Virginia,
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, -Jonathan
On Tue, Dec 29, 2009 at 8:08 AM, virginia miguel virgimiguel@yahoo.com.arwrote:
> 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 > >