Re: [modeller_usage] constant starting molecule for models

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 6/6/13 4:00 AM, Dermot Mallon wrote:
> Between models with
> identical sequence the RMSD is ~0.2

This is expected behavior. Modeller models are samples from the set of 
all models that satisfy the restraints.

> 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.

It sounds like what you're looking for is rand_method, not rand_model. 
But Modeller will still optimize to satisfy the restraints, which will 
move things around. You could just take the initial model (the *.ini 
file) which is a PDB file of the model before randomization and 
optimization. This won't change unless you change your alignment and/or 
template structures. But since it's unoptimized it could contain clashes.

	Ben Webb, Modeller Caretaker
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