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Re: [modeller_usage] Sintax error in script


Looking at your script, I see that the quote characters surrounding 'align.ali' are not the same as the ones surrounding 'atom_files' four lines above it. The ones around 'atom_files' are correct; they are standard ascii single-quotes. All the later ones are wrong; they look like the smart-quotes that word-processors use for apostrophes, to replace the ugly single-quotes. The error message says that Python doesn't like those.

Make sure you are using a plain text editor with an ascii encoding to edit your file. You can find more explanations online, e.g.  http://www.linuxplanet.com/linuxplanet/tutorials/6912/2/

I hope that helps,

On Tue, Dec 29, 2009 at 8:08 AM, virginia miguel <">> wrote:
Hi; I am trying to run the following script :

# Homology modeling with multiple templates

from modeller import *                # Load standard Modeller classes
from modeller..automodel import *      # Load the automodel class

log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

a = automodel(env,
              alnfile   = ’align.ali’,                                           # alignment filename
              knowns    = (’1bkn’, ’1b62’, ’1b63’, ’1nhh’, ’1nhi’, ’1nhj’),       # codes of the templates
              sequence  = ’PAOI’)                                               # code of the target
a.starting_model= 1                                                            # index of the first model
a.ending_model = 50                                                            # index of the last model
                                                                               # (determines how many models to calculate)
a.make()                                                                       # do the actual homology modeling

and I get the following error:

warning: Non-ASCII character '\xe2' in file model-multiple2.py on line 14, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details
  File "model-multiple2.py", line 14
    alnfile = ’align.ali’,                                           # alignment filename
SyntaxError: invalid syntax

How do I fix my script?

Thanks, Virginia