Normally, automodel generates an initial model by transferring coordinates from the templates. However, if you have a prepared PDB file containing an initial model, you can have automodel use this instead with the inifile keyword, as in the example below. (This automatically sets automodel.generate_method to generate.read_xyz for you, which is necessary for this to work.)
# Modeling using a provided initial structure file (inifile) 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 = automodel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', # codes of the templates sequence = '1fdx', # code of the target inifile = 'my-initial.pdb') # use 'my' initial structure 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 homology modeling