From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 26 2015 - 15:22:50 CST

Hi,
  It sounds like your computer has a buggy OpenGL driver, as it
should not be possible for the VMD graphics window to have a transparent
background. You didn't say what operating system or graphics hardware
you're using, but I strongly recommend that you look for an updated
graphics driver on your machine.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 20, 2015 at 01:11:46AM +0100, jing liang wrote:
> Hi,
> my VMD window which displays the molecules¬
> has a transparent background. That is, I can see
> all the applications behind that window.¬
> I had to choose a black wall paper for my linux
> desktop for that reason and also minimize any other
> ¬ application when using VMD.¬
> Have you encountered this issue?
> Thanks.

-- 
NIH Center 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/