Re: [modeller_usage] multimeric model and loop refinement

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

On 11/16/2012 03:00 AM, sdimicco wrote:
> I am trying to built a multimeric model. I would like to if I have to
> use restraints symmetry to model it.

No, just add symmetry restraints if you want it to be symmetrical. 
Obviously this would only make sense if all the subunits are identical.

> Moreover, i would like to built a model with all hydrogens and to refine
> loop automatically. How can I do that? I am trying to use allh model and
> loop model in the same script, but without success.

You can't do that because the loop modeling potential doesn't include 
parameters for hydrogen. It doesn't really make sense anyway, because 
adding hydrogens roughly doubles the number of atoms in the system and 
so roughly quadruples the compute time, for no real increase in accuracy.

	Ben Webb, Modeller Caretaker
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