From: John Stone (
Date: Tue Sep 25 2012 - 16:40:49 CDT

  I thought I'd said this already previously in our earlier email exchanges,
but in order to use the SpaceNavigator with the 6-DOF "Tools" menu, you
must set the SpaceNavigator to "tracker" mode.

You can do this by pressing the mode button until the VMD console window says:
  Info) Spaceball set to tracker mode

Once it is set to tracker mode, you can create a new tool in the Tools
menu, set it to "grab", or "tug", etc. Once it is created, and you've
associated its position/buttons with the SpaceNavigator, then, when you
press the first button (the one that usually acts as a "reset view" button
when in normal mode), that will activate the grab/tug function on whatever
molecule you have loaded.

The behavior the SpaceNavigator depends on which mode its in. In the "normal"
mode, you are correct that the buttons are set to reset the view or change
the mode. But, in "tracker" mode, the first button activates the grabbing
or pulling behavior rather than resetting the view...

Hopefully you can get this working with very little difficulty. If you
still have problems, let me know.

  John Stone

On Mon, Sep 24, 2012 at 04:40:35PM -0700, Marcos Ackel wrote:
> Hi John,
> I'm afraid you read only the initial part of my last message... Still need your help!
> The explanation about the Grab and Tug tools made clear the differences, but I still don't know how to grab the molecule.
> Let's focus on the simplest case - using the Grab tool to re-orient the view. The VMD User's manual says (at page 53):
> "The Grab Tool mimics a pair of tweezers, and can be used to move molecules around on
> the screen without any keyboard or mouse commands. Pressing a button connects the 3d
> cursor to the nearest molecule. Then, moving or rotating the tracker will cause the molecule
> to move or rotate around on the screen."
> The problem is that using the Spacenavigator (or a Joystick), there is no button to press to connect the 3d cursor (the 2 buttons are associated to reset and mode).
> What should I do to "connect the 3d cursor to the nearest molecule" ?
> Thank you again,
> Marcos Ackel
> ________________________________
> From: John Stone
> Subject: Re: vmd-l: Using Tools (grab, tug, etc)
> Hi,
>   The "Grab" tool is used just to re-orient the molecule view, much like
> the mouse does when not doing IMD.  The Grab tool doesn't apply any
> forces on the molecule or otherwise change it.  The "Tug" tool is the
> one that you would use to apply forces to molecules and change their
> structure in a running IMD simulation.  If you don't have IMD running,
> it will have no effect.  If you have trouble picking structure when using
> the Tug tool with the SpaceNavigator, be sure to try using the
> "Assigned Rep" tab of the Tool menu.  This supercedes the mouse/force/atom
> type mode you're familiar with in the Mouse menu, and allows you to apply
> the forces on the atoms that are selected in any of the currently
> active graphical representations.  This way, you can just make a rep
> for the atoms you want to pull on, and you can tell the Tool menu to
> use the molecule rep, and then you don't have to pick individual atoms
> etc.  This is the preferred way to use any of the 6DOF input devices,
> whether using something like a SpaceNavigator, or even when using more
> sophisticated haptic devices like the Sensable Phantom or the Novint Falcon.
> Let me know if you need more help getting that working.
> Cheers,
>   John Stone

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349       Fax: 217-244-6078