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[modeller_usage] request a clear method for modelling a dimeric protein

Dear sir;
I am trying to use modeller to predict the structure of a dimeric protein with no obvious symmetry between each of its subunits. My BLAST search shows that the first subunit alpha is homologous to a monomeric protein "C", while the other subunit beta is homologous to another different monomeric protein "D". Basically, I tried to align alpha with "C" and beta with "D" and I decided that the best strategy is to use a typical script from the tutorial"Building a model from multiple templates".
I am not quite sure that this procedure is the best way to build my model. Also, I found a problem in writing my alignment file especially the header section and the assignment of each of the subunits to each of the templates.
Could any body verify my alignment file and give me a clear method to deal with this situation?
Alignment file.ali:
structureX:C: 1:A:58: : : : :
structureX: D:1:A:78:::::
script file:
# Homology modeling with multiple templates
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = './'
a = automodel(env,
alnfile = 'Alignment file.ali', # alignment filename
knowns = ('C', 'D'), # codes of the templates
sequence = 'proteinX') # 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.make() # do the actual homology modeling
OTHMAN Houcemeddine
Pasteur Institute of Tunis - Tunisia