CreatePredAlphaCost pred_alpha2k alpha11 T0368.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0368.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0368.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 T0368.dssp-ehl2.constraints #include T0368.undertaker-align.sheets #include rr.constraints #Sheet constraints from t06 alignments: SheetConstraint L99 A103 F172 A168 hbond W100 100 #Helix constraints HelixConstraint K5 A23 50 HelixConstraint D27 I39 50 HelixConstraint A56 G68 50 HelixConstraint D73 F86 50 HelixConstraint S106 D112 50 HelixConstraint P122 R134 50 HelixConstraint E142 L155 50 #Hbond Constraints Hbond K141.N T138.O 30 Hbond Y166.N K163.O 30 Hbond E47.N P44.O 30 Hbond A48.N P45.O 30 Hbond A120.N G117.O 30 Hbond M121.N A118.O 30