Molecules are not rendered, black screen

Bug #1640171 reported by Jakub Krajniak
64
This bug affects 13 people
Affects Status Importance Assigned to Milestone
avogadro (Ubuntu)
Confirmed
Undecided
Unassigned

Bug Description

Description:
Recent version of avogadro package is not working properly. It is not possible to draw molecule or to display molecule from the pdb/gro file.

Ubuntu version:
Description: Ubuntu 16.10
Release: 16.10

Here is the console log:

@jakubkrajniak ~ $ avogadro
"Avogadro version: 1.1.1 Git:
LibAvogadro version: 1.1.1 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_1"
Searching for plugins in "/usr/lib/avogadro/1_1"
Searching for plugins in "/usr/lib/avogadro/1_1/colors"
Searching for plugins in "/usr/lib/avogadro/1_1/engines"
Searching for plugins in "/usr/lib/avogadro/1_1/extensions"
Searching for plugins in "/usr/lib/avogadro/1_1/tools"
Loading plugins: "/home/teodor/.avogadro/1_1/plugins"
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x55f9c0f637b0 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.
Could not find python module...
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.
GLWidget initialisation...
GLSL support enabled, OpenGL 2.0 support confirmed.
GLWidget initialised...
createObjects()
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.

Revision history for this message
Jakub Krajniak (jkrajniak) wrote :
Revision history for this message
Launchpad Janitor (janitor) wrote :

Status changed to 'Confirmed' because the bug affects multiple users.

Changed in avogadro (Ubuntu):
status: New → Confirmed
Revision history for this message
Rodrigo Azevedo (rodrigoams) wrote :

I have exactly the same problem after upgrading from Ubuntu 16.04 to Ubuntu 16.10;
Verified with Ubuntu default and Unity 8 as well as Nvidia and Intel drivers.

Revision history for this message
Akshay Sridhar (akshaysridhar) wrote :

Yes. The update to Ubuntu 16.10 broke something for me too.

Revision history for this message
Ramsus Langaard (rlangaard) wrote :

I'm having the same problem. Once I could barely se some atoms (extremely dark gray on black). Changed the background color to light gray, but to no avail. Here's my output:

rasmus@rasmus-Lenovo-Z710:~$ avogadro
"Avogadro version: 1.1.1 Git:
LibAvogadro version: 1.1.1 Git: "
Locale: "nb_NO"
Translation successfully loaded.
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 62
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action "" under id 63
Loading plugins: "/usr/bin/../lib/avogadro/1_1"
Searching for plugins in "/usr/lib/avogadro/1_1"
Searching for plugins in "/usr/lib/avogadro/1_1/colors"
Searching for plugins in "/usr/lib/avogadro/1_1/engines"
Searching for plugins in "/usr/lib/avogadro/1_1/extensions"
Searching for plugins in "/usr/lib/avogadro/1_1/tools"
Loading plugins: "/home/rasmus/.avogadro/1_1/plugins"
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x55bb862338e0 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 "Vibrasjon" is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
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

Chromaticities? Please help!

-r :-)

Revision history for this message
Ramsus Langaard (rlangaard) wrote :

I'm using this btw:

rasmus@rasmus-Lenovo-Z710:~$ uname -a
Linux rasmus-Lenovo-Z710 4.8.0-34-generic #36-Ubuntu SMP Wed Dec 21 17:24:18 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

-r :-)

Revision history for this message
Ramsus Langaard (rlangaard) wrote :

Forgot the rest of output from when I exited the program:

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.

-r :-)

Revision history for this message
luthfan (lif631g) wrote :

I'm having the same issue too (Ubuntu 16.10 Yakkety)

lirfana@velociraptor:~$ avogadro
"Avogadro version: 1.1.1 Git:
LibAvogadro version: 1.1.1 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_1"
Searching for plugins in "/usr/lib/avogadro/1_1"
Searching for plugins in "/usr/lib/avogadro/1_1/colors"
Searching for plugins in "/usr/lib/avogadro/1_1/engines"
Searching for plugins in "/usr/lib/avogadro/1_1/extensions"
Searching for plugins in "/usr/lib/avogadro/1_1/tools"
Loading plugins: "/home/lirfana/.avogadro/1_1/plugins"
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x55fae2836a80 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.
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
^CQt 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.

Thanks.

Revision history for this message
Carlos Sevcik (carlos-sevcik-s-gmail) wrote :

Same problem with Ubuntu 17.04, it renders Avogadro useless

Revision history for this message
xemard.nicolas (xemard.nicolas) wrote :

For information, same problem too with latest Debian package (cat /etc/debian_version : 9.0)
avogadro --version
"Avogadro version: 1.2.0 Git:
LibAvogadro version: 1.2.0 Git:
Locale: "fr_FR"
Translation successfully loaded.
Avogadro: 1.2.0 (Hachage )
LibAvogadro: 1.2.0 (Hachage )
Qt: 4.8.7
OpenBabel: 2.3.2

I also try white background with no success
Sometimes, depending on the rotation, molecules appear or disappear ...

Revision history for this message
Michael Banck (mbanck) wrote :

This got fixed in the Debian package 1.2.0-2.

Revision history for this message
Mike (mikejackofalltrades) wrote :

Any chance the maintainer the use the fix from the debian package? I have the same issue.

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