I want redesign my protein in flexible backbone mode. My pdb structure has some missing residues. I have two questions:
1) Should I renumber all the residues to make them continuous?
2) Which sequence should I use to construct fragment files, "complete sequence of protein" or "just sequence of the structure file"? Do missed residues introduce error(s) during fragment file construction, if so please tell me what should I do?
Thanks very much in advance for your help