CreatePredAlphaCost pred_alpha2k alpha11 T0361.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0361.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0361.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 20 \ hbond_geom_beta_pair 50 \ 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 T0361.dssp-ehl2.constraints # include T0361.undertaker-align.sheets # include rr.constraints Constraint L71.CB L98.CB -10. 7.0 14.0 0.0572100036292 # Constraint M23.CB I34.CB -10. 7.0 14.0 0.402522770318 bonus # Constraint M23.CB F37.CB -10. 7.0 14.0 0.358971475763 bonus # Constraint I88.CB L98.CB -10. 7.0 14.0 0.323147978284 bonus Constraint I34.CB L73.CB -10. 7.0 14.0 0.0317241561247 bonus Constraint L98.CB V119.CB -10. 7.0 14.0 0.0312091148191 bonus # Constraint H27.CB F37.CB -10. 7.0 14.0 0.31188292182 bonus Constraint L73.CB Y94.CB -10. 7.0 14.0 0.0311364616568 bonus