From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 03 2015 - 10:00:26 CST

Hi,
  By chance I happened to see this news story about bugs in the
X11 compositing extensino (Compiz) being fixed recently, which sounds
a lot like the transparent VMD window issue reported here a few days ago:

http://tech.slashdot.org/story/15/03/03/1329212/nvidia-fixes-old-compiz-bug
http://news.softpedia.com/news/NVIDIA-Finds-and-Corrects-Old-Compiz-Bug-that-Caused-Windows-to-Go-Black-in-Ubuntu-474723.shtml

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 26, 2015 at 03:22:50PM -0600, John Stone wrote:
> 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/

-- 
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/