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 <dwsid...@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 <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 ------------------------------------------------------------------------------ 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
