SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \ phobic_fit 2 \ sidechain 6 \ bystroff 5 \ soft_clashes 15 backbone_clashes 2 \ break 35 \ pred_alpha2 5 \ constraints 45 \ hbond_geom 0.1 \ hbond_geom_backbone 0.1 \ hbond_geom_beta 1 \ hbond_geom_beta_pair 2 // Add the following for extra-cellular proteins: # known_ssbond 0.5 # and put ssbond command in constraints file # maybe_ssbond 0.5 // For comparative modeling, increase weight of break and hbond_geom... // put any constraints here, such as helix constraints, strand constraints, // ssbond, hbond, or just arbitrary pairs of atoms. StrandConstraint H2 H7 2.0 // make His tag be extended. # include T0196.t2k.dssp-ehl2.constraints HelixConstraint G8 R17 0.6241 # StrandConstraint V42 N44 0.693 # StrandConstraint D49 E56 0.7172 # StrandConstraint M59 I60 0.6595 # too short! # StrandConstraint K65 P69 0.6478 # StrandConstraint G74 E79 0.7416 # StrandConstraint I94 I98 0.6646 # include T0196.t04.dssp-ehl2.constraints # HelixConstraint L11 K16 0.6393 # use only one from t2k # HelixConstraint E22 I28 0.6043 # use only one from t2k StrandConstraint K36 I45 0.6465 StrandConstraint V50 E56 0.6053 StrandConstraint M59 V66 0.6921 StrandConstraint G73 E79 0.6507 StrandConstraint K84 I89 0.6255 StrandConstraint G95 E99 0.6939 StrandConstraint V110 Q115 0.6214 // Try packing the initial helix against the beta unit: Constraint L15.CG G53.C 0 3.5 7 1 Constraint F12.CZ I94.CA 0 4 8 0.5 Constraint L11.CD1 G95.CA 0 3.6 7 1.0 Constraint I26.CD1 V37.CA 0 5 10 0.2 // Try // Ncap for first helix? Hbond S9.OG F12.N 2.0