[PyMOL] Auto-launching in Mac Terminal

> Actually, I've encountered this problem myself -- very annoying...
>
> What happened is that you saved the Terminal window settings while you
> had a PyMOL session open, so OS X inferred that you were indicating a
> desire to have PyMOL open as a default preference.
>
> The only way I know of changing this is to text-edit
> $HOME/Library/Preferences/com.apple.Terminal.plist and remove the
> ExecutionString entry which contains PyMOL.  That means deleting those
> two lines: the one which contains ExecutionString and the one with the
> PyMOL launch command.

The OS X Terminal.app allows you to customize various terminal windows 
by saving different sets of preferences.  What happens is that you 
somehow accidently saved the pymol-specific ones as your default.

Probably the simplest thing to do is

rm ~/Library/Preferences/com.apple.Terminal.plist

and either replace it with your carefully backed up copy, or else just 
re-set all the preferences next time you open terminal.

You can also avoid this problem by invoking pymol at the command line.  
For convenience,

alias pymol /Applications/PyMOL/Darwin/pymol.com

and then just type pymol next time you start it.  You can also open pdf 
files and/or .pml scripts in one command, eg:

alias pymol /Applications/PyMOL/Darwin/pymol.com -q 
/Users/username/pymol/alias.pml

Finally if you also are running the X-windows version, you may want to 
alias one of these to a different name (npymol or xpymol).

Bill