[modeller_usage] constant starting molecule for models

[Dermot Mallon <>]

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

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m: 07879 200800
t: 01223 336975