On 7/20/19 12:11 AM, Yoochan Myung wrote: > As mentioned in the title, is there any way to ignore/skip loop modeling > in MODELLER9v21?
To be clear, you're referring to Modeller's handling of insertions, i.e. regions of the model that don't align with a template, during comparative modeling. (Loop refinement is a separate protocol that uses a statistical potential rather than information from the alignment.)
Modeller builds a model for the sequence you give it. If you don't want to build a model for a given sequence range, remove that range from the alignment. If there's sequence on both sides of the removed region, you might want to put a chain break there ('/' residue type) to prevent Modeller from trying to make a peptide bond.
Ben Webb, Modeller Caretaker