Hi all, I used Modeller in the past to create small loops from scratch. Now I have a protein-DNA complex, and I have to build and model 4 loops of my protein. My first problem is that MODELLER does not support DNA, so I have to strip the DNA from the PDB and use the protein alone. Considering the problem that I have to "paste" the DNA to the modelled structure, I use the options *a.md_level= None* to keep the rest of the protein fixed and the option * a.loop.md_level* to model the loops. Now, these two commands work on three of the 4 loops, but I have another problem now: I have a very long loop to build (35 aa) and using these two commands, MODELLER create a very strange hairpin loop to connect these two positions. I know which will be the correct structure of this loop because I have a similar protein that present this loop, and the modelling is wrong. Finally, if I don't usage a.md_level=None, MODELLER builds a very good loop, but all the protein is in a complete different position with respect of the starting one. Any suggestion? Best regards Rubben