CreatePredAlphaCost pred_alpha2k alpha11 T0371.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0371.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0371.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 20 backbone_clashes 2 \ break 50 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 10 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ missing_atoms 1 \ maybe_metal 0.5 \ maybe_ssbond 1 // remove maybe_ssbond weight if protein known to be in reducing environment. // remove maybe_metal weight if protein known to have disulfides or // known not to bind metal ions. // Add the following for extra-cellular proteins: # known_ssbond 0.5 # and put ssbond command in constraints file // For comparative modeling, increase weight of break and hbond_geom... // put any constraints here, such as helix constraints, strand constraints, // sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms. # Sheet and Helix constraints from try7-opt2. the current highest scoring # model: SheetConstraint (T0371)K14 (T0371)D19 (T0371)E226 (T0371)G231 hbond (T0371)C15 1 SheetConstraint (T0371)C15 (T0371)D19 (T0371)D47 (T0371)V51 hbond (T0371)I16 1 SheetConstraint (T0371)L24 (T0371)K25 (T0371)A20 (T0371)F21 hbond (T0371)K25 1 SheetConstraint (T0371)L24 (T0371)T26 (T0371)L31 (T0371)G29 hbond (T0371)T26 1 SheetConstraint (T0371)Y49 (T0371)N53 (T0371)K78 (T0371)S82 hbond (T0371)I50 1 SheetConstraint (T0371)I98 (T0371)V99 (T0371)K117 (T0371)M118 hbond (T0371)V99 1 SheetConstraint (T0371)I98 (T0371)G103 (T0371)N133 (T0371)L138 hbond (T0371)A100 1 SheetConstraint (T0371)A134 (T0371)L138 (T0371)P162 (T0371)A166 hbond (T0371)L135 1 SheetConstraint (T0371)A163 (T0371)A166 (T0371)F198 (T0371)F201 hbond (T0371)V165 1 SheetConstraint (T0371)T171 (T0371)Y172 (T0371)I181 (T0371)A180 hbond (T0371)Y172 1 SheetConstraint (T0371)P173 (T0371)L174 (T0371)D178 (T0371)T177 hbond (T0371)L174 1 SheetConstraint (T0371)I227 (T0371)G231 (T0371)L246 (T0371)L250 hbond (T0371)M229 1 SheetConstraint (T0371)G269 (T0371)T273 (T0371)T248 (T0371)L252 hbond (T0371)I270 1 HelixConstraint (T0371)Q2 (T0371)L10 1 HelixConstraint (T0371)G33 (T0371)G45 1 HelixConstraint (T0371)S58 (T0371)L69 1 HelixConstraint (T0371)S81 (T0371)K93 1 HelixConstraint (T0371)T104 (T0371)D114 1 HelixConstraint (T0371)P120 (T0371)D126 1 HelixConstraint (T0371)N144 (T0371)L149 1 HelixConstraint (T0371)A182 (T0371)G195 1 HelixConstraint (T0371)S206 (T0371)M215 1 HelixConstraint (T0371)T236 (T0371)G245 1 HelixConstraint (T0371)I275 (T0371)V280 1 HelixConstraint (T0371)S278 (T0371)L283 1