VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 24 2011 - 15:45:31 CDT

Hi,
  Just tell VMD to update the atom selection every time it draws
a new frame. This is done within the "Trajectory" tab on the
graphical representations window. Select the "Update selection
every frame" button, and you should get the behavior you want.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 24, 2011 at 04:29:11PM -0400, pouyan farzinpor wrote:
> Great.
> In this way VMD shows the atoms that have this coordinate constraint in
> that "specific frame". But These atoms move during time and VMD keeps
> applying the constraint to "those atoms" not the specific region. I like
> to look at the interface of atoms and their substrate which is stationary.
> So Is it possible to apply a constraint to a region rather than the atoms?
> So when I play the render I can just see the interface.
> tnks alot
> pouyan
>
> On Fri, Jun 24, 2011 at 4:01 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Change your atom selection so it is something like
> "(some selection text) and ((z <= -3) or (z >= 4))"
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 24, 2011 at 03:53:03PM -0400, pouyan farzinpor wrote:
> > Hi,
> > Is there a way to tell VMD to hide atoms that are in specific
> region of
> > simulation box. For example I like to hide atoms that have
> z-coordinates
> > between -3 to 4.
> > tnks,
> > ~pouyan
> --
> 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 

-- 
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