I've seen this before when something went wrong with launching X11.

Have you tried launching X11 first, verifying that it works, and then launching PyMOLX11Hybrid while X11 is already running?

On Fri, Mar 13, 2009 at 1:15 PM, Atreyi Chatterjee <chatterjeea@mail.nih.gov> wrote:
I was trying to find out how to locate and use the APBS plug-in for MacPyMOL and when I mailed to the APBS-users list I was advised to rename MacPyMOL.app to PyMOLX11Hybrid.app which would make the APBS plug-in work in PyMOL.
I tried following this suggestion and being a complete novice in this field I might be missing some simple points here or making some silly mistakes. I would be really grateful if you share your thoughts with me. 
My issue is that once i rename MacPyMOL.app to PyMOLX11Hybrid.app I end up opening a version of PyMOL that has the the top area or the  "External GUI" missing. Only the bottom window containing the "Internal GUI" opens up. Since the external GUI has all the user friendly menu bars for a layman like me it is more familiar and easier to work with. The internal GUI has the secondary command line and it would be almost impossible for a person like me to work using this only. I am wondering if the PyMOLX11 version works only with commands only? 
Or, is it something that I have done that made the external GUI disappear!! 
This is what i did........when i tried opening the PyMOLX11Hybrid on my Mac, it asked me to choose an application and asked for the location of "X11". I specified it from the applications folder and it opened up w/o the external GUI.

W/o the external GUI i cannot access the wizard menu to access the APBS tools.... what am i saying, w/o it I cannot even open a file now!!!

I do not have multiple monitors connected to my computer and I am not using Leopard with spaces enabled. I cannot figure out why the top GUI is missing from my screen! 
Is there a way to bring it back?

Please help.


Atreyi Chatterjee, Ph. D.
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