Advanced G-LoSA options

-b BLOSUM62 cutoff value for filtering (default=0)
-iter number of iteration for maximum clique search (1-3, default=3)
     1: don't use maximum clique search
-f number of conserved residue(s) in a fragment pair (1-3, default=1)
     >3 : don't use fragment superposition

-surf use surface structure for alignment
(This option is only used when a whole protein structure is used for s1)
     0: don't use this option (default)
     1: use this option
-surf1 surface residues for structure 1 (n: don't use this option, default=n)
-surf1cf chemical feature for the surface residues structure (n: don't use this option, default=n)

-s2w additional structure to be transferred (PDB format) (n: don't use this option, default=n)

-s1ss secondary structure file for structure 1 (n: don't use this option, default=n)
-s2ss secondary structure file for structure 2 (n: don't use this option, default=n)
-ss check secondary structure conservation
     0: don't use this option (default)
     1: use this option

-n normalization option
     1: normalize using structure with smaller number of chemical feature points (N_min) (default)
     2: normalize using structure with larger number of chemical feature points (N_max)
     3: normalize using the average of N_min and N_max
     4: normalize using s1 structure

-o output option
     0: score only
     1: score and superposed s2 structure with matrix (default)