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
|