SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \ sidechain 6 \ bystroff 5 \ soft_clashes 10 backbone_clashes 2 \ break 20 \ pred_alpha2 5 \ constraints 20 \ hbond_geom 0.1 \ hbond_geom_backbone 0.1 \ hbond_geom_beta 0.4 \ hbond_geom_beta_pair 1 \ phobic_fit 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. # from T0206.t2k.str2.constraints StrandConstraint V110 S112 0.822 bonus #s1 StrandConstraint I118 S119 0.626 bonus #s2 StrandConstraint T125 S129 0.792 bonus #s3 StrandConstraint F133 N141 0.849 bonus #s4 StrandConstraint V147 V155 0.675 bonus #s5 StrandConstraint P159 G162 0.713 bonus #s6 StrandConstraint Q181 T184 0.4 #s7 StrandConstraint S187 I192 0.848 bonus #s8 StrandConstraint G197 L202 0.818 bonus #s9 HelixConstraint V213 H216 0.616 bonus #region 207-211 strand in str2, helix in stride # from try4 & extrapolation SheetConstraint N91 G93 G111 T109 1 bonus # ??-s1 -- loosen SheetConstraint V155 T152 G197 L200 1 # s5-s9 SheetConstraint F133 I139 V193 S187 1 # s4-s8 SheetConstraint L202 G197 T125 E130 1 # s9-s3 SheetConstraint I182 T184 G149 V147 2 # s7-s5 -- try again #SheetConstraint A201 L202 P104 D103 1 # s9-?? SheetConstraint V155 G149 V158 G164 1 # s5-s6 SheetConstraint Q181 T184 E190 S187 1 # s7-s8 SheetConstraint V127 T125 A117 S119 2 # s3-s2 -- up weight #SheetConstraint A117 S119 Q113 G111 1 # s2-s1 -- opp sides?