From: Leonardo Trabuco (
Date: Thu Apr 28 2011 - 11:12:06 CDT

Hi Sara,

As Axel said, there isn't a command-line equivalent to the GUI for the
dowser plugin (sorry!!).

The easiest way to get what you want in the short term is for you to
write a modified version of the function
::Dowser::GUI::processInputFile from dowser_gui.tcl. It basically
calls a handful of functions defined in dowser.tcl sequentially. You'd
have something like:

package require dowser
proc modifed_version_processInputFile { } {
  # define variables as in resetGUI function
  # make sure there's no call to tk_messageBox

Please let me know how it goes and if you need further help with this.


On Wed, Apr 27, 2011 at 10:34 PM, Axel Kohlmeyer <> wrote:
> hi sara,
> On Wed, Apr 27, 2011 at 3:49 PM, Sara Nichols <> wrote:
>> Is there a way to run a plugin via a script?
> for many plugins there is.
>> I want to run the first part of the dowser plugin (the part that processes
>> the input structure) via the command line with out opening VMD.
> well, you will have to launch VMD in text mode, i.e. vmd -dispdev text
> scripted VMD plugins almost always make use of some VMD extension
> to the tcl interpreter.
> now, dowser is one of the (few?) plugins, where there is no direct
> command line equivalent of the GUI.
>> If not, is the source available to get a better understanding of the
>> workflow?
> the plugin _is_ the source. it is written in Tcl/Tk. there are two files
> dowser.tcl and dowser_gui.tcl.
> you may want to search the mailing list archive, because i remember
> a similar question that was asked rather recently.
> cheers,
>    axel.
>> Thanks for any help in advance,
>> Sara
>> --
>> ==
>> Sara E. Nichols, PhD
>> UCSD Pharmacology Postdoc
>> McCammon Research Group
>> ACS COMP Div. Assistant Treasurer
>> m: 619.940.6383
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.

Leonardo Trabuco, Postdoctoral fellow (Russell group)
CellNetworks, University of Heidelberg, Germany