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
On 4/14/11 4:18 AM, email@example.com wrote: > 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'.
Like it says, there's a difference between the structureX entry in your alignment file and the sequence in the PDB file. We can't tell what the problem is without seeing your real alignment file and PDB.
Usual things to check are:
1. If you have an ending residue number and chain ID in your alignment file (structureX line), make sure to update it to match that of the ligand, not the last amino acid.
2. When you turn on env.io.hetatm, Modeller reads *all* HETATM records, not just magically the ligands you're interested in. So you need to list them all in your alignment.
3. Modeller reads the PDB file sequentially. So if your ligands are not immediately after the amino acid chain, you'll either need to include the intervening residues in your sequence or modify your PDB file so that they are.
Ben Webb, Modeller Caretaker