X11 and Yosemite

Today we had a strange problem on one of the lab computers. X11 from the XQuartz project was installed and up to date. But following a recent upgrade from Mavericks to Yosemite, none of the crystallography programs would run. The list of non-starters ran from CCP4, Coot, iMosFLM – which makes sense. They all need X11; it could be that. But the list included Phenix. I had no idea Phenix needs X11 (it’s not explicit in the notes). The GUI seems to be rendered in Qt (but I may be wrong- WxPython is still going?). Confusingly, X11 could be launched independently, and a blank prompt X11 terminal popped up when clicking the CCP4 launcher (6.4.0).

What worked? Counterintuitively, as a last resort, I reinstalled X11. Problem solved. Something got mangled by the installer. But this really makes me wonder how I updated the other computers without having this problem…

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One thought on “X11 and Yosemite

  1. Seems like Yosemite update broke X11 symlinks in /usr.

    Manually recreating the symlinks should prevent you from reinstalling X11 on all your machines.

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