On 11/29/2011 03:03 AM, flavio seixas wrote: > I was studing Modeller manual and I am not sure if there is a routine > in modeller that can refine only part of an existin model, like loop > refinement do.
Just build a new comparative model using the regular automodel class, using your original model as the template. Use a simple alignment containing two copies of the model sequence. Override select_atoms() as per the example at http://salilab.org/modeller/9.10/manual/node23.html to define the region to refine.
Note, however, that Modeller models generally do not need refinement (and if they do, using Modeller to do it probably won't make the models any better!)
> However, the region that I am interested to refine is > not a loop. Because of this, I can not use loop refinement in helical > segments, even though a region of three residues.
Loop refinement can be used for any region without a template. The protein can adopt any secondary structure, including an alpha helix. But yes, typically loop refinement will give you coil structures.
Ben Webb, Modeller Caretaker