> > > 3. in the rmsdtt dir, add downloaded file rmsdtt.tcl
> > >
> > > now, in
> > > /usr/local/spider/vmd/vmd-1.8.3/vmd-1.8.3b4/plugins/IRIX6_64/tcl/rmsdtt
> > >
> > > ls -lt shows
> > >
> > > -rwxr-xr-x 1 liw spider 535 Mar 31 10:20 pkgIndex.tcl*
> > > -rwxr-xr-x 1 liw spider 37378 Mar 31 10:13 rmsdtt.tcl*
> > >
> > > 4. in /home/liw, add .vmdrc
> > >
> > > lappend auto_path
> > > {/usr/local/spider/vmd/vmd-1.8.3/vmd-1.8.3b4/plugins/IRIX6_64/tcl/rmsdtt}
> > > if { [catch "package require rmsdtt" msg] } {
> > > puts "VMD RMSDTT package could not be loaded:\n$msg"
> > > } elseif { [catch {menu tk register "rmsdtt" rmsdtt} msg] } {
> > > puts "VMD RMSDTT could not be started:\n$msg"
> > > }
> > >
> > > Wen
> > >
> > > On Wed, 30 Mar 2005, John Stone wrote:
> > >
> > > >
> > > > Wen,
> > > > You might want to check out Luis Gracia's "RMSDTT" plugin for VMD,
> > > > as I believe it would do the alignment for you without much effort:
> > > > http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/index.html
> > > >
> > > > Once aligned, it is easy to write out the new coordinates using
> > > > 'mol writeXXX' and such.
> > > >
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Wed, Mar 30, 2005 at 04:21:26PM -0500, Wen Li wrote:
> > > > > Hello everyone,
> > > > >
> > > > > I hope that you could help me on the following question with either vmd
> > > > > or namd, or any program:
> > > > >
> > > > > I have an MD trajectory generated using AMBER, and I want to align
> > > > > snapshots of this trajectory to the coordinates of a reference structure.
> > > > > And then write out the coordinates of each aligned snapshots. Is this
> > > > > doable in VMD?
> > > > >
> > > > > Thanks,
> > > > > Wen
> > > >
> > > > --
> > > > 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
> > > >
> >
> > --
> > 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
> > 

-- 
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