Ben,
Might it be possible to set an environmental which would have the
same effect of setting...
defaults write org.x.X11_launcher app_to_run /usr/bin/true
for that run of X11.app? This is known to suppress the undesired
xterm from appearing when the pymol startup script is run.
Again, when first launched from a Terminal window, X11.app is
started and the first pymol graphics window appears without
an xterm launching. It is only the second tkinter gui window
that triggers the unwanted xterm to appear. So if we could achieve
its suppression with an enviromental setting that might be
a decent workaround that could be added to the existing pymol
startup script.
Jack
ps You can reproduced this very easily if you have fink 10.5
unstable installed. Just 'fink install pymol-py25' and execute
'pymol' from a Terminal window.
