Hi, On Thu, Dec 12, 2013 at 12:00 PM, Daniel W. Siderius <dwsid...@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 Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
