Dear Ben,
Is it possible? I know that i can model residues according to the tutorial: select the residues and use as a template to model the full structure. So i did it and the structure was severely impacted (RMSD 0.25). Loopmodel de-novo can do it without problems although i wish i could utilize my other structure file that is basically just a different conformation due to a ligand, but the deviation at the positions where the residues are missing are minuscule.
If not then i have two choices: de-novo and the automodel with a change in conformation of 0.25 RMSD. Which one would you choose?
Sincerely,
D. Boskovic