VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 20 2012 - 16:55:13 CDT

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
  vmd_at_ks.uiuc.edu

On Wed, Sep 19, 2012 at 06:14:01PM -0700, Marcos Ackel wrote:
> Hello John,
>
> (sorry - my previous message was bad formatted by Yahoo...)
>
> thanks for answering.
>
> I've already did this
> and the Spacenavigator is working in tracker mode - I can move the tool
> using the device. The problem is how to grab the molecule or part of it
> to apply forces on it.
>
> It seems that the Grab tool should work like
> tweezers (even when it's not in an Interactive MD?) but I couldn't find a
> way to grab an atom or the molecule with the tool.
>
> Also, using the Tug tool (when running an IMD) I couldn't grab any part of the molecule.
>
> I've
> tried to pick an atom (mouse/pick) but the tool seems to be completely
> disconnected from it. The (mouse/force/atom) works nicely, but only
> using the mouse.
>
> Marcos
>
> ________________________________
> From: John Stone <johns_at_ks.uiuc.edu>
> To: Marcos Ackel <mvackel_at_yahoo.com>
> Cc: VMD_List <vmd-l_at_ks.uiuc.edu>
> Sent: Tuesday, September 18, 2012 4:40 PM
> Subject: Re: vmd-l: Using Tools (grab, tug, etc)
>
>
> Hi,
>   To use a Spacenavigator with IMD, you need to set it to
> "tracker" mode, either by clicking the second button until it
> reports that it's in tracker mode, or by running this command:
>   spaceball mode tracker
>
> You'll also need to have lines like these in your .vmdsensors file:
> device SpaceballTracker     sballtracker://local/vmdlocal
> device SpaceballButtons     sballbuttons://local/vmdlocal
>
> Aside from these options that use the built-in Spacenavigator support
> in VMD, you could also run a VRPN server and register it with VMD in
> the same way that you would do so for a haptic device.
>
> Cheers,
>   John Stone
>   vmd_at_ks.uiuc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078