I am trying to construct a homology model with 4 chains, the primary one (A) being a protein and the 3 others being an RNA chain and two DNA chains.. However, when the hybridize mover starts to build the model via rosetta_scripts it throws out the nucleotide chains from the protein while I know that they should be inserted into it so I tried using constrains as suggested in the constraints guide for rosetta cm as well as using the pdb specific labels for constrains as described here in the forums but for some reason my pose includes only the protein residues without anyone of. the nucleotide chains. Originally, I threaded the full 4 chains with partial thread while leaving the nucleotides as they are in the template, and adding the nuc. chains into the fasta and alignment which seemed to work. However, apparently they're missing in the pose so I'm obviously doing something wrong.
Thanks in advance for any responses on this matter,