Urszula,

When declaring multiple known files you declare them within parenthesis as follows.

known = ( '5fd1' , '1tre' , '1j8h' )

Therefore, the completed loopmodel command would be.

a = loopmodel (env , alnfile = 'alignment.ali' , #alignment file known = ( '5fd1' , '1tre' , '1j8h' ) , #codes of the templates sequence = '1fdx' ) #code the target

This is the same for other model routines which accept more than one template.

Hope this helps.

David

On 12/1/12 2:38 PM, Urszula Uciechowska wrote: > 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 > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage