Dear sir

i have a query protein of 300 residues which has 14 zinc finger binding motifs and each motif is not identically the same. i have a template which has 3 chains with each chain having only 87 residues, all the chains being identical.

if i need to build a model to my query, i thought of chopping my query sequence in to three parts nearly such that each part resemble my template of 87 residues. it is seen that the sequence identity is nearly 50% for each part with the template.

if i build models for these independent regions, 

1. how do i join them.

2. how do i know their  relative orientation and

3. how do i account for the dna which binds to it, plz explain.