VMD-L Mailing List

From: Wen Li (liw_at_wadsworth.org)
Date: Thu Mar 31 2005 - 12:55:27 CST

Dear Dr. Stone,

Your help is really great! Adding "menu main on" brought rmsdtt in
Extensions now!

I will try to run the program!

Thanks you very much for your great help!

Best wishes,
Wen

On Thu, 31 Mar 2005, John Stone wrote:

>
> Wen,
> Make sure that the first line of your .vmdrc contains:
> menu main on
>
> If not, that's why you're not getting the main menu ;-)
>
> John
>
> On Thu, Mar 31, 2005 at 01:49:47PM -0500, Wen Li wrote:
> > Thanks you very much, Dr. Stone, for testing the procedure.
> >
> > Now either I have a .vmdrc in /home/liw, then I can't get main VMD window
> > which contains the extensions menu, or I remove .vmdrc, then Extensions
> > include Analysis, Data, Modeling, Simulation, Visualization and Tk Console.
> > No one of them include rmsdtt. Without .vmdrc, it seems like the program
> > does not take the rmsdtt plugin.
> >
> > Wen
> >
> > On Thu, 31 Mar 2005, John Stone wrote:
> >
> > >
> > > 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
> > >
>
> --
> 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
>