Re: [modeller_usage] question on mutate monomers script
To: Andrew Voronkov <>
Subject: Re: [modeller_usage] question on mutate monomers script
From: Modeller Caretaker <>
Date: Thu, 11 Mar 2010 18:33:38 -0500
Cc:
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.