CreatePredAlphaCost pred_alpha2k alpha11 T0319.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0319.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0319.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 15 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 100 \ hbond_geom_beta_pair 200 \ 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 T0319.t06.str2.constraints StrandConstraint F3 K10 17.69 StrandConstraint L25 Y27 0.691 StrandConstraint Q33 Q36 0.671 HelixConstraint P44 I50 0.7 HelixConstraint W56 E65 0.887 HelixConstraint D87 Q102 0.641 StrandConstraint A106 K111 0.681 StrandConstraint I118 K122 0.629 StrandConstraint P126 L128 0.628 include rr.0.1.constraints SheetConstraint A106 R113 N123 G116 hbond A106 10.0 SheetConstraint H117 I121 P131 N127 hbond I118 10.0 SheetConstraint N127 P131 K10 T6 hbond N127 40.0