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 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 40 backbone_clashes 2 \ break 120 \ 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 \ maybe_ssbond 0 // 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 //from decoys/try1-opt2.helices HelixConstraint (T0370)P4 (T0370)N18 1 HelixConstraint (T0370)S60 (T0370)T69 1 HelixConstraint (T0370)A95 (T0370)T109 1 //from decoys/try1-opt2.sheets, with slight changes as described in the README SheetConstraint (T0370)V24 (T0370)A31 (T0370)S44 (T0370)A37 hbond (T0370)A26 1 SheetConstraint (T0370)A26 (T0370)T30 (T0370)I76 (T0370)V72 hbond (T0370)W27 1 SheetConstraint (T0370)L53 (T0370)P57 (T0370)R124 (T0370)T120 hbond (T0370)V54 1 SheetConstraint (T0370)G70 (T0370)G77 (T0370)A89 (T0370)L82 hbond (T0370)V72 1 SheetConstraint (T0370)D81 (T0370)G87 (T0370)R134 (T0370)R128 hbond (T0370)L82 1 SheetConstraint (T0370)E86 (T0370)L92 (T0370)R128 (T0370)Y122 hbond (T0370)L90 1 SheetConstraint (T0370)R128 (T0370)E135 (T0370)D147 (T0370)S140 hbond (T0370)V130 1 SheetConstraint (T0370)L46 (T0370)D48 (T0370)L53 (T0370)T51 hbond (T0370)L53 10