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
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.