[modeller_usage] model-loop

[Urszula Uciechowska <>]

Dear Modeller users,

I am trying to use the model-loop.py script:

 Homology modeling by the automodel class
from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()
env = environ()

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

a = loopmodel(env,
              alnfile  = 'Sirt1-multi.ali',                                  # alignment 
filename
              knowns   = '1j8fAA','1j8fBB','1j8fCC','1q1aA','1yc5A','2od7A'     # codes of the 
templates
              sequence = 'Sirt1' )                                            # code of the 
target
a.starting_model= 1                 # index of the first model
a.ending_model  = 1                 # index of the last model
                                    # (determines how many models to calculate)
a.md_level = None                   # No refinement of model

a.loop.starting_model = 1           # First loop model
a.loop.ending_model   = 4           # Last loop model
a.loop.md_level       = refine.fast # Loop model refinement level

a.make()                            # do homology modeling

but i am getting the error 

'import site' failed; use -v for traceback
  File "model-loop.py", line 14
    sequence = 'Sirt1' )                                            # code of the target
           ^
SyntaxError: invalid syntax

Could someone tell me how to figure out this error?

thank you in advance



Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg