Advanced G-LoSA options
| -b | BLOSUM62 cutoff value for filtering (default=0) | |
| -iter | number of iteration for Ca atoms-based maximum clique search (1-3, default=3) | |
| 0: don't use maximum clique search | ||
| -itercf | number of iteration for chemical feature points-based maximum clique search (1-3, default=0) | |
| 0: 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 |
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| -surf | use surface structure for alignment (This option is only used when a whole protein structure is used for s1) |
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| 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) |
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| -s2w | additional structure to be transferred (PDB format) (n: don't use this option, default=n) |
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| -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 |
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| -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 |
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| -o | output option | |
| 0: score only | ||
| 1: score and superposed s2 structure with matrix (default) |