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