CreatePredAlphaCost pred_alpha2k alpha11 T0206.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0206.t04.alpha.rdb 2 alpha alpha_prev sum 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 10 backbone_clashes 2 \ break 20 \ pred_alpha2k 3 \ pred_alpha04 3 \ constraints 20 \ hbond_geom 1 \ hbond_geom_backbone 1 \ hbond_geom_beta 5 \ hbond_geom_beta_pair 10 // 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 looking at try7-opt1 (and t2k.str2 and t04.str2) StrandConstraint Y88 G93 2.0 #s0 StrandConstraint T109 G111 2.0 #s1 StrandConstraint I118 L121 2.0 #s2 StrandConstraint T125 I128 2.0 #s3 StrandConstraint Y134 A140 2.0 #s4a #StrandConstraint T144 L148 0.617 #s4b StrandConstraint L151 V155 2.0 #s5 StrandConstraint V158 G162 2.0 #s6 StrandConstraint I174 A178 2.0 #s7a StrandConstraint Q181 T185 2.0 #s7b StrandConstraint V189 V193 2.0 #s8 StrandConstraint S199 L202 2.0 #s9 HelixConstraint V213 H216 0.616 bonus #region 207-211 strand in str2, helix in stride # from visual inspection of try7 & extrapolation SheetConstraint N91 G93 G111 T109 hbond N91 8 # s0 ^v s1 SheetConstraint Y88 G93 K135 A140 hbond F90 10 # s0 || s4a SheetConstraint Y134 V138 V193 V189 hbond I192 8 # s4a ^v s8 SheetConstraint Q181 T184 I192 V189 hbond I182 8 # s7b ^v s8 SheetConstraint Q181 T185 A178 I174 hbond Q181 8 # s7b ^v s7a SheetConstraint I128 T125 I118 L121 hbond F126 8 # s3 ^v s2 SheetConstraint L202 S199 T125 I128 hbond T125 8 # s9 ^v s3 SheetConstraint V155 L151 L198 L202 hbond S199 8 # s5 ^v s9 SheetConstraint V155 L151 V158 G162 hbond V155 10 # s5 ^v s6