Re: [modeller_usage] Loop Modeling in a Protein-DNA Complex

[Modeller Caretaker <>]

On 3/15/12 9:33 PM, Alexander Predeus wrote:
> The question I wanted to ask, is what is the best assess method I can
> use, considering the nature of my task? I'm using DOPE right now, but in
> the manual I've also seen mentioning of DOPE-HR. Would it slow down the
> loop refinement process a lot (or at all)?

DOPE-HR is simply DOPE with a smaller bin size. It shouldn't be any 
slower to evaluate it than DOPE - and assessment with DOPE takes only a 
fraction of a second, so you wouldn't notice any difference anyway. DOPE 
is more widely used and tested than DOPE-HR, so I would recommend that.

	Ben Webb, Modeller Caretaker
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