I have a problem in which I am modelling a protein as a homodimer for which I am using a homodimeric template with ligands bound. When I model without ligand, it runs fine. But when I want to include heteroatoms, it says 'Number of residues between alignment and pdb file are different'. This is my script file. # Homology modeling by the automodel class 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 env.io.hetatm = True # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env,               alnfile  = 'mockali.ali',     # alignment filename               knowns   = '1COD',              # codes of the templates               sequence = 'targetfile',              # code of the target               assess_methods=(assess.DOPE, assess.GA341)) 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 This is my alignment file. >P1 sequence::::: AAAAAAAAAAA/. BBBBBBBBBBB/.* >P1 structureX:::: AAAAAAAAAAA/. BBBBBBBBBBB/.* Dr. Jayashree Ramana