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
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