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 <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 ------------------------------------------------------------------------------ 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
