PyMOL Plugin PREP fails to read prepared molecule when running from file

[marcvanderkamp]

When running with "Choose from file" (instead of "Choose from PyMOL object"), the plugin fails to read in the molecule, crashing out at this stage in __init__.py (after prep.sh has succesfully run):

        while True:
            output = p.stdout.read(1)
            if output == '' and p.wait() != None:
                break
            if output != '':
                sys.stdout.write(output)
                sys.stdout.flush()