[modeller_usage] gaps in template alignment to query sequence in case of multidomain modelling

dear modeller users, i have created a multi domain model using modeller FAQ first method aligning each template to query sequence and arranging them in PIR format in multi alignment file. but template is not available for a large C terminal region of the model. Even template alignment to query has gap regions between each domains.The model is giving poor stereochemical properties. is there any solution to this problem.

thanking you saibal das m.sc bioinformatics BIT mesra India.