CreatePredAlphaCost pred_alpha2k alpha11 T0342.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0342.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0342.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. //include T0342.dssp-ehl2.constraints //include T0342.undertaker-align.sheets //include rr.constraints //from try22-opt2.helices HelixConstraint (T0342)S1 (T0342)T10 1 HelixConstraint (T0342)L27 (T0342)N35 1 HelixConstraint (T0342)N87 (T0342)Q97 1 HelixConstraint (T0342)Y139 (T0342)G151 1 HelixConstraint (T0342)L154 (T0342)I163 1 HelixConstraint (T0342)A162 (T0342)G170 1 HelixConstraint (T0342)S173 (T0342)L188 1 //from try22-opt2.sheets SheetConstraint (T0342)S16 (T0342)A21 (T0342)N87 (T0342)V82 hbond (T0342)F17 1 SheetConstraint (T0342)F41 (T0342)D48 (T0342)W84 (T0342)D77 hbond (T0342)C42 1 SheetConstraint (T0342)V43 (T0342)L46 (T0342)Q115 (T0342)V112 hbond (T0342)R45 1 SheetConstraint (T0342)F49 (T0342)F53 (T0342)Q73 (T0342)A69 hbond (T0342)K50 1 SheetConstraint (T0342)Y105 (T0342)T114 (T0342)M127 (T0342)K118 hbond (T0342)I108 1 SheetConstraint (T0342)C122 (T0342)S124 (T0342)L18 (T0342)F20 hbond (T0342)R123 1