[modeller_usage] reproduction

hi,

i would like to ask for a bit of an input. you see, i have an alignment of two proteins, one is an xray structure, serves as a template. the other one is the target. the template consists of a globular domain which gets reproduced very nicely, and of an extended part, which gets somehow randomized, or differs substantially from the template. the question of mine is, how to inform modeller to reproduce this part, of just the whole protein which as little deviation as possible (ie. to closely resemble the template) ? thank you for any input,

best,

jean-paul