[modeller_usage] loop refinement

[Urszula Uciechowska <>]

Dear Modeller users, 

I was trying to use the script for the loop refinement, however I want to use several templates codes. 
I tried to add them as:  knowns   = '5fd1', '1tre', '1j8h' ,             # codes of the templates
 and received an error: 

 File "loop_model.py", line 13
    knowns   = '1tcrA','3mbeC','2q86A','3c6lA','1j8hD', #templates
SyntaxError: non-keyword arg after keyword arg

How should I specify them? 

# 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  = 'alignment.ali',     # alignment filename
              knowns   = '5fd1',              # codes of the templates
              sequence = '1fdx')              # 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

thanks a lot for your help 

/Urszula