I commented in the ticket, but just thought I'd respond here as well. This sounds like a graphics driver issue. I'd report it at http://bugreport.apple.com On May 15, 2010, at 11:44, Jack Howarth wrote:
I have had reports of pymol crashing under X11 when used with a secondary display...
https://trac.macports.org/ticket/24895
Unfortunately. I don't have any dual headed systems to test this with. Could someone with that configuration take a look at this with the MacPorts pymol package to see if it is a Xquartz bug? Also, if the Pymol viewer window flashes, starting the program with 'pymol -M' will suppress that by launching pymol in non-stereo mode. Jack
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