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Hi, Indeed it is a problem with X11. I had the same problem with coot and other programs which uses the X11 (e.g. PymolX11Hybrid). When you update Mac OS X or install Xcode you should reinstall X11. So you don't have to delete anything. This was I found on a site: "Released on 05.17.2009, X11 2.3.3.2 contains Xquartz-1.4.2-apple42. To install, download X11-2.3.3.2.dmg, and double-click the disk image to mount and begin installation. There are currently two situations where you need to re-install X11: 1- after future OS, and Security Updates delivered through Apple's Software Update; 2- after installing Xcode." An update and latest version of the X11 you can find on this site: http://mac.softpedia.com/get/System-Utilities/XQuartz.shtml regards, Ruben