Avogadro molecule display and image question

General Discussion
1

Hi,

I’m having a problem with Avogadro and I hope you can help me.

I am using Avogadro 0.9.4 on Linux - Ubuntu 9.04

The Molecule Display window (where the molecule appears) goes blank whenever Avogadro opens a menu or new panel that overlaps the molecular display. If I click in the molecule area it comes right back. This only seems to be a problem when I try to Export to an image file - instead of an image of the molecule, I get an image of the desktop or some other window.

Is this what you see happen, or is it just me? Do you know why it may be doing this, or if there is something I can do to fix it?

I’m new to Linux - could it have something to do with the graphics settings, or the version of some graphics library?

I would try to compile the latest release of Avogadro, but I’m not sure exactly how to do that. Instead I got the version in the Debichem repository as described here:
http://avogadro.openmolecules.net/wiki/Distribution_Packages

Thanks for your help,

Steve

Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

2

Steven Wathen wrote:

Hi,

I’m having a problem with Avogadro and I hope you can help me.

I am using Avogadro 0.9.4 on Linux - Ubuntu 9.04

The Molecule Display window (where the molecule appears) goes blank whenever Avogadro opens a menu or new panel that overlaps the molecular display. If I click in the molecule area it comes right back. This only seems to be a problem when I try to Export to an image file - instead of an image of the molecule, I get an image of the desktop or some other window.

Do you have any kind of compositing enabled? It might be desktop
effects, compiz or similar. The compositing desktop effects do no
interact well with OpenGL based applications such as Avogadro. You could
try disabling this if that is the case. I have been working with an
Ubuntu developer, and I think at least Avogadro 0.9.6 should now be
available from the DebiChem PPA (hope that means something to you).

Is this what you see happen, or is it just me? Do you know why it may be doing this, or if there is something I can do to fix it?

I use KDE 4.3 on a Gentoo amd64 Linux machine and don’t see that. We did
have some issues with getting snapshots, I am sure they were fixed for
0.9.6 but might be present in 0.9.4. It would be great if you could try
the updated version and let us know how well it works for you.

I’m new to Linux - could it have something to do with the graphics settings, or the version of some graphics library?

I would try to compile the latest release of Avogadro, but I’m not sure exactly how to do that. Instead I got the version in the Debichem repository as described here:
http://avogadro.openmolecules.net/wiki/Distribution_Packages

If you update then I think 0.9.6 should be in there now.

Thanks,

Marcus

3

Marcus,

Thanks for the help.

I did manage to upgrade to Avogadro 0.9.6

That by itself did not solve my problem, but disabling the visual effects did the trick. I had to set the Visual Effects to “None” and now the molecule window is stable and I can save image files without problems.

Thanks,

Steve

Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

From: Marcus D. Hanwell [marcus@cryos.org]
Sent: Saturday, August 01, 2009 11:26 AM
To: Steven Wathen
Cc: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Avogadro molecule display and image question

Steven Wathen wrote:

Hi,

I’m having a problem with Avogadro and I hope you can help me.

I am using Avogadro 0.9.4 on Linux - Ubuntu 9.04

The Molecule Display window (where the molecule appears) goes blank whenever Avogadro opens a menu or new panel that overlaps the molecular display. If I click in the molecule area it comes right back. This only seems to be a problem when I try to Export to an image file - instead of an image of the molecule, I get an image of the desktop or some other window.

Do you have any kind of compositing enabled? It might be desktop
effects, compiz or similar. The compositing desktop effects do no
interact well with OpenGL based applications such as Avogadro. You could
try disabling this if that is the case. I have been working with an
Ubuntu developer, and I think at least Avogadro 0.9.6 should now be
available from the DebiChem PPA (hope that means something to you).

Is this what you see happen, or is it just me? Do you know why it may be doing this, or if there is something I can do to fix it?

I use KDE 4.3 on a Gentoo amd64 Linux machine and don’t see that. We did
have some issues with getting snapshots, I am sure they were fixed for
0.9.6 but might be present in 0.9.4. It would be great if you could try
the updated version and let us know how well it works for you.

I’m new to Linux - could it have something to do with the graphics settings, or the version of some graphics library?

I would try to compile the latest release of Avogadro, but I’m not sure exactly how to do that. Instead I got the version in the Debichem repository as described here:
http://avogadro.openmolecules.net/wiki/Distribution_Packages

If you update then I think 0.9.6 should be in there now.

Thanks,

Marcus

4

Steven Wathen wrote:

Marcus,

Thanks for the help.

I did manage to upgrade to Avogadro 0.9.6

That by itself did not solve my problem, but disabling the visual effects did the trick. I had to set the Visual Effects to “None” and now the molecule window is stable and I can save image files without problems.

Hi Steve,

Glad that solved your problem. I love the visual effects in KDE 4, but
if I turn them on then Avogadro slows to a crawl. I also get artifacts
as you described. Hopefully this situation will improve as driver
support is improved.

We are working on getting our 1.0 release ready, so any and all feedback
at this stage is especially helpful. Perhaps we should start an FAQ with
some of these items, I know the visual effects on Linux issue has been
hit by quite a few people (myself included).

Thanks,

Marcus