From: Marcos Ackel (
Date: Mon Sep 24 2012 - 18:40:35 CDT

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)

  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.

  John Stone