I am trying to model difference versions of a protein; each differing by one or two amino acids.

I am then looking at differences in electrostatics.

The effect size I am looking at is quite small and there is considerable difference simply from differences in modeller - I believe this is because it starts at a different amino acid. Between models with identical sequence the RMSD is ~0.2, which although small is abolishing any meaningful difference I could expect to see form the one or two amino acid change.

Therefore, I wonder if there is a way to ask modeller to start at the same point in these molecules? I tried a.rand_model = None, but that doesn't appear to be the correct option.

Does anyone know how I can achieve this?

Many thanks for your help.

-- D Mallon Clinical Research Fellow

e: dhm31@cam.ac.uk m: 07879 200800 t: 01223 336975