> 1) Should I renumber all the residues to make them continuous?
there is an opetion -use_pdb_numbering but I’m not sure if it works with fragments. In any case, if you mean that you want to renumber the protein to omit the residues that are missing in the density, I would not do that. You want to model those residues right? So you need to keep them in the fasta file and in the numbering.
> 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?
Use the full sequence, including the residues that are missing in the density in your fasta file. Fragment files are constructed from teh fasta file of your sequence, it does not matter that their are residues missing from the density of the structure (indeed, you don’t even need an experimental structure to construct a fragment file).
> Thanks very much in advance for your help