[modeller_usage] Modeller homology modelling loops

Dear all,

I have two molecules in two different conformations due to two different ligands (CRISPR crRNA/crRNA+target RNA). When i compare the structures where the loops are missing the RMSD are 1.4 and 2.0 (20-30 total non-loop residues aligned). Would you use homology modeling or de novo? I think considering the RMSD that one might be able to model it using the missing residues as a template and homology model the target structure with loop refinement but this is my first attempt at doing homology modeling hence i am very reluctant to take any of my deductions as 100% viable solutions.

Thanks,

D. B.