Reading molecular file failed error

Hello,

I have a recurring problem with Avogadro on an Ubuntu Linux machine.
When I open any molecular file (.XYZ, .CIF, .PDB, etc.), it returns an
error “Reading molecular file failed,file [path to filename”. This
problem occurs with every installation of Avogadro that I have tried.
The first was an installation using the Ubuntu Software Center. When
that did not work, I tried building Avogadro from source (which worked,
after building some dependencies from scratch), but the same error is
returned.

When I open avogadro from a terminal, here is the screen output:
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
QStackedLayout::setCurrentWidget: Widget 0x2cd9e60 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

The program window opens just fine. Then if I try to open a file (say,
1AKI.pdb, which is the structure of Lysozyme in the Protein DataBank), I
get a pop-up window stating “Reading molecular file failed,file [path to
filename]”. There is no other output in the debugging window.

Does anyone have an idea where to start looking for a fix? Avogadro runs
fine on my MacBook, but I have never managed to get it working on my
Ubuntu machine. Other details that may help:

System:
Ubuntu 12.04 LTS [kept up to date]
Qt4 installation from Ubuntu repo (apt-get install libqt4-dev)
Self-built OpenBabel 2.3.2
Self-built cmake 2.8.10
Self-built Eigen2

Sorry to be sparse on details, but Avogadro is not giving me much
feedback for debugging.

Thanks,
Dan

Hi,

On Thu, Dec 12, 2013 at 12:00 PM, Daniel W. Siderius dwsideri@gmail.com wrote:

Hello,

I have a recurring problem with Avogadro on an Ubuntu Linux machine. When I open any molecular file (.XYZ, .CIF, .PDB, etc.), it returns an error “Reading molecular file failed,file [path to filename”. This problem occurs with every installation of Avogadro that I have tried. The first was an installation using the Ubuntu Software Center. When that did not work, I tried building Avogadro from source (which worked, after building some dependencies from scratch), but the same error is returned.

When I open avogadro from a terminal, here is the screen output:
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
QStackedLayout::setCurrentWidget: Widget 0x2cd9e60 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

The program window opens just fine. Then if I try to open a file (say, 1AKI.pdb, which is the structure of Lysozyme in the Protein DataBank), I get a pop-up window stating “Reading molecular file failed,file [path to filename]”. There is no other output in the debugging window.

Does anyone have an idea where to start looking for a fix? Avogadro runs fine on my MacBook, but I have never managed to get it working on my Ubuntu machine. Other details that may help:

System:
Ubuntu 12.04 LTS [kept up to date]
Qt4 installation from Ubuntu repo (apt-get install libqt4-dev)
Self-built OpenBabel 2.3.2
Self-built cmake 2.8.10
Self-built Eigen2

Sorry to be sparse on details, but Avogadro is not giving me much feedback for debugging.

Can you confirm that Avogadro is linked to your Open Babel library,
and also perhaps try obabel on the file to ensure it is able to read
the PDB? An easy test is converting a PDB to XYZ or similar. Avogadro
is using Open Babel to do most file IO, and it sounds like this isn’t
working for some reason. I have a laptop with 12.04 LTS and Avogadro
works fine there.

Marcus

Marcus,

You pointed me in the right direction. obabel was not working because my
BABEL_LIBDIR environment variable was not set. I’ve now set that
variable in my shell rc file and Avogadro reads the various files.

Thanks,
Dan

On 12/12/2013 01:01 PM, Marcus D. Hanwell wrote:

Hi,

On Thu, Dec 12, 2013 at 12:00 PM, Daniel W. Siderius dwsideri@gmail.com wrote:

Hello,

I have a recurring problem with Avogadro on an Ubuntu Linux machine. When I open any molecular file (.XYZ, .CIF, .PDB, etc.), it returns an error “Reading molecular file failed,file [path to filename”. This problem occurs with every installation of Avogadro that I have tried. The first was an installation using the Ubuntu Software Center. When that did not work, I tried building Avogadro from source (which worked, after building some dependencies from scratch), but the same error is returned.

When I open avogadro from a terminal, here is the screen output:
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
QStackedLayout::setCurrentWidget: Widget 0x2cd9e60 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

The program window opens just fine. Then if I try to open a file (say, 1AKI.pdb, which is the structure of Lysozyme in the Protein DataBank), I get a pop-up window stating “Reading molecular file failed,file [path to filename]”. There is no other output in the debugging window.

Does anyone have an idea where to start looking for a fix? Avogadro runs fine on my MacBook, but I have never managed to get it working on my Ubuntu machine. Other details that may help:

System:
Ubuntu 12.04 LTS [kept up to date]
Qt4 installation from Ubuntu repo (apt-get install libqt4-dev)
Self-built OpenBabel 2.3.2
Self-built cmake 2.8.10
Self-built Eigen2

Sorry to be sparse on details, but Avogadro is not giving me much feedback for debugging.

Can you confirm that Avogadro is linked to your Open Babel library,
and also perhaps try obabel on the file to ensure it is able to read
the PDB? An easy test is converting a PDB to XYZ or similar. Avogadro
is using Open Babel to do most file IO, and it sounds like this isn’t
working for some reason. I have a laptop with 12.04 LTS and Avogadro
works fine there.

Marcus


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Dan,

Glad you managed to get to the bottom of it! We try to test in as many
different environments as possible, that is one of the reasons I kept
12.04LTS on my Sputnik2 laptop. Thanks for sharing your fix.

Marcus

On Thu, Dec 12, 2013 at 1:39 PM, Daniel W. Siderius dwsideri@gmail.com wrote:

Marcus,

You pointed me in the right direction. obabel was not working because my
BABEL_LIBDIR environment variable was not set. I’ve now set that
variable in my shell rc file and Avogadro reads the various files.

Thanks,
Dan

On 12/12/2013 01:01 PM, Marcus D. Hanwell wrote:

Hi,

On Thu, Dec 12, 2013 at 12:00 PM, Daniel W. Siderius dwsideri@gmail.com wrote:

Hello,

I have a recurring problem with Avogadro on an Ubuntu Linux machine. When I open any molecular file (.XYZ, .CIF, .PDB, etc.), it returns an error “Reading molecular file failed,file [path to filename”. This problem occurs with every installation of Avogadro that I have tried. The first was an installation using the Ubuntu Software Center. When that did not work, I tried building Avogadro from source (which worked, after building some dependencies from scratch), but the same error is returned.

When I open avogadro from a terminal, here is the screen output:
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
QStackedLayout::setCurrentWidget: Widget 0x2cd9e60 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

The program window opens just fine. Then if I try to open a file (say, 1AKI.pdb, which is the structure of Lysozyme in the Protein DataBank), I get a pop-up window stating “Reading molecular file failed,file [path to filename]”. There is no other output in the debugging window.

Does anyone have an idea where to start looking for a fix? Avogadro runs fine on my MacBook, but I have never managed to get it working on my Ubuntu machine. Other details that may help:

System:
Ubuntu 12.04 LTS [kept up to date]
Qt4 installation from Ubuntu repo (apt-get install libqt4-dev)
Self-built OpenBabel 2.3.2
Self-built cmake 2.8.10
Self-built Eigen2

Sorry to be sparse on details, but Avogadro is not giving me much feedback for debugging.

Can you confirm that Avogadro is linked to your Open Babel library,
and also perhaps try obabel on the file to ensure it is able to read
the PDB? An easy test is converting a PDB to XYZ or similar. Avogadro
is using Open Babel to do most file IO, and it sounds like this isn’t
working for some reason. I have a laptop with 12.04 LTS and Avogadro
works fine there.

Marcus


Rapidly troubleshoot problems before they affect your business. Most IT
organizations don’t have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk


Avogadro-Discuss mailing list
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https://lists.sourceforge.net/lists/listinfo/avogadro-discuss


Rapidly troubleshoot problems before they affect your business. Most IT
organizations don’t have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk


Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss