From: Per Larsson (
Date: Wed Nov 10 2021 - 02:07:52 CST

Thanks John for input.

The window manager is Gnome. Running

$ lspci -nnk | grep -i vga -A3

I get

Kernel driver in use: wmwgfx
Kernel modules: vmwgfx

This is a virtual server so it does not have a proper GPU - might that be the issue?

I can also add that running the glxgears software also results in transparent windows, but not e.g. xmgrace for plotting.


> 9 nov. 2021 kl. 22:36 skrev John Stone <>:
> Hi,
> What GPU and video drivers are you using? This could also be a but in
> the desktop compositing-based window manager -- what window manager are
> you using? Gnome? KDE? Something else, what version? I've heard of
> two other users encountering something that sounded like this on recent
> Ubuntu systems with unknown hardware/software configurations, but
> otherwise I've not heard of anything like this in recent times.
> It strikes me as a bug in your system software however.
> The warning from VMD about the "Composite" extension is only
> relevant to stereoscopic rendering. Today, most window managers
> use compositing and stereoscopic displays are extremely rare, so
> the current test versions of VMD 1.9.4 no longer emit this warning
> even though it's still an issue.
> Best,
> John Stone
> On Tue, Nov 09, 2021 at 09:33:47PM +0100, Per Larsson wrote:
>> Hi all,
>> I have installed VMD version 1.9.3 on a machine which runs RedHat linux. The machine is a virtual server which I access using Remote Desktop and the rdp-protocol.
>> The installation itself was ok and the program starts and runs, but the problem is that some of the windows, in particular the ???VMD Main??? window have semi-transparent drop-down menus (File, Molecule, Graphics etc???). I say semi-transparent, because the degree of transparency seems to be dependent on the background color. A black background gives almost no transparency, whereas opening the menus against a white background results in almost full transparency making it very hard to read the text.
>> Upon startup I get the message ???Detected X11 ???Composite??? extension: if incorrect display occurs try disabling this X server option. This seems relevant, but after some googling I have still not been able to identify where I need to look to disable this extension. I am also not sure if the fact that I am using Remote Desktop complicates things. I did reach out to our universities support, and they told me to try asking for help here first. I would appreciate any hints about what I could do to solve this issue.
>> Kind regards
>> /Per Larsson, Uppsala University.
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Phone: 217-244-3349