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

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