[modeller_usage] Modeling core residues without loop regions

Dear MODELLER users, I was looking for answers to the following questions? 1. What is the best approach to model proteins with large insertions (approximately 50residues) at different parts of the protein. Example AAAAAA---------------------------------BBBBBB---------------------------------------------CCCC Even if the alignment is good, I get an exceeded maxmolpdf error in the model building stage. I am not sure what value to set for the maxmolpdf . 2.Is it possible to build only the core residues without the insertions? It would be helpful if you can point me to references related to the same. -- Vimalkumar Velayudhan