CreatePredAlphaCost pred_alpha2k alpha11 T0370.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0370.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0370.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 7 bad_peptide 10 \ bystroff 5 \ soft_clashes 30 backbone_clashes 2 \ break 80 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 25 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ missing_atoms 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. //include T0370.dssp-ehl2.constraints //include T0370.undertaker-align.sheets //include rr.constraints SheetConstraint (T0370)R129 (T0370)E135 (T0370)M145 (T0370)L139 hbond (T0370)V130 20 SheetConstraint (T0370)R142 (T0370)R146 (T0370)D154 (T0370)W150 hbond (T0370)L144 20 SheetConstraint (T0370)R80 (T0370)G87 (T0370)E135 (T0370)R128 hbond (T0370)L82 10