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Re: [modeller_usage] question on mutate monomers script

On 3/11/10 9:06 AM, Andrew Voronkov wrote:

I am trying to mutate several aminoacids in the PDB file. I ve used
the scrtipt (mutate.py) attached for this, but I get the error given
below. What can be the problem? As I understand I need only PDB file
for this script execution. Do I need to write path to the libraries
in the explicit way or it should get it from the environment setup? I
haven't specified the full path.
Here's the reply I sent you on March 2nd the first time you asked me this question (maybe that email got lost somewhere): 


:~/Mutate>  mod9v7 mutate.py
warning: Non-ASCII character '\xe2' in file mutate.py on line 11, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details
File "mutate.py", line 11
env.libs.topology.read(file=’$(LIB)/top_heav.lib’)
^
SyntaxError: invalid syntax
This is a Python error, not a Modeller one, but it is telling you exactly what the problem is. You have to use regular quote characters (') but you've used fancy quotes (something that looks like a quote character, but isn't). To fix this, use regular quotes, such as those used in the immediately preceding line which sets atom_files_directory. 

	Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
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