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
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