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