[modeller_usage] Re: Question about the loop modeling

On 12/7/22 2:39 PM, Ecem Güngör via modeller_usage wrote: > I have an X-ray structure where I want to model some loop regions. > However, while modeling these loops, I do not want to either optimize or > refine them. How should I proceed for that?

"model", "optimize" and "refine" are essentially synonyms - they all mean "move some atoms in an attempt to reduce the value of the scoring function" so what you're asking for doesn't really make sense, unless I am not understanding you correctly. Do you perhaps mean that you want to model the loops without affecting the rest of the protein? If so, that's what the loop modeling protocol does by default; see https://salilab.org/modeller/10.4/manual/node36.html

Ben Webb, Modeller Caretaker