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cryos / avogadro

Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
http://avogadro.cc/
GNU General Public License v2.0
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Molecules not shown #880

Open leofedep opened 7 years ago

leofedep commented 7 years ago

When I open avogadro the molecules are present, but they don't show. When debugger is enabled I could see the number or atoms and bonds. If I execute from terminal, this is what it comes:

Gtk-Message: Failed to load module "canberra-gtk-module"
"Avogadro version:  1.2.0   Git:    
LibAvogadro version:    1.2.0   Git:    " 
Locale:  "en_US" 
Libavogadro translations not found. 
System has OpenGL support. 
About to test OpenGL capabilities. 
OpenGL capabilities found: 
    Double Buffering.
    Direct Rendering.
    Antialiasing.
Loading plugins: "/usr/bin/../lib/avogadro/1_2" 
Searching for plugins in "/usr/lib/avogadro/1_2" 
Searching for plugins in "/usr/lib/avogadro/1_2/colors" 
Searching for plugins in "/usr/lib/avogadro/1_2/engines" 
Searching for plugins in "/usr/lib/avogadro/1_2/extensions" 
Searching for plugins in "/usr/lib/avogadro/1_2/tools" 
Loading plugins: "/home/leofedep/.avogadro/1_2/plugins" 
Settings are missing for the next engines: () 
QStackedLayout::setCurrentWidget: Widget 0x5652f1c42f10 not contained in stack
dev warning: Extension "GAMESS" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. 
dev warning: Extension "Orbitals" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. 
dev warning: Extension "Python Terminal" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. 
dev warning: Extension "Vibration" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. 
HOMO at:  -1 
GLWidget initialisation... 
GLSL support enabled, OpenGL 2.0 support confirmed. 
GLWidget initialised... 
createObjects() 
OpenGL extension GL_ARB_texture_rectangle is present. 
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: cHRM: invalid chromaticities
Qt has caught an exception thrown from an event handler. Throwing
exceptions from an event handler is not supported in Qt. You must
reimplement QApplication::notify() and catch all exceptions there.

Avogadro versions: Application and library: 1.2.0 Open babel: 2.3.2 Qt: 4.8.7

Debian version (Gnome 3.22.2) Linux XXXXX 4.9.0-3-amd64 #1 SMP Debian 4.9.30-2+deb9u2 (2017-06-26) x86_64 GNU/Linux

Thanks in advance!!!! screenshot from 2017-07-11 17-17-18

lmmentel commented 7 years ago

I have exactly the same issue and I'm also on debian9. The molecules are not shown independently of the format loaded. However I found that when I tried to rotate and zoom (a lot) I was able to find some positions in which the molecules were (partially) visible but disappeared when I rotated/zoomed a bit more.

leofedep commented 7 years ago

Immentel is exactly the same for me.

esmuigors commented 7 years ago

Same for me, also after installing Debian 9 (MATE 1.16.2). There is also no difference as whether avogadro is launched with Intel of Nvidia GPU. If I could try to add my bit to what lmmentel said, the molecules seem to emerge from some plane when rotated, or they disappear beneath that plane. All properties of the molecule are accessible, i.e., the program definitely knows there is one. Also, axes sometimes disappear during the addition of atoms, too; when this happens, coordinates of all atoms that have been just added are displayed as nan, and molecular mechanics fails to run with such input data. Actually, I have also seen something like this for Gabedit – on the same freshly installed Debian 9. But, just the opposite, it happens only for certain zooms – the molecule dips beneath some plane when being rotated. So this is probably Debian issue. But which package is responsible for it? In the "Issues to be aware of for stretch" there is chapter "Perl changes that may break third-party software". Maybe this is the reason for some incompatibilities? I tried installing CGI Perl packages, as well as libmodule-build-perl (with its literally 50 dependencies) – the packages specifically cited in the chapter I mentioned earlier – but this did not help.

JefersonGP commented 7 years ago

Me too, i have ubuntu 17.04, Avogadro 1.2.0, and by terminal : "Avogadro version: 1.2.0 Git:
LibAvogadro version: 1.2.0 Git: " Locale: "en_US" Libavogadro translations not found. System has OpenGL support. About to test OpenGL capabilities. OpenGL capabilities found: Double Buffering. Direct Rendering. Antialiasing. void DBusMenuExporterPrivate::addAction(QAction, int): Already tracking action "" under id 63 void DBusMenuExporterPrivate::addAction(QAction, int): Already tracking action "" under id 64 Loading plugins: "/usr/bin/../lib/avogadro/1_2" Searching for plugins in "/usr/lib/avogadro/1_2" Searching for plugins in "/usr/lib/avogadro/1_2/colors" Searching for plugins in "/usr/lib/avogadro/1_2/engines" Searching for plugins in "/usr/lib/avogadro/1_2/extensions" Searching for plugins in "/usr/lib/avogadro/1_2/tools" Loading plugins: "/home/jefersong/.avogadro/1_2/plugins" Settings are missing for the next engines: () QStackedLayout::setCurrentWidget: Widget 0x561577317c90 not contained in stack dev warning: Extension "GAMESS" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. dev warning: Extension "Orbitals" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. dev warning: Extension "Python Terminal" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. dev warning: Extension "Vibration" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation. HOMO at: -1 GLWidget initialisation... GLSL support enabled, OpenGL 2.0 support confirmed. GLWidget initialised... read 1 molecules. Old molecule deleted... No matching basis set file found: "/home/jefersong/Downloads/937.mol" HOMO at: -1 libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: iCCP: known incorrect sRGB profile libpng warning: cHRM: invalid chromaticities createObjects() OpenGL extension GL_ARB_texture_rectangle is present.

esmuigors commented 7 years ago

Today I have installed updates, among which was python-avogadro (to 1.2.0-1+dev9u1 version). After this, problems were gone for me. Hope for the rest of You also.

If nobody else complains, I consider that this bug is fixed then?

leofedep commented 7 years ago

It's fixed for me. Thank you!!!!

beangoben commented 7 years ago

This works for the newest ubuntu 17.04...but if you are using anything below (16.10)...you are stuck and still have to deal with this problem.

beangoben commented 7 years ago

Not fixed, updated to ubuntu 17.04 which uses 1.2.0-1build1 and it is still not working. Can provide screenshot and console messages is needed.

s-ansa commented 3 years ago

The same problem. Ubuntu 19.10 Avogadro 1.2.0 Open Babel 2.4.1 Qt 4.8.7