Hi,

> import os, __main__, time
> 
> os.environ['PYMOL_PATH'] = "C:\Python27\PyMOL"
> 
> __main__.pymol_argv = [ 'pymol', "-qx"] # Quiet and no GUI
> import pymol
> pymol.finish_launching()
> 
> pymol.cmd.load("water.pdb")
> time.sleep(1)
> pymol.cmd.window("position", 500, 300)
> 
> ...in Python, Pymol freezes. If I remove the sleep command, it freezes
> before even displaying the test water molecules.

I couldn't reproduce it. 
On my Ubuntu with PyMOL 1.5.0.1 & Python 2.7, your script works just fine.

As I don't use Windows version of PyMOL, I cannot test more.

Best regards,

Takanori Nakane

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