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Hi Barry: It is an X11.app bug that has persisted for years now. (It isn’t specific to coot). Briefly, this happens unless you uncheck the checkbox for “Displays have Separate Spaces” in System Preferences>Mission Control William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu > On Sep 23, 2017, at 12:11 PM, Barry Finzel <[log in to unmask]> wrote: > > I've been trying to get coot running on my MacBook Pro after upgrading to OS X El Capitan (10.11.6). I have installed as part of ccp4, Phenix (1.9-1692) or standalone (0.8.8) (As provided by the Scott lab at UCSC). I'm also running X11 (2.7.11). It seems to be fine, unless I have my big Mac Cinema HD Display connected (via USB). When the big monitor is plugged in, all coot windows just disappear. They reappear on the notebook screen if I disconnect the remote monitor. > > Never had this problem with the same hardware and older versions of the Mac OS, an have not had problems with windows from other software, either - just coot. > > Is this a problem others have observed and/or dealt with? > > --Barry Finzel