If I understand well, for a protein with known secondary structure, I think I need to supply two files : seq.dat and seq.ss
A few questions...
1. Is seq.ss really necessary? from looking at the scripts, it seems to me that only seq.dat is actually used as input for other steps/programs.
2. For a protein of known 3D structure, I used DSSP to assign secondary structure. Would DSSP be the recommended SS to use? Or is STRIDE better to use in relation to I-TASSER?
3. What is the recommended "reliability" for seq.dat when SS is known? 9 for everything as shown below?
1 MET 1 9
2 ALA 1 9
3 ILE 4 9
4 ILE 4 9
5 THR 4 9
6 VAL 4 9
7 THR 4 9
8 ALA 4 9
9 GLN 4 9
10 ALA 1 9
11 ASN 1 9
12 GLU 1 9